From 547b31cde6e500d63b8b34826239824d974b7e48 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 6 Feb 2024 22:18:28 -0800 Subject: [PATCH 1/7] First pass at LinkML schema definition. --- schema/v1.1.0/metadata.yaml | 328 ++++++++++++++++++++++++++++++++++++ 1 file changed, 328 insertions(+) create mode 100644 schema/v1.1.0/metadata.yaml diff --git a/schema/v1.1.0/metadata.yaml b/schema/v1.1.0/metadata.yaml new file mode 100644 index 000000000..53fca648b --- /dev/null +++ b/schema/v1.1.0/metadata.yaml @@ -0,0 +1,328 @@ +id: https://cryoetdataportal.czscience.com/cetdp +name: cdp-meta +prefixes: + linkml: https://w3id.org/linkml/ + ORCID: https://orcid.org/ + ROR: https://ror.org/ + UBERON: http://purl.obolibrary.org/obo/UBERON_ + CL: http://purl.obolibrary.org/obo/CL_ + GO: http://purl.obolibrary.org/obo/GO_ +imports: + - linkml:types +default_range: string + +slots: + # ============================================================================ + # Common slots + # ============================================================================ + ORCID: + description: An ORCID identifier. + range: string + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + + affiliation_identifier: + description: A research organization registry identifier. + range: string + pattern: '^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$' + +enums: + # ============================================================================ + # Controlled vocabularies + # ============================================================================ + + sample_type: + description: Type of sample imaged in a CryoET study. + permissible_values: + cell: + description: Tomographic data of whole cells or cell sections. + tissue: + description: Tomographic data of tissue sections. + organism: + description: Tomographic data of sections through multicellular organisms. + organelle: + description: Tomographic data of purified organelles. + virus: + description: Tomographic data of purified viruses or VLPs. + in vitro: + description: Tomographic data of in vitro reconstituted systems or mixtures of proteins. + in silico: + description: Simulated tomographic data. + other: + description: Other type of sample. + +classes: + # ============================================================================ + # Author and Annotator information + # ============================================================================ + + Author: + description: An author of a scientific data entity. + attributes: + name: + range: string + required: true + description: The full name of the author. + email: + range: string + description: The email of the author. + affiliation_name: + range: string + description: The name of the author's affiliation. + affiliation_address: + range: string + description: The address of the author's affiliation. + is_corresponding: + range: boolean + description: Whether the author is the corresponding author. + is_primary_author: + range: boolean + description: Whether the author is the primary author. + alias: is_primary_annotator + + slots: + - ORCID + - affiliation_identifier + slot_usage: + orcid: + recommended: true + affiliation_identifier: + recommended: true + + # ============================================================================ + # Funding source information + # ============================================================================ + + Funding: + description: A funding source for a scientific data entity. + attributes: + funding_agency_name: + range: string + recommended: true + description: The name of the funding source. + grant_id: + range: string + recommended: true + description: Grant identifier provided by the funding agency + + # ============================================================================ + # Deposition, release and last modified dates + # ============================================================================ + + Dates: + description: A set of dates. + attributes: + deposition_date: + range: date + required: true + description: The date a piece of data was deposited to the cryoET data portal. + release_date: + range: date + required: true + description: The date a piece of data was made public on the cryoET data portal. + last_modified_date: + range: date + required: true + description: The date a piece of data was last modified on the cryoET data portal. + + # ============================================================================ + # Snapshot / Thumbnail + # ============================================================================ + + PictureLocations: + description: A set of paths to representative images of a piece of data. + attributes: + snapshot: + range: string + description: Path to an associated (larger) snapshot image relative to the dataset directory root. + thumbnail: + range: string + description: Path to an associated (smaller) thumbnail image relative to the dataset directory root. + + + # ============================================================================ + # Experimental metadata + # ============================================================================ + + Species: + description: The species from which the sample was derived. + attributes: + name: + range: string + recommended: true + description: The name of the species. + taxonomy_id: + range: integer + recommended: true + description: The NCBI taxonomy identifier for the species. + + Tissue: + description: The type of tissue from which the sample was derived. + attributes: + name: + range: string + recommended: true + description: The name of the tissue. + id: + range: string + recommended: true + description: The UBERON identifier for the tissue. + + CellType: + description: The cell type from which the sample was derived. + attributes: + name: + range: string + recommended: true + description: The name of the cell type. + id: + range: string + recommended: true + description: The CL identifier for the cell type. + + CellStrain: + description: The strain or cell line from which the sample was derived. + attributes: + name: + range: string + recommended: true + description: The name of the cell line or strain. + id: + range: string + recommended: true + description: The CL identifier for the cell line or strain. + + CellComponent: + description: The cellular component from which the sample was derived. + attributes: + name: + range: string + recommended: true + description: The name of the cellular component. + id: + range: string + recommended: true + description: The GO identifier for the cellular component. + + ExperimentalMetadata: + description: Metadata describing sample and sample preparation methods used in a cryoET dataset. + attributes: + sample_type: + range: sample_type + required: true + description: The type of sample imaged in a CryoET study. + organism: + range: Species + description: The species from which the sample was derived. + tissue: + range: Tissue + description: The type of tissue from which the sample was derived. + cell_type: + range: CellType + description: The cell type from which the sample was derived. + cell_strain: + range: CellStrain + description: The strain or cell line from which the sample was derived. + cell_component: + range: CellComponent + description: The cellular component from which the sample was derived. + sample_preparation: + range: string + description: A description of the sample preparation. + grid_preparation: + range: string + description: A description of the grid preparation. + other_setup: + range: string + description: Any other experimental setup information not covered by the other fields. + + + # ============================================================================ + # Dataset + # ============================================================================ + + CrossReferences: + description: A set of cross-references to other databases. + attributes: + dataset_publications: + range: string + description: Comma-separated list of DOIs for publications associated with the dataset. + related_database_entries: + range: string + description: Comma-separated list of related database entries for the dataset. + related_database_links: + range: string + description: Comma-separated list of related database links for the dataset. + dataset_citations: + range: string + description: Comma-separated list of DOIs for publications citing the dataset. + + Dataset: + description: High-level description of a cryoET dataset. + mixins: + - TimestampedEntity + - AuthoredEntity + - FundedEntity + - PreviewableEntity + - ExperimentalMetadata + attributes: + dataset_identifier: + range: integer + required: true + description: The unique identifier of the dataset on the cryoET data portal. + dataset_title: + range: string + required: true + description: The title of the dataset. + dataset_description: + range: string + required: true + description: A short description of the CryoET dataset. + cross_references: + range: CrossReferences + description: A set of cross-references to other databases and publications. + snapshot: + range: string + description: Path to an associated snapshot image relative to the dataset directory root. + thumbnail: + range: string + description: Path to an associated thumbnail image relative to the dataset directory root. + + + # ============================================================================ + # Meta-Mixins + # ============================================================================ + + TimestampedEntity: + description: An entity with associated deposition, release and last modified dates. + attributes: + dates: + range: Dates + required: true + description: The dates at which the entity was deposited, released and last modified. + + AuthoredEntity: + description: An entity with associated authors. + attributes: + authors: + range: Author + required: true + description: An ordered list of authors of the entity. + multivalued: true + inlined_as_list : true + + FundedEntity: + description: An entity with associated funding sources. + attributes: + funding: + range: Funding + recommended: true + description: An ordered list of funding sources for the entity. + multivalued: true + + PreviewableEntity: + description: An entity with associated preview images. + attributes: + key_photos: + range: PictureLocations + description: A set of paths to representative images of the entity. + multivalued: false \ No newline at end of file From 1df29d9f0542a8dfbab298130c0f21c9ed29abbb Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 6 Feb 2024 22:30:30 -0800 Subject: [PATCH 2/7] Fix FundedEntity listing. --- schema/v1.1.0/metadata.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/schema/v1.1.0/metadata.yaml b/schema/v1.1.0/metadata.yaml index 53fca648b..3a9368d7b 100644 --- a/schema/v1.1.0/metadata.yaml +++ b/schema/v1.1.0/metadata.yaml @@ -318,6 +318,7 @@ classes: recommended: true description: An ordered list of funding sources for the entity. multivalued: true + inlined_as_list : true PreviewableEntity: description: An entity with associated preview images. From 1780bc48679be0e0c867dc5165491345d85115c2 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 5 Mar 2024 17:43:08 -0800 Subject: [PATCH 3/7] LinkML schema, documentation and codegen. --- schema/v1.1.0/Makefile | 13 + schema/v1.1.0/README.md | 50 + schema/v1.1.0/common.yaml | 697 ++++++ schema/v1.1.0/metadata-docs/Annotation.md | 512 ++++ .../metadata-docs/AnnotationConfidence.md | 204 ++ schema/v1.1.0/metadata-docs/AnnotationFile.md | 235 ++ .../metadata-docs/AnnotationMethodTypeEnum.md | 70 + .../v1.1.0/metadata-docs/AnnotationObject.md | 251 ++ .../metadata-docs/AnnotationShapeEnum.md | 64 + schema/v1.1.0/metadata-docs/Annotator.md | 368 +++ .../v1.1.0/metadata-docs/AnnotatoredEntity.md | 141 ++ schema/v1.1.0/metadata-docs/Author.md | 401 +++ schema/v1.1.0/metadata-docs/AuthoredEntity.md | 144 ++ schema/v1.1.0/metadata-docs/Camera.md | 70 + schema/v1.1.0/metadata-docs/CellComponent.md | 182 ++ schema/v1.1.0/metadata-docs/CellStrain.md | 182 ++ schema/v1.1.0/metadata-docs/CellType.md | 182 ++ .../metadata-docs/CrossReferencedEntity.md | 131 + .../v1.1.0/metadata-docs/CrossReferences.md | 224 ++ schema/v1.1.0/metadata-docs/Dataset.md | 675 +++++ schema/v1.1.0/metadata-docs/DateStamp.md | 245 ++ .../v1.1.0/metadata-docs/DatestampedEntity.md | 138 ++ .../metadata-docs/ExperimentalMetadata.md | 399 +++ .../FiducialAlignmentStatusEnum.md | 66 + schema/v1.1.0/metadata-docs/FundedEntity.md | 139 ++ schema/v1.1.0/metadata-docs/Funding.md | 54 + schema/v1.1.0/metadata-docs/Microscope.md | 70 + .../metadata-docs/MicroscopeOpticalSetup.md | 200 ++ schema/v1.1.0/metadata-docs/ORCID.md | 54 + schema/v1.1.0/metadata-docs/Organism.md | 54 + schema/v1.1.0/metadata-docs/PicturePath.md | 165 ++ schema/v1.1.0/metadata-docs/PicturedEntity.md | 136 ++ schema/v1.1.0/metadata-docs/SampleTypeEnum.md | 91 + schema/v1.1.0/metadata-docs/TiltRange.md | 167 ++ schema/v1.1.0/metadata-docs/TiltSeries.md | 645 +++++ schema/v1.1.0/metadata-docs/Tissue.md | 54 + schema/v1.1.0/metadata-docs/Tomogram.md | 545 +++++ schema/v1.1.0/metadata-docs/TomogramOffset.md | 196 ++ schema/v1.1.0/metadata-docs/TomogramSize.md | 208 ++ .../v1.1.0/metadata-docs/TomogramTypeEnum.md | 56 + .../metadata-docs/acceleration_voltage.md | 72 + .../metadata-docs/affiliation_address.md | 54 + .../metadata-docs/affiliation_identifier.md | 54 + .../v1.1.0/metadata-docs/affiliation_name.md | 54 + .../affine_transformation_matrix.md | 73 + .../aligned_tiltseries_binning.md | 72 + .../v1.1.0/metadata-docs/annotation_method.md | 73 + .../metadata-docs/annotation_method_type.md | 72 + .../v1.1.0/metadata-docs/annotation_object.md | 70 + .../metadata-docs/annotation_publications.md | 73 + .../metadata-docs/annotation_software.md | 72 + schema/v1.1.0/metadata-docs/authors.md | 60 + .../metadata-docs/binning_from_frames.md | 72 + schema/v1.1.0/metadata-docs/cdp-meta.md | 6 + schema/v1.1.0/metadata-docs/cell_component.md | 54 + schema/v1.1.0/metadata-docs/cell_strain.md | 54 + schema/v1.1.0/metadata-docs/cell_type.md | 54 + schema/v1.1.0/metadata-docs/confidence.md | 70 + .../v1.1.0/metadata-docs/cross_references.md | 54 + schema/v1.1.0/metadata-docs/ctf_corrected.md | 72 + .../data_acquisition_software.md | 72 + .../v1.1.0/metadata-docs/dataset_citations.md | 70 + .../metadata-docs/dataset_description.md | 73 + .../metadata-docs/dataset_identifier.md | 73 + .../metadata-docs/dataset_publications.md | 73 + schema/v1.1.0/metadata-docs/dataset_title.md | 72 + schema/v1.1.0/metadata-docs/dates.md | 56 + .../v1.1.0/metadata-docs/deposition_date.md | 73 + schema/v1.1.0/metadata-docs/description.md | 74 + schema/v1.1.0/metadata-docs/email.md | 54 + schema/v1.1.0/metadata-docs/energy_filter.md | 72 + .../fiducial_alignment_status.md | 72 + schema/v1.1.0/metadata-docs/files.md | 74 + schema/v1.1.0/metadata-docs/format.md | 72 + schema/v1.1.0/metadata-docs/frames_count.md | 72 + .../metadata-docs/funding_agency_name.md | 72 + schema/v1.1.0/metadata-docs/grant_id.md | 72 + .../v1.1.0/metadata-docs/grid_preparation.md | 54 + .../metadata-docs/ground_truth_status.md | 73 + .../v1.1.0/metadata-docs/ground_truth_used.md | 72 + schema/v1.1.0/metadata-docs/id.md | 60 + .../v1.1.0/metadata-docs/image_corrector.md | 72 + schema/v1.1.0/metadata-docs/index.md | 171 ++ .../v1.1.0/metadata-docs/is_corresponding.md | 54 + .../metadata-docs/is_curator_recommended.md | 73 + .../metadata-docs/is_primary_annotator.md | 72 + .../v1.1.0/metadata-docs/is_primary_author.md | 72 + .../metadata-docs/is_visualization_default.md | 72 + schema/v1.1.0/metadata-docs/key_photos.md | 56 + .../metadata-docs/last_modified_date.md | 74 + schema/v1.1.0/metadata-docs/manufacturer.md | 54 + schema/v1.1.0/metadata-docs/max.md | 72 + .../microscope_additional_info.md | 73 + .../metadata-docs/microscope_optical_setup.md | 70 + schema/v1.1.0/metadata-docs/min.md | 72 + schema/v1.1.0/metadata-docs/model.md | 54 + schema/v1.1.0/metadata-docs/name.md | 66 + schema/v1.1.0/metadata-docs/object_count.md | 72 + schema/v1.1.0/metadata-docs/offset.md | 71 + schema/v1.1.0/metadata-docs/other_setup.md | 54 + schema/v1.1.0/metadata-docs/path.md | 72 + schema/v1.1.0/metadata-docs/phase_plate.md | 72 + schema/v1.1.0/metadata-docs/pixel_spacing.md | 72 + schema/v1.1.0/metadata-docs/precision.md | 73 + schema/v1.1.0/metadata-docs/processing.md | 72 + .../metadata-docs/processing_software.md | 72 + schema/v1.1.0/metadata-docs/recall.md | 73 + .../metadata-docs/reconstruction_method.md | 72 + .../metadata-docs/reconstruction_software.md | 72 + .../metadata-docs/related_database_entries.md | 73 + .../metadata-docs/related_database_links.md | 70 + schema/v1.1.0/metadata-docs/release_date.md | 74 + .../metadata-docs/sample_preparation.md | 54 + schema/v1.1.0/metadata-docs/sample_type.md | 54 + schema/v1.1.0/metadata-docs/shape.md | 73 + schema/v1.1.0/metadata-docs/size.md | 70 + schema/v1.1.0/metadata-docs/snapshot.md | 70 + .../spherical_aberration_constant.md | 72 + schema/v1.1.0/metadata-docs/state.md | 72 + schema/v1.1.0/metadata-docs/taxonomy_id.md | 72 + schema/v1.1.0/metadata-docs/thumbnail.md | 71 + schema/v1.1.0/metadata-docs/tilt_axis.md | 72 + schema/v1.1.0/metadata-docs/tilt_range.md | 70 + .../metadata-docs/tilt_series_quality.md | 73 + schema/v1.1.0/metadata-docs/tilt_step.md | 72 + schema/v1.1.0/metadata-docs/tilting_scheme.md | 72 + .../v1.1.0/metadata-docs/tomogram_version.md | 74 + schema/v1.1.0/metadata-docs/total_flux.md | 73 + schema/v1.1.0/metadata-docs/types.md | 6 + schema/v1.1.0/metadata-docs/voxel_spacing.md | 72 + schema/v1.1.0/metadata-docs/x.md | 54 + schema/v1.1.0/metadata-docs/y.md | 54 + schema/v1.1.0/metadata-docs/z.md | 54 + schema/v1.1.0/metadata.yaml | 677 ++++-- schema/v1.1.0/metadata_materialized.yaml | 2162 +++++++++++++++++ schema/v1.1.0/metadata_models.py | 512 ++++ schema/v1.1.0/schema.py | 103 + test_infra/seed_moto.sh | 2 +- 138 files changed, 18009 insertions(+), 210 deletions(-) create mode 100644 schema/v1.1.0/Makefile create mode 100644 schema/v1.1.0/README.md create mode 100644 schema/v1.1.0/common.yaml create mode 100644 schema/v1.1.0/metadata-docs/Annotation.md create mode 100644 schema/v1.1.0/metadata-docs/AnnotationConfidence.md create mode 100644 schema/v1.1.0/metadata-docs/AnnotationFile.md create mode 100644 schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md create mode 100644 schema/v1.1.0/metadata-docs/AnnotationObject.md create mode 100644 schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md create mode 100644 schema/v1.1.0/metadata-docs/Annotator.md create mode 100644 schema/v1.1.0/metadata-docs/AnnotatoredEntity.md create mode 100644 schema/v1.1.0/metadata-docs/Author.md create mode 100644 schema/v1.1.0/metadata-docs/AuthoredEntity.md create mode 100644 schema/v1.1.0/metadata-docs/Camera.md create mode 100644 schema/v1.1.0/metadata-docs/CellComponent.md create mode 100644 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schema/v1.1.0/metadata-docs/manufacturer.md create mode 100644 schema/v1.1.0/metadata-docs/max.md create mode 100644 schema/v1.1.0/metadata-docs/microscope_additional_info.md create mode 100644 schema/v1.1.0/metadata-docs/microscope_optical_setup.md create mode 100644 schema/v1.1.0/metadata-docs/min.md create mode 100644 schema/v1.1.0/metadata-docs/model.md create mode 100644 schema/v1.1.0/metadata-docs/name.md create mode 100644 schema/v1.1.0/metadata-docs/object_count.md create mode 100644 schema/v1.1.0/metadata-docs/offset.md create mode 100644 schema/v1.1.0/metadata-docs/other_setup.md create mode 100644 schema/v1.1.0/metadata-docs/path.md create mode 100644 schema/v1.1.0/metadata-docs/phase_plate.md create mode 100644 schema/v1.1.0/metadata-docs/pixel_spacing.md create mode 100644 schema/v1.1.0/metadata-docs/precision.md create mode 100644 schema/v1.1.0/metadata-docs/processing.md create mode 100644 schema/v1.1.0/metadata-docs/processing_software.md create mode 100644 schema/v1.1.0/metadata-docs/recall.md create mode 100644 schema/v1.1.0/metadata-docs/reconstruction_method.md create mode 100644 schema/v1.1.0/metadata-docs/reconstruction_software.md create mode 100644 schema/v1.1.0/metadata-docs/related_database_entries.md create mode 100644 schema/v1.1.0/metadata-docs/related_database_links.md create mode 100644 schema/v1.1.0/metadata-docs/release_date.md create mode 100644 schema/v1.1.0/metadata-docs/sample_preparation.md create mode 100644 schema/v1.1.0/metadata-docs/sample_type.md create mode 100644 schema/v1.1.0/metadata-docs/shape.md create mode 100644 schema/v1.1.0/metadata-docs/size.md create mode 100644 schema/v1.1.0/metadata-docs/snapshot.md create mode 100644 schema/v1.1.0/metadata-docs/spherical_aberration_constant.md create mode 100644 schema/v1.1.0/metadata-docs/state.md create mode 100644 schema/v1.1.0/metadata-docs/taxonomy_id.md create mode 100644 schema/v1.1.0/metadata-docs/thumbnail.md create mode 100644 schema/v1.1.0/metadata-docs/tilt_axis.md create mode 100644 schema/v1.1.0/metadata-docs/tilt_range.md create mode 100644 schema/v1.1.0/metadata-docs/tilt_series_quality.md create mode 100644 schema/v1.1.0/metadata-docs/tilt_step.md create mode 100644 schema/v1.1.0/metadata-docs/tilting_scheme.md create mode 100644 schema/v1.1.0/metadata-docs/tomogram_version.md create mode 100644 schema/v1.1.0/metadata-docs/total_flux.md create mode 100644 schema/v1.1.0/metadata-docs/types.md create mode 100644 schema/v1.1.0/metadata-docs/voxel_spacing.md create mode 100644 schema/v1.1.0/metadata-docs/x.md create mode 100644 schema/v1.1.0/metadata-docs/y.md create mode 100644 schema/v1.1.0/metadata-docs/z.md create mode 100644 schema/v1.1.0/metadata_materialized.yaml create mode 100644 schema/v1.1.0/metadata_models.py create mode 100644 schema/v1.1.0/schema.py diff --git a/schema/v1.1.0/Makefile b/schema/v1.1.0/Makefile new file mode 100644 index 000000000..a42602a5a --- /dev/null +++ b/schema/v1.1.0/Makefile @@ -0,0 +1,13 @@ +.DEFAULT_GOAL := build + +.PHONY: clean +clean: + rm -rf metadata-docs + rm -rf metadata_materialized.yaml + rm -rf metadata_models.py + +.PHONY: build +build: + python schema.py materialize metadata.yaml common.yaml metadata_materialized.yaml + gen-doc -d metadata-docs --no-mergeimports --hierarchical-class-view --stacktrace metadata_materialized.yaml + gen-pydantic --pydantic-version 2 metadata_materialized.yaml > metadata_models.py diff --git a/schema/v1.1.0/README.md b/schema/v1.1.0/README.md new file mode 100644 index 000000000..24e6d8c4f --- /dev/null +++ b/schema/v1.1.0/README.md @@ -0,0 +1,50 @@ +# cryoET data portal metadata schema + +This directory contains the metadata schema for the cryoET data portal. Browse contained classes [here](metadata-docs/index.md). + +Metadata file and directory layout specs: + +
+[dataset_identifier]/
+|-- dataset_metadata.json
+|-- [run_name]/
+|   |-- run_metadata.json
+|   |-- Frames/
+|   |   |-- [tiff|eer|mrc]
+|   |   |-- Gain_reference.mrc|dm4
+|   |   |-- frame_acquisition_order.json
+|   |-- TiltSeries/
+|   |   |-- tiltseries_metadata.json
+|   |   |-- [run_name].mrc
+|   |   |-- [run_name].zarr/
+|   |   |   |-- [subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+|   |   |-- [run_name].mdoc [optional, sometimes]
+|   |   |-- [run_name].rawtlt [optional, sometimes]
+|   |   |-- [run_name].tlt [optional, sometimes]
+|   |-- Tomograms/
+|   |   |-- VoxelSpacing[xx.yyy]
+|   |   |   |-- CanonicalTomogram
+|   |   |   |   |-- tomogram_metadata.json
+|   |   |   |   |-- neuroglancer_config.json
+|   |   |   |   |-- [run_name].mrc
+|   |   |   |   |-- [run_name].xf [optional, sometimes]
+|   |   |   |   |-- [run_name].zarr/
+|   |   |   |   |   |-- [subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+|   |   |   |-- Annotations/
+|   |   |   |   |-- XXX_[object_name]_[version]_point.ndjson
+|   |   |   |   |-- XXX_[object_name]_[version].json
+|   |   |   |   |-- YYY_[object_name]_[version]_segmentationmask.mrc
+|   |   |   |   |-- YYY_[object_name]_[version]_segmentationmask.zarr
+|   |   |   |   |   |-- [subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+|   |   |   |   |-- YYY_[object_name]_[version].json
+
+
+ +## Building the schema and docs + +To build the schema, markdown docs and pydantic classes: + +```bash +cd schema/v1.1.0 +make build +``` diff --git a/schema/v1.1.0/common.yaml b/schema/v1.1.0/common.yaml new file mode 100644 index 000000000..c99bb37fe --- /dev/null +++ b/schema/v1.1.0/common.yaml @@ -0,0 +1,697 @@ +id: https://cryoetdataportal.czscience.com/schema-docs/common +name: cdp-common +version: 1.1.0 +prefixes: + linkml: https://w3id.org/linkml/ + cdp-common: https://cryoetdataportal.czscience.com/schema/common/ + ROR: https://ror.org/ + UBERON: http://purl.obolibrary.org/obo/UBERON_ + CL: http://purl.obolibrary.org/obo/CL_ + GO: http://purl.obolibrary.org/obo/GO_ + IAO: http://purl.obolibrary.org/obo/IAO_ + FOAF: http://xmlns.com/foaf/0.1/ +imports: + - linkml:types +default_prefix: cdp-common +default_range: string + + +slots: + # ============================================================================ + # Common Identifiers + # ============================================================================ + orcid: + description: >- + A unique, persistent identifier for researchers, provided by ORCID. + range: string + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + exact_mappings: + - IAO:0000708 + + affiliation_identifier: + description: >- + A Research Organization Registry (ROR) identifier. + range: string + pattern: '^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$' + # ============================================================================ + + # ============================================================================ + # Dates (re-used in Dataset, Tomogram, Tiltseries, Annotation) + # ============================================================================ + deposition_date: + range: date + required: true + description: >- + The date a data item was received by the cryoET data portal. + + release_date: + range: date + required: true + description: >- + The date a data item was received by the cryoET data portal. + + last_modified_date: + range: date + required: true + description: >- + The date a piece of data was last modified on the cryoET data portal. + # ============================================================================ + + # ============================================================================ + # Author slots + # ============================================================================ + author_name: + range: string + required: true + description: >- + The full name of the author. + close_mappings: + - FOAF:name + + author_email: + range: string + description: >- + The email address of the author. + close_mappings: + - FOAF:mbox + + author_affiliation_name: + range: string + description: >- + The name of the author's affiliation. + + author_affiliation_address: + range: string + description: >- + The address of the author's affiliation. + + author_corresponding_author_status: + range: boolean + description: >- + Whether the author is a corresponding author. + + author_primary_author_status: + range: boolean + description: >- + Whether the author is a primary author. + + author_primary_annotator_status: + range: boolean + description: >- + Whether the author is a primary annotator. + + author_list_order: + range: integer + required: true + description: >- + The position of the author in the author list. + # ============================================================================ + + # ============================================================================ + # Dataset slots + # ============================================================================ + dataset_identifier: + identifier: true + range: integer + required: true + description: >- + An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory + name in data tree. + dataset_title: + range: string + required: true + description: >- + Title of a CryoET dataset. + dataset_description: + range: string + required: true + description: >- + A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. + + dataset_key_photo_url: + range: string + description: >- + URL for the dataset preview image. + dataset_key_photo_thumbnail_url: + range: string + description: >- + URL for the thumbnail of preview image. + dataset_s3_prefix: + range: string + description: >- + The S3 public bucket path where this dataset is contained. + dataset_https_prefix: + range: string + description: >- + The HTTPS directory path where this dataset is contained. + # ============================================================================ + + # ============================================================================ + # Funding information slots + # ============================================================================ + funding_agency_name: + range: string + recommended: true + description: The name of the funding source. + funding_grant_id: + range: string + recommended: true + description: Grant identifier provided by the funding agency + # ============================================================================ + + # ============================================================================ + # Experimental metadata slots + # ============================================================================ + # Organism/Species + organism_name: + range: string + recommended: true + description: >- + Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens. + organism_taxid: + range: string + recommended: true + description: >- + NCBI taxonomy identifier for the organism, e.g. 9606 + + # Tissue + tissue_name: + range: string + recommended: true + description: >- + Name of the tissue from which a biological sample used in a CryoET study is derived from. + tissue_id: + range: string + recommended: true + description: >- + The UBERON identifier for the tissue. + + # Cell Type + cell_name: + range: string + recommended: true + description: >- + Name of the cell type from which a biological sample used in a CryoET study is derived from. + cell_type_id: + range: string + recommended: true + description: >- + Cell Ontology identifier for the cell type + + # Cell Strain + cell_strain_name: + range: string + recommended: true + description: >- + Cell line or strain for the sample. + cell_strain_id: + range: string + recommended: true + description: >- + Link to more information about the cell strain. + + # Cell Component + cell_component_name: + range: string + recommended: true + description: >- + Name of the cellular component. + cell_component_id: + range: string + recommended: true + description: >- + The GO identifier for the cellular component. + + # Preparation + preparation_sample_type: + range: sample_type_enum + required: true + description: >- + Type of sample imaged in a CryoET study. + sample_preparation: + range: string + recommended: true + description: >- + Describes how the sample was prepared. + grid_preparation: + range: string + recommended: true + description: >- + Describes Cryo-ET grid preparation. + preparation_other_setup: + range: string + recommended: true + description: >- + Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in + the same publication. + # ============================================================================ + + # ============================================================================ + # Run slots + # ============================================================================ + + # ============================================================================ + + # ============================================================================ + # TomogramVoxelSpacing slots + # ============================================================================ + + # ============================================================================ + + # ============================================================================ + # TiltSeries slots + # ============================================================================ + # id: + # range: integer + # description: Numeric identifier for this tilt series (this may change!) + #run (Run): An object relationship with the run this tiltseries is a part of + tiltseries_run_id: + range: integer + description: Reference to the run this tiltseries is a part of + tiltseries_acceleration_voltage: + range: integer + description: Electron Microscope Accelerator voltage in volts + unit: + descriptive_name: volts + symbol: V + tiltseries_aligned_tiltseries_binning: + range: integer + description: Binning factor of the aligned tilt series + tiltseries_binning_from_frames: + range: float + description: Describes the binning factor from frames to tilt series file + tiltseries_camera_manufacturer: + range: string + description: Name of the camera manufacturer + tiltseries_camera_model: + range: string + description: Camera model name + tiltseries_data_acquisition_software: + range: string + description: Software used to collect data + tiltseries_frames_count: + range: integer + description: Number of frames associated with this tiltseries + tiltseries_https_alignment_file: + range: string + description: HTTPS path to the alignment file for this tiltseries + tiltseries_https_angle_list: + range: string + description: HTTPS path to the angle list file for this tiltseries + tiltseries_https_collection_metadata: + range: string + description: HTTPS path to the collection metadata file for this tiltseries + tiltseries_https_mrc_bin1: + range: string + description: HTTPS path to this tiltseries in MRC format (no scaling) + tiltseries_https_omezarr_dir: + range: string + description: HTTPS path to this tiltseries in multiscale OME-Zarr format + tiltseries_microscope_additional_info: + range: string + description: Other microscope optical setup information, in addition to energy filter, phase plate and image corrector + tiltseries_microscope_energy_filter: + range: string + description: Energy filter setup used + tiltseries_microscope_image_corrector: + range: string + description: Image corrector setup + tiltseries_microscope_manufacturer: + range: string + description: Name of the microscope manufacturer + tiltseries_microscope_model: + range: string + description: Microscope model name + tiltseries_microscope_phase_plate: + range: string + description: Phase plate configuration + tiltseries_pixel_spacing: + range: float + description: Pixel spacing for the tilt series + unit: + descriptive_name: Angstroms per pixel + symbol: Å/px + tiltseries_related_empiar_entry: + range: string + description: If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier + tiltseries_s3_alignment_file: + range: string + description: S3 path to the alignment file for this tiltseries + tiltseries_s3_angle_list: + range: string + description: S3 path to the angle list file for this tiltseries + tiltseries_s3_collection_metadata: + range: string + description: S3 path to the collection metadata file for this tiltseries + tiltseries_s3_mrc_bin1: + range: string + description: S3 path to this tiltseries in MRC format (no scaling) + tiltseries_s3_omezarr_dir: + range: string + description: S3 path to this tiltseries in multiscale OME-Zarr format + tiltseries_spherical_aberration_constant: + range: float + description: Spherical Aberration Constant of the objective lens in millimeters + unit: + descriptive_name: millimeters + symbol: mm + tiltseries_tilt_axis: + range: float + description: Rotation angle in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_max: + range: float + description: Maximal tilt angle in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_min: + range: float + description: Minimal tilt angle in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_range: + range: float + description: Total tilt range in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_series_quality: + range: integer + description: Author assessment of tilt series quality within the dataset (1-5, 5 is best) + tiltseries_tilt_step: + range: float + description: Tilt step in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilting_scheme: + range: string + description: The order of stage tilting during acquisition of the data + tiltseries_total_flux: + range: float + description: Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series + unit: + descriptive_name: electrons per square Angstrom + symbol: e^-/Å^2 + # ============================================================================ + + + # ============================================================================ + # Tomogram slots + # ============================================================================ + tomogram_affine_transformation_matrix: + range: string + description: The flip or rotation transformation of this author submitted tomogram is indicated here + tomogram_ctf_corrected: + range: boolean + description: Whether this tomogram is CTF corrected + #dataset (Dataset): An object relationship with the dataset this tomogram is a part of + tomogram_dataset_id: + range: integer + description: Reference to the dataset this tomogram is a part of + tomogram_fiducial_alignment_status: + range: fiducial_alignment_status_enum + description: Whether the tomographic alignment was computed based on fiducial markers. + tomogram_https_mrc_scale0: + range: string + description: HTTPS path to this tomogram in MRC format (no scaling) + tomogram_https_omezarr_dir: + range: string + description: HTTPS path to this tomogram in multiscale OME-Zarr format + tomogram_is_canonical: + range: boolean + description: Is this tomogram considered the canonical tomogram for the run experiment? + tomogram_key_photo_thumbnail_url: + range: string + description: URL for the thumbnail of key photo + tomogram_key_photo_url: + range: string + description: URL for the key photo + tomogram_name: + range: string + description: Short name for this tomogram + tomogram_neuroglancer_config: + range: string + description: the compact json of neuroglancer config + tomogram_offset_x: + range: integer + description: x offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + tomogram_offset_y: + range: integer + description: y offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + tomogram_offset_z: + range: integer + description: z offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + tomogram_processing: + range: string + description: Describe additional processing used to derive the tomogram + tomogram_processing_software: + range: string + description: Processing software used to derive the tomogram + tomogram_reconstruction_method: + range: string + description: Describe reconstruction method (Weighted back-projection, SART, SIRT) + tomogram_reconstruction_software: + range: string + description: Name of software used for reconstruction + tomogram_s3_mrc_scale0: + range: string + description: S3 path to this tomogram in MRC format (no scaling) + tomogram_s3_omezarr_dir: + range: string + description: S3 path to this tomogram in multiscale OME-Zarr format + tomogram_scale0_dimensions: + range: string + description: comma separated x,y,z dimensions of the unscaled tomogram + tomogram_scale1_dimensions: + range: string + description: comma separated x,y,z dimensions of the scale1 tomogram + tomogram_scale2_dimensions: + range: string + description: comma separated x,y,z dimensions of the scale2 tomogram + tomogram_size_x: + range: integer + description: Number of pixels in the 3D data fast axis + tomogram_size_y: + range: integer + description: Number of pixels in the 3D data medium axis + tomogram_size_z: + range: integer + description: Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt + tomogram_version: + range: string + description: Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version + #tomogram_voxel_spacing (TomogramVoxelSpacing): An object relationship with a specific voxel spacing for this experiment run + tomogram_type: + range: string + description: "Tomogram purpose (ex: CANONICAL)" + tomogram_voxel_spacing: + range: float + description: Voxel spacing equal in all three axes in angstroms + unit: + descriptive_name: Angstroms per voxel + symbol: Å/voxel + # ============================================================================ + + # ============================================================================ + # Annotation slots + # ============================================================================ + #id (int): Numeric identifier (May change!) + annotation_method: + range: string + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) + annotation_method_type: + range: annotation_method_type_enum + description: Classification of the annotation method based on supervision. + annotation_publication: + range: string + description: DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. + annotation_software: + range: string + description: Software used for generating this annotation + #authors (list[Author]): An array relationship with the authors of this annotation + annotation_confidence_precision: + range: float + description: Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive + annotation_confidence_recall: + range: float + description: Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly + #deposition_date (date): Date when an annotation set is initially received by the Data Portal. + annotation_ground_truth_status: + range: boolean + description: Whether an annotation is considered ground truth, as determined by the annotator. + annotation_ground_truth_used: + range: string + description: Annotation filename used as ground truth for precision and recall + https_metadata_path: + range: string + description: HTTPS path for the metadata json file for this annotation + #last_modified_date (date): Date when an annotation was last modified in the Data Portal + annotation_object_count: + range: integer + description: Number of objects identified + annotation_object_description: + range: string + description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. + annotation_object_id: + range: string + description: Gene Ontology Cellular Component identifier for the annotation object + annotation_object_name: + range: string + description: Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) + annotation_object_state: + range: string + description: Molecule state annotated (e.g. open, closed) + #release_date (date): Date when annotation data is made public by the Data Portal. + #tomogram_voxel_spacing (TomogramVoxelSpacing): An object relationship with a specific voxel spacing for this annotation + tomogram_voxel_spacing_id: + range: integer + description: Reference to the tomogram voxel spacing group this annotation applies to + s3_metadata_path: + range: string + description: S3 path for the metadata json file for this annotation + annotation_is_curator_recommended: + range: boolean + description: This annotation is recommended by the curator to be preferred for this object type. + + # ============================================================================ + # Annotation File slots + # ============================================================================ + #id (int): Numeric identifier (May change!) + annotation_file_format: + range: string + description: File format for this file + annotation_file_https_path: + range: string + description: HTTPS url for the annotation file + annotation_file_s3_path: + range: string + description: S3 path for the annotation file + annotation_file_shape_type: + range: string + description: Describe whether this is a Point, OrientedPoint, or SegmentationMask file + annotation_file_annotation_id: + range: integer + description: Reference to the annotation this file applies to + annotation_file_path: + range: string + description: Path to the annotation file relative to the dataset root. + annotation_file_is_visualization_default: + range: boolean + description: This annotation will be rendered in neuroglancer by default. + #Annotation (Annotation): The annotation this file is a part of + +enums: + # ============================================================================ + # Controlled vocabularies + # ============================================================================ + sample_type_enum: + description: Type of sample imaged in a CryoET study. + permissible_values: + cell: + description: Tomographic data of whole cells or cell sections. + tissue: + description: Tomographic data of tissue sections. + organism: + description: Tomographic data of sections through multicellular organisms. + organelle: + description: Tomographic data of purified organelles. + virus: + description: Tomographic data of purified viruses or VLPs. + in_vitro: + description: Tomographic data of in vitro reconstituted systems or mixtures of proteins. + in_silico: + description: Simulated tomographic data. + other: + description: Other type of sample. + + fiducial_alignment_status_enum: + description: Fiducial Alignment method + permissible_values: + FIDUCIAL: + description: Alignment computed based on fiducial markers + NON_FIDUCIAL: + description: Alignment computed without fiducial markers + + tomogram_type_enum: + description: Tomogram type + permissible_values: + CANONICAL: + description: Canonical tomogram (basis geometry for all annotations) + + annotation_method_type_enum: + description: Describes how the annotations were generated. + permissible_values: + manual: + description: Annotations were generated manually. + automated: + description: Annotations were generated semi-automatically. + hybrid: + description: Annotations were generated automatically. + + annotation_shape_enum: + description: Annotation shape types available on the data portal. + permissible_values: + Point: + description: Annotations were generated manually. + OrientedPoint: + description: Annotations were generated semi-automatically. + SegmentationMask: + description: Annotations were generated automatically. + + +classes: + # ============================================================================ + # Deposition, release and last modified dates + # ============================================================================ + DateStamp: + abstract: true + description: A set of dates at which a data item was deposited, published and last modified. + slots: + - deposition_date + - release_date + - last_modified_date + slot_usage: + deposition_date: + required: true + release_date: + recommended: true + last_modified_date: + recommended: true + + # ============================================================================ + # Cross-references to other databases and publications + # ============================================================================ + CrossReferences: + description: A set of cross-references to other databases and publications. + attributes: + dataset_publications: + range: string + recommended: true + description: Comma-separated list of DOIs for publications associated with the dataset. + related_database_entries: + range: string + recommended: true + description: Comma-separated list of related database entries for the dataset. + related_database_links: + range: string + description: Comma-separated list of related database links for the dataset. + dataset_citations: + range: string + description: Comma-separated list of DOIs for publications citing the dataset. + + + diff --git a/schema/v1.1.0/metadata-docs/Annotation.md b/schema/v1.1.0/metadata-docs/Annotation.md new file mode 100644 index 000000000..28d3fe09a --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Annotation.md @@ -0,0 +1,512 @@ +# Class: Annotation + + +_Metadata describing an annotation._ + + + + + +URI: [cdp-meta:Annotation](https://cryoetdataportal.czscience.com/schema/metadata/Annotation) + + + + +```mermaid + classDiagram + class Annotation + DatestampedEntity <|-- Annotation + AnnotatoredEntity <|-- Annotation + + Annotation : annotation_method + + Annotation --> string : annotation_method + + Annotation : annotation_method_type + + Annotation --> annotation_method_type_enum : annotation_method_type + + Annotation : annotation_object + + Annotation --> AnnotationObject : annotation_object + + Annotation : annotation_publications + + Annotation --> string : annotation_publications + + Annotation : annotation_software + + Annotation --> string : annotation_software + + Annotation : authors + + Annotation --> Annotator : authors + + Annotation : confidence + + Annotation --> AnnotationConfidence : confidence + + Annotation : dates + + Annotation --> DateStamp : dates + + Annotation : files + + Annotation --> AnnotationFile : files + + Annotation : ground_truth_status + + Annotation --> boolean : ground_truth_status + + Annotation : is_curator_recommended + + Annotation --> boolean : is_curator_recommended + + Annotation : object_count + + Annotation --> integer : object_count + + +``` + + + + + +## Inheritance +* **Annotation** [ [DatestampedEntity](DatestampedEntity.md) [AnnotatoredEntity](AnnotatoredEntity.md)] + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [annotation_method](annotation_method.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describe how the annotation is made (e | direct | +| [annotation_method_type](annotation_method_type.md) | 0..1
[AnnotationMethodTypeEnum](AnnotationMethodTypeEnum.md) | Classification of the annotation method based on supervision | direct | +| [annotation_publications](annotation_publications.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | DOIs for publications that describe the dataset | direct | +| [annotation_software](annotation_software.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Software used for generating this annotation | direct | +| [ground_truth_status](ground_truth_status.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | Whether an annotation is considered ground truth, as determined by the annota... | direct | +| [object_count](object_count.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Number of objects identified | direct | +| [is_curator_recommended](is_curator_recommended.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | This annotation is recommended by the curator to be preferred for this object... | direct | +| [files](files.md) | 0..*
[AnnotationFile](AnnotationFile.md) | Metadata describing a file containing an annotation | direct | +| [confidence](confidence.md) | 0..1
[AnnotationConfidence](AnnotationConfidence.md) | Metadata describing the confidence of an annotation | direct | +| [annotation_object](annotation_object.md) | 0..1
[AnnotationObject](AnnotationObject.md) | Metadata describing the object being annotated | direct | +| [dates](dates.md) | 1..1
[DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modifie... | direct | +| [authors](authors.md) | 1..*
[Annotator](Annotator.md) | Annotator of a scientific data entity | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:Annotation | +| native | cdp-meta:Annotation | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: Annotation +description: Metadata describing an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +mixins: +- DatestampedEntity +- AnnotatoredEntity +attributes: + annotation_method: + name: annotation_method + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive + Unlabeled Learning, template matching) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_method + rank: 1000 + alias: annotation_method + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_method_type: + name: annotation_method_type + description: Classification of the annotation method based on supervision. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_method_type + rank: 1000 + alias: annotation_method_type + owner: Annotation + domain_of: + - Annotation + range: annotation_method_type_enum + inlined: true + inlined_as_list: true + annotation_publications: + name: annotation_publications + description: DOIs for publications that describe the dataset. Use a comma to separate + multiple DOIs. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_publication + rank: 1000 + alias: annotation_publications + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_software: + name: annotation_software + description: Software used for generating this annotation + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_software + rank: 1000 + alias: annotation_software + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + ground_truth_status: + name: ground_truth_status + description: Whether an annotation is considered ground truth, as determined by + the annotator. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_ground_truth_status + rank: 1000 + alias: ground_truth_status + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + object_count: + name: object_count + description: Number of objects identified + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_count + rank: 1000 + alias: object_count + owner: Annotation + domain_of: + - Annotation + range: integer + inlined: true + inlined_as_list: true + is_curator_recommended: + name: is_curator_recommended + description: This annotation is recommended by the curator to be preferred for + this object type. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_is_curator_recommended + rank: 1000 + alias: is_curator_recommended + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + files: + name: files + description: Metadata describing a file containing an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + multivalued: true + list_elements_ordered: true + alias: files + owner: Annotation + domain_of: + - Annotation + range: AnnotationFile + inlined: true + inlined_as_list: true + confidence: + name: confidence + description: Metadata describing the confidence of an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: confidence + owner: Annotation + domain_of: + - Annotation + range: AnnotationConfidence + inlined: true + inlined_as_list: true + annotation_object: + name: annotation_object + description: Metadata describing the object being annotated. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: annotation_object + owner: Annotation + domain_of: + - Annotation + range: AnnotationObject + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: Annotation + domain_of: + - DatestampedEntity + - Dataset + - Annotation + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Annotation + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Annotator + required: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: Annotation +description: Metadata describing an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +mixins: +- DatestampedEntity +- AnnotatoredEntity +attributes: + annotation_method: + name: annotation_method + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive + Unlabeled Learning, template matching) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_method + rank: 1000 + alias: annotation_method + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_method_type: + name: annotation_method_type + description: Classification of the annotation method based on supervision. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_method_type + rank: 1000 + alias: annotation_method_type + owner: Annotation + domain_of: + - Annotation + range: annotation_method_type_enum + inlined: true + inlined_as_list: true + annotation_publications: + name: annotation_publications + description: DOIs for publications that describe the dataset. Use a comma to separate + multiple DOIs. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_publication + rank: 1000 + alias: annotation_publications + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_software: + name: annotation_software + description: Software used for generating this annotation + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_software + rank: 1000 + alias: annotation_software + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + ground_truth_status: + name: ground_truth_status + description: Whether an annotation is considered ground truth, as determined by + the annotator. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_ground_truth_status + rank: 1000 + alias: ground_truth_status + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + object_count: + name: object_count + description: Number of objects identified + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_count + rank: 1000 + alias: object_count + owner: Annotation + domain_of: + - Annotation + range: integer + inlined: true + inlined_as_list: true + is_curator_recommended: + name: is_curator_recommended + description: This annotation is recommended by the curator to be preferred for + this object type. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_is_curator_recommended + rank: 1000 + alias: is_curator_recommended + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + files: + name: files + description: Metadata describing a file containing an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + multivalued: true + list_elements_ordered: true + alias: files + owner: Annotation + domain_of: + - Annotation + range: AnnotationFile + inlined: true + inlined_as_list: true + confidence: + name: confidence + description: Metadata describing the confidence of an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: confidence + owner: Annotation + domain_of: + - Annotation + range: AnnotationConfidence + inlined: true + inlined_as_list: true + annotation_object: + name: annotation_object + description: Metadata describing the object being annotated. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: annotation_object + owner: Annotation + domain_of: + - Annotation + range: AnnotationObject + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: Annotation + domain_of: + - DatestampedEntity + - Dataset + - Annotation + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Annotation + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Annotator + required: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/AnnotationConfidence.md b/schema/v1.1.0/metadata-docs/AnnotationConfidence.md new file mode 100644 index 000000000..a06ff2574 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AnnotationConfidence.md @@ -0,0 +1,204 @@ +# Class: AnnotationConfidence + + +_Metadata describing the confidence of an annotation._ + + + + + +URI: [cdp-meta:AnnotationConfidence](https://cryoetdataportal.czscience.com/schema/metadata/AnnotationConfidence) + + + + +```mermaid + classDiagram + class AnnotationConfidence + AnnotationConfidence : ground_truth_used + + AnnotationConfidence --> string : ground_truth_used + + AnnotationConfidence : precision + + AnnotationConfidence --> float : precision + + AnnotationConfidence : recall + + AnnotationConfidence --> float : recall + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [precision](precision.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Describe the confidence level of the annotation | direct | +| [recall](recall.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Describe the confidence level of the annotation | direct | +| [ground_truth_used](ground_truth_used.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Annotation filename used as ground truth for precision and recall | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [Annotation](Annotation.md) | [confidence](confidence.md) | range | [AnnotationConfidence](AnnotationConfidence.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:AnnotationConfidence | +| native | cdp-meta:AnnotationConfidence | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: AnnotationConfidence +description: Metadata describing the confidence of an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + precision: + name: precision + description: Describe the confidence level of the annotation. Precision is defined + as the % of annotation objects being true positive + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_confidence_precision + rank: 1000 + alias: precision + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + recall: + name: recall + description: Describe the confidence level of the annotation. Recall is defined + as the % of true positives being annotated correctly + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_confidence_recall + rank: 1000 + alias: recall + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + ground_truth_used: + name: ground_truth_used + description: Annotation filename used as ground truth for precision and recall + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_ground_truth_used + rank: 1000 + alias: ground_truth_used + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: AnnotationConfidence +description: Metadata describing the confidence of an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + precision: + name: precision + description: Describe the confidence level of the annotation. Precision is defined + as the % of annotation objects being true positive + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_confidence_precision + rank: 1000 + alias: precision + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + recall: + name: recall + description: Describe the confidence level of the annotation. Recall is defined + as the % of true positives being annotated correctly + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_confidence_recall + rank: 1000 + alias: recall + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + ground_truth_used: + name: ground_truth_used + description: Annotation filename used as ground truth for precision and recall + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_ground_truth_used + rank: 1000 + alias: ground_truth_used + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/AnnotationFile.md b/schema/v1.1.0/metadata-docs/AnnotationFile.md new file mode 100644 index 000000000..2007ccde5 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AnnotationFile.md @@ -0,0 +1,235 @@ +# Class: AnnotationFile + + +_Metadata describing a file containing an annotation._ + + + + + +URI: [cdp-meta:AnnotationFile](https://cryoetdataportal.czscience.com/schema/metadata/AnnotationFile) + + + + +```mermaid + classDiagram + class AnnotationFile + AnnotationFile : format + + AnnotationFile --> string : format + + AnnotationFile : is_visualization_default + + AnnotationFile --> boolean : is_visualization_default + + AnnotationFile : path + + AnnotationFile --> string : path + + AnnotationFile : shape + + AnnotationFile --> string : shape + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [format](format.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | File format for this file | direct | +| [shape](shape.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describe whether this is a Point, OrientedPoint, or SegmentationMask file | direct | +| [path](path.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Path to the annotation file relative to the dataset root | direct | +| [is_visualization_default](is_visualization_default.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | This annotation will be rendered in neuroglancer by default | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [Annotation](Annotation.md) | [files](files.md) | range | [AnnotationFile](AnnotationFile.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:AnnotationFile | +| native | cdp-meta:AnnotationFile | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: AnnotationFile +description: Metadata describing a file containing an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + format: + name: format + description: File format for this file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_format + rank: 1000 + alias: format + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + shape: + name: shape + description: Describe whether this is a Point, OrientedPoint, or SegmentationMask + file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_shape_type + rank: 1000 + alias: shape + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + path: + name: path + description: Path to the annotation file relative to the dataset root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_path + rank: 1000 + alias: path + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_is_visualization_default + rank: 1000 + alias: is_visualization_default + owner: AnnotationFile + domain_of: + - AnnotationFile + range: boolean + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: AnnotationFile +description: Metadata describing a file containing an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + format: + name: format + description: File format for this file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_format + rank: 1000 + alias: format + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + shape: + name: shape + description: Describe whether this is a Point, OrientedPoint, or SegmentationMask + file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_shape_type + rank: 1000 + alias: shape + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + path: + name: path + description: Path to the annotation file relative to the dataset root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_path + rank: 1000 + alias: path + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_is_visualization_default + rank: 1000 + alias: is_visualization_default + owner: AnnotationFile + domain_of: + - AnnotationFile + range: boolean + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md b/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md new file mode 100644 index 000000000..6a669921e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md @@ -0,0 +1,70 @@ +# Enum: AnnotationMethodTypeEnum + + + + +_Describes how the annotations were generated._ + + + +URI: [AnnotationMethodTypeEnum](AnnotationMethodTypeEnum.md) + +## Permissible Values + +| Value | Meaning | Description | +| --- | --- | --- | +| manual | None | Annotations were generated manually | +| automated | None | Annotations were generated semi-automatically | +| hybrid | None | Annotations were generated automatically | + + + + +## Slots + +| Name | Description | +| --- | --- | +| [annotation_method_type](annotation_method_type.md) | Classification of the annotation method based on supervision | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_method_type_enum +description: Describes how the annotations were generated. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +permissible_values: + manual: + text: manual + description: Annotations were generated manually. + automated: + text: automated + description: Annotations were generated semi-automatically. + hybrid: + text: hybrid + description: Annotations were generated automatically. + +``` +
diff --git a/schema/v1.1.0/metadata-docs/AnnotationObject.md b/schema/v1.1.0/metadata-docs/AnnotationObject.md new file mode 100644 index 000000000..65fa57d2e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AnnotationObject.md @@ -0,0 +1,251 @@ +# Class: AnnotationObject + + +_Metadata describing the object being annotated._ + + + + + +URI: [cdp-meta:AnnotationObject](https://cryoetdataportal.czscience.com/schema/metadata/AnnotationObject) + + + + +```mermaid + classDiagram + class AnnotationObject + AnnotationObject : description + + AnnotationObject --> string : description + + AnnotationObject : id + + AnnotationObject --> string : id + + AnnotationObject : name + + AnnotationObject --> string : name + + AnnotationObject : state + + AnnotationObject --> string : state + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [id](id.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [name](name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [description](description.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | A textual description of the annotation object, can be a longer description t... | direct | +| [state](state.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Molecule state annotated (e | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [Annotation](Annotation.md) | [annotation_object](annotation_object.md) | range | [AnnotationObject](AnnotationObject.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:AnnotationObject | +| native | cdp-meta:AnnotationObject | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: AnnotationObject +description: Metadata describing the object being annotated. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_id + alias: id + owner: AnnotationObject + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_name + alias: name + owner: AnnotationObject + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + description: + name: description + description: A textual description of the annotation object, can be a longer description + to include additional information not covered by the Annotation object name + and state. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_description + rank: 1000 + alias: description + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + state: + name: state + description: Molecule state annotated (e.g. open, closed) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_state + rank: 1000 + alias: state + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: AnnotationObject +description: Metadata describing the object being annotated. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_id + alias: id + owner: AnnotationObject + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_name + alias: name + owner: AnnotationObject + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + description: + name: description + description: A textual description of the annotation object, can be a longer description + to include additional information not covered by the Annotation object name + and state. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_description + rank: 1000 + alias: description + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + state: + name: state + description: Molecule state annotated (e.g. open, closed) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_state + rank: 1000 + alias: state + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md b/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md new file mode 100644 index 000000000..40882de1d --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md @@ -0,0 +1,64 @@ +# Enum: AnnotationShapeEnum + + + + +_Annotation shape types available on the data portal._ + + + +URI: [AnnotationShapeEnum](AnnotationShapeEnum.md) + +## Permissible Values + +| Value | Meaning | Description | +| --- | --- | --- | +| Point | None | Annotations were generated manually | +| OrientedPoint | None | Annotations were generated semi-automatically | +| SegmentationMask | None | Annotations were generated automatically | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_shape_enum +description: Annotation shape types available on the data portal. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +permissible_values: + Point: + text: Point + description: Annotations were generated manually. + OrientedPoint: + text: OrientedPoint + description: Annotations were generated semi-automatically. + SegmentationMask: + text: SegmentationMask + description: Annotations were generated automatically. + +``` +
diff --git a/schema/v1.1.0/metadata-docs/Annotator.md b/schema/v1.1.0/metadata-docs/Annotator.md new file mode 100644 index 000000000..c832469f5 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Annotator.md @@ -0,0 +1,368 @@ +# Class: Annotator + + +_Annotator of a scientific data entity._ + + + + + +URI: [cdp-meta:Annotator](https://cryoetdataportal.czscience.com/schema/metadata/Annotator) + + + + +```mermaid + classDiagram + class Annotator + Annotator : affiliation_address + + Annotator --> string : affiliation_address + + Annotator : affiliation_identifier + + Annotator --> string : affiliation_identifier + + Annotator : affiliation_name + + Annotator --> string : affiliation_name + + Annotator : email + + Annotator --> string : email + + Annotator : is_corresponding + + Annotator --> string : is_corresponding + + Annotator : is_primary_annotator + + Annotator --> boolean : is_primary_annotator + + Annotator : name + + Annotator --> string : name + + Annotator : ORCID + + Annotator --> string : ORCID + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [name](name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [email](email.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [affiliation_name](affiliation_name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [affiliation_address](affiliation_address.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [affiliation_identifier](affiliation_identifier.md) | 0..1 _recommended_
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [is_corresponding](is_corresponding.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [is_primary_annotator](is_primary_annotator.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | Whether the author is a primary author | direct | +| [ORCID](ORCID.md) | 0..1 _recommended_
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [AnnotatoredEntity](AnnotatoredEntity.md) | [authors](authors.md) | range | [Annotator](Annotator.md) | +| [Annotation](Annotation.md) | [authors](authors.md) | range | [Annotator](Annotator.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:Annotator | +| native | cdp-meta:Annotator | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: Annotator +description: Annotator of a scientific data entity. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_name + alias: name + owner: Annotator + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + email: + name: email + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_email + alias: email + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:affiliation_identifier + alias: affiliation_identifier + owner: Annotator + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + is_corresponding: + name: is_corresponding + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + alias: is_corresponding + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + is_primary_annotator: + name: is_primary_annotator + description: Whether the author is a primary author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_primary_author_status + rank: 1000 + alias: is_primary_annotator + owner: Annotator + domain_of: + - Annotator + range: boolean + inlined: true + inlined_as_list: true + ORCID: + name: ORCID + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:orcid + alias: ORCID + owner: Annotator + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: Annotator +description: Annotator of a scientific data entity. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_name + alias: name + owner: Annotator + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + email: + name: email + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_email + alias: email + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:affiliation_identifier + alias: affiliation_identifier + owner: Annotator + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + is_corresponding: + name: is_corresponding + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + alias: is_corresponding + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + is_primary_annotator: + name: is_primary_annotator + description: Whether the author is a primary author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_primary_author_status + rank: 1000 + alias: is_primary_annotator + owner: Annotator + domain_of: + - Annotator + range: boolean + inlined: true + inlined_as_list: true + ORCID: + name: ORCID + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:orcid + alias: ORCID + owner: Annotator + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md b/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md new file mode 100644 index 000000000..a09931ec9 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md @@ -0,0 +1,141 @@ +# Class: AnnotatoredEntity + + +_An entity with associated annotation authors._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:AnnotatoredEntity](https://cryoetdataportal.czscience.com/schema/metadata/AnnotatoredEntity) + + + + +```mermaid + classDiagram + class AnnotatoredEntity + AnnotatoredEntity <|-- Annotation + + AnnotatoredEntity : authors + + AnnotatoredEntity --> Annotator : authors + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [authors](authors.md) | 1..*
[Annotator](Annotator.md) | Annotator of a scientific data entity | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:AnnotatoredEntity | +| native | cdp-meta:AnnotatoredEntity | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: AnnotatoredEntity +description: An entity with associated annotation authors. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + authors: + name: authors + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: AnnotatoredEntity + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Annotator + required: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: AnnotatoredEntity +description: An entity with associated annotation authors. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + authors: + name: authors + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: AnnotatoredEntity + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Annotator + required: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Author.md b/schema/v1.1.0/metadata-docs/Author.md new file mode 100644 index 000000000..52d7a85e3 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Author.md @@ -0,0 +1,401 @@ +# Class: Author + + +_Author of a scientific data entity._ + + + + + +URI: [cdp-meta:Author](https://cryoetdataportal.czscience.com/schema/metadata/Author) + + + + +```mermaid + classDiagram + class Author + Author : affiliation_address + + Author --> string : affiliation_address + + Author : affiliation_identifier + + Author --> string : affiliation_identifier + + Author : affiliation_name + + Author --> string : affiliation_name + + Author : email + + Author --> string : email + + Author : is_corresponding + + Author --> boolean : is_corresponding + + Author : is_primary_author + + Author --> boolean : is_primary_author + + Author : name + + Author --> string : name + + Author : ORCID + + Author --> string : ORCID + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [name](name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | The full name of the author | direct | +| [email](email.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | The email address of the author | direct | +| [affiliation_name](affiliation_name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | The name of the author's affiliation | direct | +| [affiliation_address](affiliation_address.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | The address of the author's affiliation | direct | +| [affiliation_identifier](affiliation_identifier.md) | 0..1 _recommended_
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | A Research Organization Registry (ROR) identifier | direct | +| [is_corresponding](is_corresponding.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | Whether the author is a corresponding author | direct | +| [is_primary_author](is_primary_author.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | Whether the author is a primary author | direct | +| [ORCID](ORCID.md) | 0..1 _recommended_
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | A unique, persistent identifier for researchers, provided by ORCID | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [AuthoredEntity](AuthoredEntity.md) | [authors](authors.md) | range | [Author](Author.md) | +| [Dataset](Dataset.md) | [authors](authors.md) | range | [Author](Author.md) | +| [Tomogram](Tomogram.md) | [authors](authors.md) | range | [Author](Author.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:Author | +| native | cdp-meta:Author | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: Author +description: Author of a scientific data entity. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + description: The full name of the author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_name + rank: 1000 + alias: name + owner: Author + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_email + rank: 1000 + alias: email + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_name + rank: 1000 + alias: affiliation_name + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_address + rank: 1000 + alias: affiliation_address + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:affiliation_identifier + rank: 1000 + alias: affiliation_identifier + owner: Author + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$ + is_corresponding: + name: is_corresponding + description: Whether the author is a corresponding author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + rank: 1000 + alias: is_corresponding + owner: Author + domain_of: + - Author + - Annotator + range: boolean + inlined: true + inlined_as_list: true + is_primary_author: + name: is_primary_author + description: Whether the author is a primary author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_primary_author_status + rank: 1000 + alias: is_primary_author + owner: Author + domain_of: + - Author + range: boolean + inlined: true + inlined_as_list: true + ORCID: + name: ORCID + description: A unique, persistent identifier for researchers, provided by ORCID. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:orcid + rank: 1000 + alias: ORCID + owner: Author + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + +``` +
+ +### Induced + +
+```yaml +name: Author +description: Author of a scientific data entity. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + description: The full name of the author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_name + rank: 1000 + alias: name + owner: Author + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_email + rank: 1000 + alias: email + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_name + rank: 1000 + alias: affiliation_name + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_address + rank: 1000 + alias: affiliation_address + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:affiliation_identifier + rank: 1000 + alias: affiliation_identifier + owner: Author + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$ + is_corresponding: + name: is_corresponding + description: Whether the author is a corresponding author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + rank: 1000 + alias: is_corresponding + owner: Author + domain_of: + - Author + - Annotator + range: boolean + inlined: true + inlined_as_list: true + is_primary_author: + name: is_primary_author + description: Whether the author is a primary author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_primary_author_status + rank: 1000 + alias: is_primary_author + owner: Author + domain_of: + - Author + range: boolean + inlined: true + inlined_as_list: true + ORCID: + name: ORCID + description: A unique, persistent identifier for researchers, provided by ORCID. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:orcid + rank: 1000 + alias: ORCID + owner: Author + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/AuthoredEntity.md b/schema/v1.1.0/metadata-docs/AuthoredEntity.md new file mode 100644 index 000000000..ed2db70d6 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/AuthoredEntity.md @@ -0,0 +1,144 @@ +# Class: AuthoredEntity + + +_An entity with associated authors._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:AuthoredEntity](https://cryoetdataportal.czscience.com/schema/metadata/AuthoredEntity) + + + + +```mermaid + classDiagram + class AuthoredEntity + AuthoredEntity <|-- Dataset + AuthoredEntity <|-- Tomogram + + AuthoredEntity : authors + + AuthoredEntity --> Author : authors + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [authors](authors.md) | 1..*
[Author](Author.md) | Author of a scientific data entity | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:AuthoredEntity | +| native | cdp-meta:AuthoredEntity | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: AuthoredEntity +description: An entity with associated authors. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + multivalued: true + list_elements_ordered: true + alias: authors + owner: AuthoredEntity + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Author + required: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: AuthoredEntity +description: An entity with associated authors. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + multivalued: true + list_elements_ordered: true + alias: authors + owner: AuthoredEntity + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Author + required: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Camera.md b/schema/v1.1.0/metadata-docs/Camera.md new file mode 100644 index 000000000..1977fdff5 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Camera.md @@ -0,0 +1,70 @@ +# Slot: camera + + +_The camera used to collect the tilt series._ + + + +URI: [cdp-meta:camera](https://cryoetdataportal.czscience.com/schema/metadata/camera) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [Camera](Camera.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: camera +description: The camera used to collect the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: camera +owner: TiltSeries +domain_of: +- TiltSeries +range: Camera +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/CellComponent.md b/schema/v1.1.0/metadata-docs/CellComponent.md new file mode 100644 index 000000000..f1a057b81 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/CellComponent.md @@ -0,0 +1,182 @@ +# Class: CellComponent + + +_The cellular component from which the sample was derived._ + + + + + +URI: [cdp-meta:CellComponent](https://cryoetdataportal.czscience.com/schema/metadata/CellComponent) + + + + +```mermaid + classDiagram + class CellComponent + CellComponent : id + + CellComponent --> string : id + + CellComponent : name + + CellComponent --> string : name + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [name](name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [id](id.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [ExperimentalMetadata](ExperimentalMetadata.md) | [cell_component](cell_component.md) | range | [CellComponent](CellComponent.md) | +| [Dataset](Dataset.md) | [cell_component](cell_component.md) | range | [CellComponent](CellComponent.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:CellComponent | +| native | cdp-meta:CellComponent | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: CellComponent +description: The cellular component from which the sample was derived. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_component_name + alias: name + owner: CellComponent + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_component_id + alias: id + owner: CellComponent + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: CellComponent +description: The cellular component from which the sample was derived. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_component_name + alias: name + owner: CellComponent + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_component_id + alias: id + owner: CellComponent + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/CellStrain.md b/schema/v1.1.0/metadata-docs/CellStrain.md new file mode 100644 index 000000000..273177312 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/CellStrain.md @@ -0,0 +1,182 @@ +# Class: CellStrain + + +_The strain or cell line from which the sample was derived._ + + + + + +URI: [cdp-meta:CellStrain](https://cryoetdataportal.czscience.com/schema/metadata/CellStrain) + + + + +```mermaid + classDiagram + class CellStrain + CellStrain : id + + CellStrain --> string : id + + CellStrain : name + + CellStrain --> string : name + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [name](name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [id](id.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [ExperimentalMetadata](ExperimentalMetadata.md) | [cell_strain](cell_strain.md) | range | [CellStrain](CellStrain.md) | +| [Dataset](Dataset.md) | [cell_strain](cell_strain.md) | range | [CellStrain](CellStrain.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:CellStrain | +| native | cdp-meta:CellStrain | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: CellStrain +description: The strain or cell line from which the sample was derived. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_strain_name + alias: name + owner: CellStrain + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_strain_id + alias: id + owner: CellStrain + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: CellStrain +description: The strain or cell line from which the sample was derived. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_strain_name + alias: name + owner: CellStrain + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_strain_id + alias: id + owner: CellStrain + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/CellType.md b/schema/v1.1.0/metadata-docs/CellType.md new file mode 100644 index 000000000..00f5caef8 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/CellType.md @@ -0,0 +1,182 @@ +# Class: CellType + + +_The cell type from which the sample was derived._ + + + + + +URI: [cdp-meta:CellType](https://cryoetdataportal.czscience.com/schema/metadata/CellType) + + + + +```mermaid + classDiagram + class CellType + CellType : id + + CellType --> string : id + + CellType : name + + CellType --> string : name + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [name](name.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [id](id.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [ExperimentalMetadata](ExperimentalMetadata.md) | [cell_type](cell_type.md) | range | [CellType](CellType.md) | +| [Dataset](Dataset.md) | [cell_type](cell_type.md) | range | [CellType](CellType.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:CellType | +| native | cdp-meta:CellType | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: CellType +description: The cell type from which the sample was derived. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_name + alias: name + owner: CellType + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_type_id + alias: id + owner: CellType + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: CellType +description: The cell type from which the sample was derived. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_name + alias: name + owner: CellType + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_type_id + alias: id + owner: CellType + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md b/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md new file mode 100644 index 000000000..bf84aeb08 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md @@ -0,0 +1,131 @@ +# Class: CrossReferencedEntity + + +_An entity with associated cross-references to other databases and publications._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:CrossReferencedEntity](https://cryoetdataportal.czscience.com/schema/metadata/CrossReferencedEntity) + + + + +```mermaid + classDiagram + class CrossReferencedEntity + CrossReferencedEntity <|-- Dataset + + CrossReferencedEntity : cross_references + + CrossReferencedEntity --> CrossReferences : cross_references + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [cross_references](cross_references.md) | 0..1
[CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:CrossReferencedEntity | +| native | cdp-meta:CrossReferencedEntity | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: CrossReferencedEntity +description: An entity with associated cross-references to other databases and publications. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cross_references + owner: CrossReferencedEntity + domain_of: + - CrossReferencedEntity + - Dataset + range: CrossReferences + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: CrossReferencedEntity +description: An entity with associated cross-references to other databases and publications. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cross_references + owner: CrossReferencedEntity + domain_of: + - CrossReferencedEntity + - Dataset + range: CrossReferences + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/CrossReferences.md b/schema/v1.1.0/metadata-docs/CrossReferences.md new file mode 100644 index 000000000..e326d3c69 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/CrossReferences.md @@ -0,0 +1,224 @@ +# Class: CrossReferences + + +_A set of cross-references to other databases and publications._ + + + + + +URI: [cdp-meta:CrossReferences](https://cryoetdataportal.czscience.com/schema/metadata/CrossReferences) + + + + +```mermaid + classDiagram + class CrossReferences + CrossReferences : dataset_citations + + CrossReferences --> string : dataset_citations + + CrossReferences : dataset_publications + + CrossReferences --> string : dataset_publications + + CrossReferences : related_database_entries + + CrossReferences --> string : related_database_entries + + CrossReferences : related_database_links + + CrossReferences --> string : related_database_links + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [dataset_publications](dataset_publications.md) | 0..1 _recommended_
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Comma-separated list of DOIs for publications associated with the dataset | direct | +| [related_database_entries](related_database_entries.md) | 0..1 _recommended_
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Comma-separated list of related database entries for the dataset | direct | +| [related_database_links](related_database_links.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Comma-separated list of related database links for the dataset | direct | +| [dataset_citations](dataset_citations.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Comma-separated list of DOIs for publications citing the dataset | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [CrossReferencedEntity](CrossReferencedEntity.md) | [cross_references](cross_references.md) | range | [CrossReferences](CrossReferences.md) | +| [Dataset](Dataset.md) | [cross_references](cross_references.md) | range | [CrossReferences](CrossReferences.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:CrossReferences | +| native | cdp-meta:CrossReferences | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: CrossReferences +description: A set of cross-references to other databases and publications. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + dataset_publications: + name: dataset_publications + description: Comma-separated list of DOIs for publications associated with the + dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: dataset_publications + owner: CrossReferences + domain_of: + - CrossReferences + range: string + recommended: true + inlined: true + inlined_as_list: true + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: related_database_entries + owner: CrossReferences + domain_of: + - CrossReferences + range: string + recommended: true + inlined: true + inlined_as_list: true + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: related_database_links + owner: CrossReferences + domain_of: + - CrossReferences + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: dataset_citations + owner: CrossReferences + domain_of: + - CrossReferences + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: CrossReferences +description: A set of cross-references to other databases and publications. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + dataset_publications: + name: dataset_publications + description: Comma-separated list of DOIs for publications associated with the + dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: dataset_publications + owner: CrossReferences + domain_of: + - CrossReferences + range: string + recommended: true + inlined: true + inlined_as_list: true + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: related_database_entries + owner: CrossReferences + domain_of: + - CrossReferences + range: string + recommended: true + inlined: true + inlined_as_list: true + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: related_database_links + owner: CrossReferences + domain_of: + - CrossReferences + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: dataset_citations + owner: CrossReferences + domain_of: + - CrossReferences + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Dataset.md b/schema/v1.1.0/metadata-docs/Dataset.md new file mode 100644 index 000000000..a0b1c4845 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Dataset.md @@ -0,0 +1,675 @@ +# Class: Dataset + + +_High-level description of a cryoET dataset._ + + + + + +URI: [cdp-meta:Dataset](https://cryoetdataportal.czscience.com/schema/metadata/Dataset) + + + + +```mermaid + classDiagram + class Dataset + DatestampedEntity <|-- Dataset + AuthoredEntity <|-- Dataset + FundedEntity <|-- Dataset + PicturedEntity <|-- Dataset + CrossReferencedEntity <|-- Dataset + ExperimentalMetadata <|-- Dataset + + Dataset : authors + + Dataset --> Author : authors + + Dataset : cell_component + + Dataset --> CellComponent : cell_component + + Dataset : cell_strain + + Dataset --> CellStrain : cell_strain + + Dataset : cell_type + + Dataset --> CellType : cell_type + + Dataset : cross_references + + Dataset --> CrossReferences : cross_references + + Dataset : dataset_description + + Dataset --> string : dataset_description + + Dataset : dataset_identifier + + Dataset --> integer : dataset_identifier + + Dataset : dataset_title + + Dataset --> string : dataset_title + + Dataset : dates + + Dataset --> DateStamp : dates + + Dataset : funding + + Dataset --> Funding : funding + + Dataset : grid_preparation + + Dataset --> string : grid_preparation + + Dataset : key_photos + + Dataset --> PicturePath : key_photos + + Dataset : organism + + Dataset --> Organism : organism + + Dataset : other_setup + + Dataset --> string : other_setup + + Dataset : sample_preparation + + Dataset --> string : sample_preparation + + Dataset : sample_type + + Dataset --> string : sample_type + + Dataset : tissue + + Dataset --> Tissue : tissue + + +``` + + + + + +## Inheritance +* **Dataset** [ [DatestampedEntity](DatestampedEntity.md) [AuthoredEntity](AuthoredEntity.md) [FundedEntity](FundedEntity.md) [PicturedEntity](PicturedEntity.md) [CrossReferencedEntity](CrossReferencedEntity.md) [ExperimentalMetadata](ExperimentalMetadata.md)] + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [dataset_identifier](dataset_identifier.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | An identifier for a CryoET dataset, assigned by the Data Portal | direct | +| [dataset_title](dataset_title.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Title of a CryoET dataset | direct | +| [dataset_description](dataset_description.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | A short description of a CryoET dataset, similar to an abstract for a journal... | direct | +| [dates](dates.md) | 1..1
[DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modifie... | direct | +| [authors](authors.md) | 1..*
[Author](Author.md) | Author of a scientific data entity | direct | +| [funding](funding.md) | 0..* _recommended_
[Funding](Funding.md) | A funding source for a scientific data entity (base for JSON and DB represent... | direct | +| [key_photos](key_photos.md) | 1..1
[PicturePath](PicturePath.md) | A set of paths to representative images of a piece of data | direct | +| [cross_references](cross_references.md) | 0..1
[CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications | direct | +| [sample_type](sample_type.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Type of sample imaged in a CryoET study | direct | +| [sample_preparation](sample_preparation.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describes how the sample was prepared | direct | +| [grid_preparation](grid_preparation.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describes Cryo-ET grid preparation | direct | +| [other_setup](other_setup.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describes other setup not covered by sample preparation or grid preparation t... | direct | +| [organism](organism.md) | 0..1
[Organism](Organism.md) | The species from which the sample was derived | direct | +| [tissue](tissue.md) | 0..1
[Tissue](Tissue.md) | The type of tissue from which the sample was derived | direct | +| [cell_type](cell_type.md) | 0..1
[CellType](CellType.md) | The cell type from which the sample was derived | direct | +| [cell_strain](cell_strain.md) | 0..1
[CellStrain](CellStrain.md) | The strain or cell line from which the sample was derived | direct | +| [cell_component](cell_component.md) | 0..1
[CellComponent](CellComponent.md) | The cellular component from which the sample was derived | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:Dataset | +| native | cdp-meta:Dataset | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: Dataset +description: High-level description of a cryoET dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +mixins: +- DatestampedEntity +- AuthoredEntity +- FundedEntity +- PicturedEntity +- CrossReferencedEntity +- ExperimentalMetadata +attributes: + dataset_identifier: + name: dataset_identifier + description: An identifier for a CryoET dataset, assigned by the Data Portal. + Used to identify the dataset as the directory name in data tree. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_identifier + rank: 1000 + alias: dataset_identifier + owner: Dataset + domain_of: + - Dataset + range: integer + inlined: true + inlined_as_list: true + dataset_title: + name: dataset_title + description: Title of a CryoET dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_title + rank: 1000 + alias: dataset_title + owner: Dataset + domain_of: + - Dataset + range: string + inlined: true + inlined_as_list: true + dataset_description: + name: dataset_description + description: A short description of a CryoET dataset, similar to an abstract for + a journal article or dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_description + rank: 1000 + alias: dataset_description + owner: Dataset + domain_of: + - Dataset + range: string + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: Dataset + domain_of: + - DatestampedEntity + - Dataset + - Annotation + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Dataset + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Author + required: true + inlined: true + inlined_as_list: true + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON and + DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: funding + owner: Dataset + domain_of: + - FundedEntity + - Dataset + range: Funding + recommended: true + inlined: true + inlined_as_list: true + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: Dataset + domain_of: + - PicturedEntity + - Dataset + - Tomogram + range: PicturePath + required: true + inlined: true + inlined_as_list: true + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cross_references + owner: Dataset + domain_of: + - CrossReferencedEntity + - Dataset + range: CrossReferences + inlined: true + inlined_as_list: true + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid preparation + that may make this dataset unique in the same publication. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: organism + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: Organism + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: tissue + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: Tissue + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_type + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_strain + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_component + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: CellComponent + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: Dataset +description: High-level description of a cryoET dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +mixins: +- DatestampedEntity +- AuthoredEntity +- FundedEntity +- PicturedEntity +- CrossReferencedEntity +- ExperimentalMetadata +attributes: + dataset_identifier: + name: dataset_identifier + description: An identifier for a CryoET dataset, assigned by the Data Portal. + Used to identify the dataset as the directory name in data tree. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_identifier + rank: 1000 + alias: dataset_identifier + owner: Dataset + domain_of: + - Dataset + range: integer + inlined: true + inlined_as_list: true + dataset_title: + name: dataset_title + description: Title of a CryoET dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_title + rank: 1000 + alias: dataset_title + owner: Dataset + domain_of: + - Dataset + range: string + inlined: true + inlined_as_list: true + dataset_description: + name: dataset_description + description: A short description of a CryoET dataset, similar to an abstract for + a journal article or dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_description + rank: 1000 + alias: dataset_description + owner: Dataset + domain_of: + - Dataset + range: string + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: Dataset + domain_of: + - DatestampedEntity + - Dataset + - Annotation + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Dataset + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Author + required: true + inlined: true + inlined_as_list: true + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON and + DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: funding + owner: Dataset + domain_of: + - FundedEntity + - Dataset + range: Funding + recommended: true + inlined: true + inlined_as_list: true + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: Dataset + domain_of: + - PicturedEntity + - Dataset + - Tomogram + range: PicturePath + required: true + inlined: true + inlined_as_list: true + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cross_references + owner: Dataset + domain_of: + - CrossReferencedEntity + - Dataset + range: CrossReferences + inlined: true + inlined_as_list: true + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid preparation + that may make this dataset unique in the same publication. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: organism + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: Organism + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: tissue + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: Tissue + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_type + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_strain + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_component + owner: Dataset + domain_of: + - ExperimentalMetadata + - Dataset + range: CellComponent + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/DateStamp.md b/schema/v1.1.0/metadata-docs/DateStamp.md new file mode 100644 index 000000000..18cd3fc7e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/DateStamp.md @@ -0,0 +1,245 @@ +# Class: DateStamp + + +_A set of dates at which a data item was deposited, published and last modified._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:DateStamp](https://cryoetdataportal.czscience.com/schema/metadata/DateStamp) + + + + +```mermaid + classDiagram + class DateStamp + DateStamp : deposition_date + + DateStamp --> date : deposition_date + + DateStamp : last_modified_date + + DateStamp --> date : last_modified_date + + DateStamp : release_date + + DateStamp --> date : release_date + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [deposition_date](deposition_date.md) | 1..1
[xsd:date](http://www.w3.org/2001/XMLSchema#date) | The date a data item was received by the cryoET data portal | direct | +| [release_date](release_date.md) | 1..1 _recommended_
[xsd:date](http://www.w3.org/2001/XMLSchema#date) | The date a data item was received by the cryoET data portal | direct | +| [last_modified_date](last_modified_date.md) | 1..1 _recommended_
[xsd:date](http://www.w3.org/2001/XMLSchema#date) | The date a piece of data was last modified on the cryoET data portal | direct | +| [deposition_date](deposition_date.md) | 1..1
[xsd:date](http://www.w3.org/2001/XMLSchema#date) | The date a data item was received by the cryoET data portal | direct | +| [release_date](release_date.md) | 1..1 _recommended_
[xsd:date](http://www.w3.org/2001/XMLSchema#date) | The date a data item was received by the cryoET data portal | direct | +| [last_modified_date](last_modified_date.md) | 1..1 _recommended_
[xsd:date](http://www.w3.org/2001/XMLSchema#date) | The date a piece of data was last modified on the cryoET data portal | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [DatestampedEntity](DatestampedEntity.md) | [dates](dates.md) | range | [DateStamp](DateStamp.md) | +| [Dataset](Dataset.md) | [dates](dates.md) | range | [DateStamp](DateStamp.md) | +| [Annotation](Annotation.md) | [dates](dates.md) | range | [DateStamp](DateStamp.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:DateStamp | +| native | cdp-meta:DateStamp | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: DateStamp +description: A set of dates at which a data item was deposited, published and last + modified. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +slots: +- deposition_date +- release_date +- last_modified_date +slot_usage: + deposition_date: + name: deposition_date + domain_of: + - DateStamp + required: true + release_date: + name: release_date + domain_of: + - DateStamp + recommended: true + last_modified_date: + name: last_modified_date + domain_of: + - DateStamp + recommended: true +attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: deposition_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: release_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + recommended: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: last_modified_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + recommended: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: DateStamp +description: A set of dates at which a data item was deposited, published and last + modified. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +slot_usage: + deposition_date: + name: deposition_date + domain_of: + - DateStamp + required: true + release_date: + name: release_date + domain_of: + - DateStamp + recommended: true + last_modified_date: + name: last_modified_date + domain_of: + - DateStamp + recommended: true +attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: deposition_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: release_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + recommended: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: last_modified_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + recommended: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/DatestampedEntity.md b/schema/v1.1.0/metadata-docs/DatestampedEntity.md new file mode 100644 index 000000000..6a40b8618 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/DatestampedEntity.md @@ -0,0 +1,138 @@ +# Class: DatestampedEntity + + +_An entity with associated deposition, release and last modified dates._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:DatestampedEntity](https://cryoetdataportal.czscience.com/schema/metadata/DatestampedEntity) + + + + +```mermaid + classDiagram + class DatestampedEntity + DatestampedEntity <|-- Dataset + DatestampedEntity <|-- Annotation + + DatestampedEntity : dates + + DatestampedEntity --> DateStamp : dates + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [dates](dates.md) | 1..1
[DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modifie... | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:DatestampedEntity | +| native | cdp-meta:DatestampedEntity | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: DatestampedEntity +description: An entity with associated deposition, release and last modified dates. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + dates: + name: dates + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: dates + owner: DatestampedEntity + domain_of: + - DatestampedEntity + - Dataset + - Annotation + range: DateStamp + required: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: DatestampedEntity +description: An entity with associated deposition, release and last modified dates. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + dates: + name: dates + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: dates + owner: DatestampedEntity + domain_of: + - DatestampedEntity + - Dataset + - Annotation + range: DateStamp + required: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md b/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md new file mode 100644 index 000000000..aa3949de6 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md @@ -0,0 +1,399 @@ +# Class: ExperimentalMetadata + + +_Metadata describing sample and sample preparation methods used in a cryoET dataset._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:ExperimentalMetadata](https://cryoetdataportal.czscience.com/schema/metadata/ExperimentalMetadata) + + + + +```mermaid + classDiagram + class ExperimentalMetadata + ExperimentalMetadata <|-- Dataset + + ExperimentalMetadata : cell_component + + ExperimentalMetadata --> CellComponent : cell_component + + ExperimentalMetadata : cell_strain + + ExperimentalMetadata --> CellStrain : cell_strain + + ExperimentalMetadata : cell_type + + ExperimentalMetadata --> CellType : cell_type + + ExperimentalMetadata : grid_preparation + + ExperimentalMetadata --> string : grid_preparation + + ExperimentalMetadata : organism + + ExperimentalMetadata --> Organism : organism + + ExperimentalMetadata : other_setup + + ExperimentalMetadata --> string : other_setup + + ExperimentalMetadata : sample_preparation + + ExperimentalMetadata --> string : sample_preparation + + ExperimentalMetadata : sample_type + + ExperimentalMetadata --> sample_type_enum : sample_type + + ExperimentalMetadata : tissue + + ExperimentalMetadata --> Tissue : tissue + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [sample_type](sample_type.md) | 0..1
[SampleTypeEnum](SampleTypeEnum.md) | Type of sample imaged in a CryoET study | direct | +| [sample_preparation](sample_preparation.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describes how the sample was prepared | direct | +| [grid_preparation](grid_preparation.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describes Cryo-ET grid preparation | direct | +| [other_setup](other_setup.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describes other setup not covered by sample preparation or grid preparation t... | direct | +| [organism](organism.md) | 0..1
[Organism](Organism.md) | The species from which the sample was derived | direct | +| [tissue](tissue.md) | 0..1
[Tissue](Tissue.md) | The type of tissue from which the sample was derived | direct | +| [cell_type](cell_type.md) | 0..1
[CellType](CellType.md) | The cell type from which the sample was derived | direct | +| [cell_strain](cell_strain.md) | 0..1
[CellStrain](CellStrain.md) | The strain or cell line from which the sample was derived | direct | +| [cell_component](cell_component.md) | 0..1
[CellComponent](CellComponent.md) | The cellular component from which the sample was derived | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:ExperimentalMetadata | +| native | cdp-meta:ExperimentalMetadata | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: ExperimentalMetadata +description: Metadata describing sample and sample preparation methods used in a cryoET + dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_sample_type + rank: 1000 + alias: sample_type + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: sample_type_enum + inlined: true + inlined_as_list: true + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:sample_preparation + rank: 1000 + alias: sample_preparation + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:grid_preparation + rank: 1000 + alias: grid_preparation + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid preparation + that may make this dataset unique in the same publication. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_other_setup + rank: 1000 + alias: other_setup + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: organism + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: Organism + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: tissue + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: Tissue + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cell_type + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cell_strain + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cell_component + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: CellComponent + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: ExperimentalMetadata +description: Metadata describing sample and sample preparation methods used in a cryoET + dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_sample_type + rank: 1000 + alias: sample_type + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: sample_type_enum + inlined: true + inlined_as_list: true + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:sample_preparation + rank: 1000 + alias: sample_preparation + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:grid_preparation + rank: 1000 + alias: grid_preparation + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid preparation + that may make this dataset unique in the same publication. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_other_setup + rank: 1000 + alias: other_setup + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: string + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: organism + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: Organism + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: tissue + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: Tissue + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cell_type + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cell_strain + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: cell_component + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + - Dataset + range: CellComponent + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md b/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md new file mode 100644 index 000000000..5a1afc62c --- /dev/null +++ b/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md @@ -0,0 +1,66 @@ +# Enum: FiducialAlignmentStatusEnum + + + + +_Fiducial Alignment method_ + + + +URI: [FiducialAlignmentStatusEnum](FiducialAlignmentStatusEnum.md) + +## Permissible Values + +| Value | Meaning | Description | +| --- | --- | --- | +| FIDUCIAL | None | Alignment computed based on fiducial markers | +| NON_FIDUCIAL | None | Alignment computed without fiducial markers | + + + + +## Slots + +| Name | Description | +| --- | --- | +| [fiducial_alignment_status](fiducial_alignment_status.md) | Whether the tomographic alignment was computed based on fiducial markers | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: fiducial_alignment_status_enum +description: Fiducial Alignment method +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +permissible_values: + FIDUCIAL: + text: FIDUCIAL + description: Alignment computed based on fiducial markers + NON_FIDUCIAL: + text: NON_FIDUCIAL + description: Alignment computed without fiducial markers + +``` +
diff --git a/schema/v1.1.0/metadata-docs/FundedEntity.md b/schema/v1.1.0/metadata-docs/FundedEntity.md new file mode 100644 index 000000000..12df0f8b2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/FundedEntity.md @@ -0,0 +1,139 @@ +# Class: FundedEntity + + +_An entity with associated funding sources._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:FundedEntity](https://cryoetdataportal.czscience.com/schema/metadata/FundedEntity) + + + + +```mermaid + classDiagram + class FundedEntity + FundedEntity <|-- Dataset + + FundedEntity : funding + + FundedEntity --> Funding : funding + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [funding](funding.md) | 0..* _recommended_
[Funding](Funding.md) | A funding source for a scientific data entity (base for JSON and DB represent... | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:FundedEntity | +| native | cdp-meta:FundedEntity | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: FundedEntity +description: An entity with associated funding sources. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON and + DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + multivalued: true + list_elements_ordered: true + alias: funding + owner: FundedEntity + domain_of: + - FundedEntity + - Dataset + range: Funding + recommended: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: FundedEntity +description: An entity with associated funding sources. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON and + DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + multivalued: true + list_elements_ordered: true + alias: funding + owner: FundedEntity + domain_of: + - FundedEntity + - Dataset + range: Funding + recommended: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Funding.md b/schema/v1.1.0/metadata-docs/Funding.md new file mode 100644 index 000000000..e1e25d6a3 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Funding.md @@ -0,0 +1,54 @@ +# Slot: funding + +URI: [cdp-meta:funding](https://cryoetdataportal.czscience.com/schema/metadata/funding) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[FundedEntity](FundedEntity.md) | An entity with associated funding sources | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: funding +alias: funding +domain_of: +- FundedEntity +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Microscope.md b/schema/v1.1.0/metadata-docs/Microscope.md new file mode 100644 index 000000000..6dcc714e8 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Microscope.md @@ -0,0 +1,70 @@ +# Slot: microscope + + +_The microscope used to collect the tilt series._ + + + +URI: [cdp-meta:microscope](https://cryoetdataportal.czscience.com/schema/metadata/microscope) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [Microscope](Microscope.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: microscope +description: The microscope used to collect the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: microscope +owner: TiltSeries +domain_of: +- TiltSeries +range: Microscope +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md b/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md new file mode 100644 index 000000000..77fcb49a9 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md @@ -0,0 +1,200 @@ +# Class: MicroscopeOpticalSetup + + +_The optical setup of the microscope used to collect the tilt series._ + + + + + +URI: [cdp-meta:MicroscopeOpticalSetup](https://cryoetdataportal.czscience.com/schema/metadata/MicroscopeOpticalSetup) + + + + +```mermaid + classDiagram + class MicroscopeOpticalSetup + MicroscopeOpticalSetup : energy_filter + + MicroscopeOpticalSetup --> string : energy_filter + + MicroscopeOpticalSetup : image_corrector + + MicroscopeOpticalSetup --> string : image_corrector + + MicroscopeOpticalSetup : phase_plate + + MicroscopeOpticalSetup --> string : phase_plate + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [energy_filter](energy_filter.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Energy filter setup used | direct | +| [phase_plate](phase_plate.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Phase plate configuration | direct | +| [image_corrector](image_corrector.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Image corrector setup | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [TiltSeries](TiltSeries.md) | [microscope_optical_setup](microscope_optical_setup.md) | range | [MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:MicroscopeOpticalSetup | +| native | cdp-meta:MicroscopeOpticalSetup | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: MicroscopeOpticalSetup +description: The optical setup of the microscope used to collect the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + energy_filter: + name: energy_filter + description: Energy filter setup used + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + rank: 1000 + alias: energy_filter + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + phase_plate: + name: phase_plate + description: Phase plate configuration + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + rank: 1000 + alias: phase_plate + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + image_corrector: + name: image_corrector + description: Image corrector setup + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + rank: 1000 + alias: image_corrector + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: MicroscopeOpticalSetup +description: The optical setup of the microscope used to collect the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + energy_filter: + name: energy_filter + description: Energy filter setup used + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + rank: 1000 + alias: energy_filter + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + phase_plate: + name: phase_plate + description: Phase plate configuration + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + rank: 1000 + alias: phase_plate + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + image_corrector: + name: image_corrector + description: Image corrector setup + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + rank: 1000 + alias: image_corrector + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/ORCID.md b/schema/v1.1.0/metadata-docs/ORCID.md new file mode 100644 index 000000000..e9d1a7385 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/ORCID.md @@ -0,0 +1,54 @@ +# Slot: ORCID + +URI: [cdp-meta:ORCID](https://cryoetdataportal.czscience.com/schema/metadata/ORCID) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: ORCID +alias: ORCID +domain_of: +- Author +- Annotator +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Organism.md b/schema/v1.1.0/metadata-docs/Organism.md new file mode 100644 index 000000000..1bfc9127c --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Organism.md @@ -0,0 +1,54 @@ +# Slot: organism + +URI: [cdp-meta:organism](https://cryoetdataportal.czscience.com/schema/metadata/organism) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: organism +alias: organism +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/PicturePath.md b/schema/v1.1.0/metadata-docs/PicturePath.md new file mode 100644 index 000000000..6c294a339 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/PicturePath.md @@ -0,0 +1,165 @@ +# Class: PicturePath + + +_A set of paths to representative images of a piece of data._ + + + + + +URI: [cdp-meta:PicturePath](https://cryoetdataportal.czscience.com/schema/metadata/PicturePath) + + + + +```mermaid + classDiagram + class PicturePath + PicturePath : snapshot + + PicturePath --> string : snapshot + + PicturePath : thumbnail + + PicturePath --> string : thumbnail + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [snapshot](snapshot.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Path to the dataset preview image relative to the dataset directory root | direct | +| [thumbnail](thumbnail.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Path to the thumbnail of preview image relative to the dataset directory root | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [PicturedEntity](PicturedEntity.md) | [key_photos](key_photos.md) | range | [PicturePath](PicturePath.md) | +| [Dataset](Dataset.md) | [key_photos](key_photos.md) | range | [PicturePath](PicturePath.md) | +| [Tomogram](Tomogram.md) | [key_photos](key_photos.md) | range | [PicturePath](PicturePath.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:PicturePath | +| native | cdp-meta:PicturePath | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: PicturePath +description: A set of paths to representative images of a piece of data. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + snapshot: + name: snapshot + description: Path to the dataset preview image relative to the dataset directory + root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: snapshot + owner: PicturePath + domain_of: + - PicturePath + range: string + inlined: true + inlined_as_list: true + thumbnail: + name: thumbnail + description: Path to the thumbnail of preview image relative to the dataset directory + root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: thumbnail + owner: PicturePath + domain_of: + - PicturePath + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: PicturePath +description: A set of paths to representative images of a piece of data. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + snapshot: + name: snapshot + description: Path to the dataset preview image relative to the dataset directory + root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: snapshot + owner: PicturePath + domain_of: + - PicturePath + range: string + inlined: true + inlined_as_list: true + thumbnail: + name: thumbnail + description: Path to the thumbnail of preview image relative to the dataset directory + root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: thumbnail + owner: PicturePath + domain_of: + - PicturePath + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/PicturedEntity.md b/schema/v1.1.0/metadata-docs/PicturedEntity.md new file mode 100644 index 000000000..671f4bc5b --- /dev/null +++ b/schema/v1.1.0/metadata-docs/PicturedEntity.md @@ -0,0 +1,136 @@ +# Class: PicturedEntity + + +_An entity with associated preview images._ + + + + +* __NOTE__: this is an abstract class and should not be instantiated directly + + +URI: [cdp-meta:PicturedEntity](https://cryoetdataportal.czscience.com/schema/metadata/PicturedEntity) + + + + +```mermaid + classDiagram + class PicturedEntity + PicturedEntity <|-- Dataset + PicturedEntity <|-- Tomogram + + PicturedEntity : key_photos + + PicturedEntity --> PicturePath : key_photos + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [key_photos](key_photos.md) | 1..1
[PicturePath](PicturePath.md) | A set of paths to representative images of a piece of data | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:PicturedEntity | +| native | cdp-meta:PicturedEntity | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: PicturedEntity +description: An entity with associated preview images. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: key_photos + owner: PicturedEntity + domain_of: + - PicturedEntity + - Dataset + - Tomogram + range: PicturePath + required: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: PicturedEntity +description: An entity with associated preview images. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +abstract: true +attributes: + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: key_photos + owner: PicturedEntity + domain_of: + - PicturedEntity + - Dataset + - Tomogram + range: PicturePath + required: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/SampleTypeEnum.md b/schema/v1.1.0/metadata-docs/SampleTypeEnum.md new file mode 100644 index 000000000..964361694 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/SampleTypeEnum.md @@ -0,0 +1,91 @@ +# Enum: SampleTypeEnum + + + + +_Type of sample imaged in a CryoET study._ + + + +URI: [SampleTypeEnum](SampleTypeEnum.md) + +## Permissible Values + +| Value | Meaning | Description | +| --- | --- | --- | +| cell | None | Tomographic data of whole cells or cell sections | +| tissue | None | Tomographic data of tissue sections | +| organism | None | Tomographic data of sections through multicellular organisms | +| organelle | None | Tomographic data of purified organelles | +| virus | None | Tomographic data of purified viruses or VLPs | +| in_vitro | None | Tomographic data of in vitro reconstituted systems or mixtures of proteins | +| in_silico | None | Simulated tomographic data | +| other | None | Other type of sample | + + + + +## Slots + +| Name | Description | +| --- | --- | +| [sample_type](sample_type.md) | Type of sample imaged in a CryoET study | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: sample_type_enum +description: Type of sample imaged in a CryoET study. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +permissible_values: + cell: + text: cell + description: Tomographic data of whole cells or cell sections. + tissue: + text: tissue + description: Tomographic data of tissue sections. + organism: + text: organism + description: Tomographic data of sections through multicellular organisms. + organelle: + text: organelle + description: Tomographic data of purified organelles. + virus: + text: virus + description: Tomographic data of purified viruses or VLPs. + in_vitro: + text: in_vitro + description: Tomographic data of in vitro reconstituted systems or mixtures of + proteins. + in_silico: + text: in_silico + description: Simulated tomographic data. + other: + text: other + description: Other type of sample. + +``` +
diff --git a/schema/v1.1.0/metadata-docs/TiltRange.md b/schema/v1.1.0/metadata-docs/TiltRange.md new file mode 100644 index 000000000..a77942631 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/TiltRange.md @@ -0,0 +1,167 @@ +# Class: TiltRange + + +_The range of tilt angles in the tilt series._ + + + + + +URI: [cdp-meta:TiltRange](https://cryoetdataportal.czscience.com/schema/metadata/TiltRange) + + + + +```mermaid + classDiagram + class TiltRange + TiltRange : max + + TiltRange --> float : max + + TiltRange : min + + TiltRange --> float : min + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [min](min.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Minimal tilt angle in degrees | direct | +| [max](max.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Maximal tilt angle in degrees | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [TiltSeries](TiltSeries.md) | [tilt_range](tilt_range.md) | range | [TiltRange](TiltRange.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:TiltRange | +| native | cdp-meta:TiltRange | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: TiltRange +description: The range of tilt angles in the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + min: + name: min + description: Minimal tilt angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_min + rank: 1000 + alias: min + owner: TiltRange + domain_of: + - TiltRange + range: float + inlined: true + inlined_as_list: true + max: + name: max + description: Maximal tilt angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_max + rank: 1000 + alias: max + owner: TiltRange + domain_of: + - TiltRange + range: float + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: TiltRange +description: The range of tilt angles in the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + min: + name: min + description: Minimal tilt angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_min + rank: 1000 + alias: min + owner: TiltRange + domain_of: + - TiltRange + range: float + inlined: true + inlined_as_list: true + max: + name: max + description: Maximal tilt angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_max + rank: 1000 + alias: max + owner: TiltRange + domain_of: + - TiltRange + range: float + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/TiltSeries.md b/schema/v1.1.0/metadata-docs/TiltSeries.md new file mode 100644 index 000000000..5dac42624 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/TiltSeries.md @@ -0,0 +1,645 @@ +# Class: TiltSeries + + +_Metadata describing a tilt series._ + + + + + +URI: [cdp-meta:TiltSeries](https://cryoetdataportal.czscience.com/schema/metadata/TiltSeries) + + + + +```mermaid + classDiagram + class TiltSeries + TiltSeries : acceleration_voltage + + TiltSeries --> integer : acceleration_voltage + + TiltSeries : aligned_tiltseries_binning + + TiltSeries --> integer : aligned_tiltseries_binning + + TiltSeries : binning_from_frames + + TiltSeries --> float : binning_from_frames + + TiltSeries : camera + + TiltSeries --> Camera : camera + + TiltSeries : data_acquisition_software + + TiltSeries --> string : data_acquisition_software + + TiltSeries : frames_count + + TiltSeries --> integer : frames_count + + TiltSeries : microscope + + TiltSeries --> Microscope : microscope + + TiltSeries : microscope_additional_info + + TiltSeries --> string : microscope_additional_info + + TiltSeries : microscope_optical_setup + + TiltSeries --> MicroscopeOpticalSetup : microscope_optical_setup + + TiltSeries : pixel_spacing + + TiltSeries --> float : pixel_spacing + + TiltSeries : spherical_aberration_constant + + TiltSeries --> float : spherical_aberration_constant + + TiltSeries : tilt_axis + + TiltSeries --> float : tilt_axis + + TiltSeries : tilt_range + + TiltSeries --> TiltRange : tilt_range + + TiltSeries : tilt_series_quality + + TiltSeries --> integer : tilt_series_quality + + TiltSeries : tilt_step + + TiltSeries --> float : tilt_step + + TiltSeries : tilting_scheme + + TiltSeries --> string : tilting_scheme + + TiltSeries : total_flux + + TiltSeries --> float : total_flux + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [acceleration_voltage](acceleration_voltage.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Electron Microscope Accelerator voltage in volts | direct | +| [spherical_aberration_constant](spherical_aberration_constant.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Spherical Aberration Constant of the objective lens in millimeters | direct | +| [microscope_additional_info](microscope_additional_info.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Other microscope optical setup information, in addition to energy filter, pha... | direct | +| [tilt_axis](tilt_axis.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Rotation angle in degrees | direct | +| [tilt_step](tilt_step.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Tilt step in degrees | direct | +| [tilting_scheme](tilting_scheme.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | The order of stage tilting during acquisition of the data | direct | +| [total_flux](total_flux.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Number of Electrons reaching the specimen in a square Angstrom area for the e... | direct | +| [data_acquisition_software](data_acquisition_software.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Software used to collect data | direct | +| [binning_from_frames](binning_from_frames.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Describes the binning factor from frames to tilt series file | direct | +| [tilt_series_quality](tilt_series_quality.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Author assessment of tilt series quality within the dataset (1-5, 5 is best) | direct | +| [pixel_spacing](pixel_spacing.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Pixel spacing for the tilt series | direct | +| [aligned_tiltseries_binning](aligned_tiltseries_binning.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Binning factor of the aligned tilt series | direct | +| [frames_count](frames_count.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Number of frames associated with this tiltseries | direct | +| [camera](camera.md) | 0..1
[Camera](Camera.md) | The camera used to collect the tilt series | direct | +| [microscope](microscope.md) | 0..1
[Microscope](Microscope.md) | The microscope used to collect the tilt series | direct | +| [microscope_optical_setup](microscope_optical_setup.md) | 0..1
[MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) | The optical setup of the microscope used to collect the tilt series | direct | +| [tilt_range](tilt_range.md) | 0..1
[TiltRange](TiltRange.md) | The range of tilt angles in the tilt series | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:TiltSeries | +| native | cdp-meta:TiltSeries | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: TiltSeries +description: Metadata describing a tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + acceleration_voltage: + name: acceleration_voltage + description: Electron Microscope Accelerator voltage in volts + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + rank: 1000 + alias: acceleration_voltage + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + spherical_aberration_constant: + name: spherical_aberration_constant + description: Spherical Aberration Constant of the objective lens in millimeters + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_spherical_aberration_constant + rank: 1000 + alias: spherical_aberration_constant + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + microscope_additional_info: + name: microscope_additional_info + description: Other microscope optical setup information, in addition to energy + filter, phase plate and image corrector + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + rank: 1000 + alias: microscope_additional_info + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + tilt_axis: + name: tilt_axis + description: Rotation angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_axis + rank: 1000 + alias: tilt_axis + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilt_step: + name: tilt_step + description: Tilt step in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_step + rank: 1000 + alias: tilt_step + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilting_scheme: + name: tilting_scheme + description: The order of stage tilting during acquisition of the data + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + rank: 1000 + alias: tilting_scheme + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + total_flux: + name: total_flux + description: Number of Electrons reaching the specimen in a square Angstrom area + for the entire tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_total_flux + rank: 1000 + alias: total_flux + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + data_acquisition_software: + name: data_acquisition_software + description: Software used to collect data + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + rank: 1000 + alias: data_acquisition_software + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + binning_from_frames: + name: binning_from_frames + description: Describes the binning factor from frames to tilt series file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_binning_from_frames + rank: 1000 + alias: binning_from_frames + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilt_series_quality: + name: tilt_series_quality + description: Author assessment of tilt series quality within the dataset (1-5, + 5 is best) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_series_quality + rank: 1000 + alias: tilt_series_quality + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + pixel_spacing: + name: pixel_spacing + description: Pixel spacing for the tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_pixel_spacing + rank: 1000 + alias: pixel_spacing + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + aligned_tiltseries_binning: + name: aligned_tiltseries_binning + description: Binning factor of the aligned tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_aligned_tiltseries_binning + rank: 1000 + alias: aligned_tiltseries_binning + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + frames_count: + name: frames_count + description: Number of frames associated with this tiltseries + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_frames_count + rank: 1000 + alias: frames_count + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + camera: + name: camera + description: The camera used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: camera + owner: TiltSeries + domain_of: + - TiltSeries + range: Camera + inlined: true + inlined_as_list: true + microscope: + name: microscope + description: The microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: microscope + owner: TiltSeries + domain_of: + - TiltSeries + range: Microscope + inlined: true + inlined_as_list: true + microscope_optical_setup: + name: microscope_optical_setup + description: The optical setup of the microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: microscope_optical_setup + owner: TiltSeries + domain_of: + - TiltSeries + range: MicroscopeOpticalSetup + inlined: true + inlined_as_list: true + tilt_range: + name: tilt_range + description: The range of tilt angles in the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: tilt_range + owner: TiltSeries + domain_of: + - TiltSeries + range: TiltRange + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: TiltSeries +description: Metadata describing a tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + acceleration_voltage: + name: acceleration_voltage + description: Electron Microscope Accelerator voltage in volts + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + rank: 1000 + alias: acceleration_voltage + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + spherical_aberration_constant: + name: spherical_aberration_constant + description: Spherical Aberration Constant of the objective lens in millimeters + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_spherical_aberration_constant + rank: 1000 + alias: spherical_aberration_constant + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + microscope_additional_info: + name: microscope_additional_info + description: Other microscope optical setup information, in addition to energy + filter, phase plate and image corrector + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + rank: 1000 + alias: microscope_additional_info + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + tilt_axis: + name: tilt_axis + description: Rotation angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_axis + rank: 1000 + alias: tilt_axis + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilt_step: + name: tilt_step + description: Tilt step in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_step + rank: 1000 + alias: tilt_step + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilting_scheme: + name: tilting_scheme + description: The order of stage tilting during acquisition of the data + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + rank: 1000 + alias: tilting_scheme + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + total_flux: + name: total_flux + description: Number of Electrons reaching the specimen in a square Angstrom area + for the entire tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_total_flux + rank: 1000 + alias: total_flux + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + data_acquisition_software: + name: data_acquisition_software + description: Software used to collect data + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + rank: 1000 + alias: data_acquisition_software + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + binning_from_frames: + name: binning_from_frames + description: Describes the binning factor from frames to tilt series file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_binning_from_frames + rank: 1000 + alias: binning_from_frames + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilt_series_quality: + name: tilt_series_quality + description: Author assessment of tilt series quality within the dataset (1-5, + 5 is best) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_series_quality + rank: 1000 + alias: tilt_series_quality + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + pixel_spacing: + name: pixel_spacing + description: Pixel spacing for the tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_pixel_spacing + rank: 1000 + alias: pixel_spacing + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + aligned_tiltseries_binning: + name: aligned_tiltseries_binning + description: Binning factor of the aligned tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_aligned_tiltseries_binning + rank: 1000 + alias: aligned_tiltseries_binning + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + frames_count: + name: frames_count + description: Number of frames associated with this tiltseries + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_frames_count + rank: 1000 + alias: frames_count + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + camera: + name: camera + description: The camera used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: camera + owner: TiltSeries + domain_of: + - TiltSeries + range: Camera + inlined: true + inlined_as_list: true + microscope: + name: microscope + description: The microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: microscope + owner: TiltSeries + domain_of: + - TiltSeries + range: Microscope + inlined: true + inlined_as_list: true + microscope_optical_setup: + name: microscope_optical_setup + description: The optical setup of the microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: microscope_optical_setup + owner: TiltSeries + domain_of: + - TiltSeries + range: MicroscopeOpticalSetup + inlined: true + inlined_as_list: true + tilt_range: + name: tilt_range + description: The range of tilt angles in the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: tilt_range + owner: TiltSeries + domain_of: + - TiltSeries + range: TiltRange + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Tissue.md b/schema/v1.1.0/metadata-docs/Tissue.md new file mode 100644 index 000000000..bcecda29b --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Tissue.md @@ -0,0 +1,54 @@ +# Slot: tissue + +URI: [cdp-meta:tissue](https://cryoetdataportal.czscience.com/schema/metadata/tissue) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: tissue +alias: tissue +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/Tomogram.md b/schema/v1.1.0/metadata-docs/Tomogram.md new file mode 100644 index 000000000..80f7562bf --- /dev/null +++ b/schema/v1.1.0/metadata-docs/Tomogram.md @@ -0,0 +1,545 @@ +# Class: Tomogram + + +_Metadata describing a tomogram._ + + + + + +URI: [cdp-meta:Tomogram](https://cryoetdataportal.czscience.com/schema/metadata/Tomogram) + + + + +```mermaid + classDiagram + class Tomogram + AuthoredEntity <|-- Tomogram + PicturedEntity <|-- Tomogram + + Tomogram : affine_transformation_matrix + + Tomogram --> string : affine_transformation_matrix + + Tomogram : authors + + Tomogram --> Author : authors + + Tomogram : ctf_corrected + + Tomogram --> boolean : ctf_corrected + + Tomogram : fiducial_alignment_status + + Tomogram --> fiducial_alignment_status_enum : fiducial_alignment_status + + Tomogram : key_photos + + Tomogram --> PicturePath : key_photos + + Tomogram : offset + + Tomogram --> TomogramOffset : offset + + Tomogram : processing + + Tomogram --> string : processing + + Tomogram : processing_software + + Tomogram --> string : processing_software + + Tomogram : reconstruction_method + + Tomogram --> string : reconstruction_method + + Tomogram : reconstruction_software + + Tomogram --> string : reconstruction_software + + Tomogram : size + + Tomogram --> TomogramSize : size + + Tomogram : tomogram_version + + Tomogram --> string : tomogram_version + + Tomogram : voxel_spacing + + Tomogram --> float : voxel_spacing + + +``` + + + + + +## Inheritance +* **Tomogram** [ [AuthoredEntity](AuthoredEntity.md) [PicturedEntity](PicturedEntity.md)] + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [voxel_spacing](voxel_spacing.md) | 0..1
[xsd:float](http://www.w3.org/2001/XMLSchema#float) | Voxel spacing equal in all three axes in angstroms | direct | +| [fiducial_alignment_status](fiducial_alignment_status.md) | 0..1
[FiducialAlignmentStatusEnum](FiducialAlignmentStatusEnum.md) | Whether the tomographic alignment was computed based on fiducial markers | direct | +| [ctf_corrected](ctf_corrected.md) | 0..1
[xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | Whether this tomogram is CTF corrected | direct | +| [reconstruction_method](reconstruction_method.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describe reconstruction method (Weighted back-projection, SART, SIRT) | direct | +| [reconstruction_software](reconstruction_software.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Name of software used for reconstruction | direct | +| [processing](processing.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Describe additional processing used to derive the tomogram | direct | +| [processing_software](processing_software.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Processing software used to derive the tomogram | direct | +| [tomogram_version](tomogram_version.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | Version of tomogram using the same software and post-processing | direct | +| [affine_transformation_matrix](affine_transformation_matrix.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | The flip or rotation transformation of this author submitted tomogram is indi... | direct | +| [size](size.md) | 0..1
[TomogramSize](TomogramSize.md) | The size of a tomogram in voxels in each dimension | direct | +| [offset](offset.md) | 0..1
[TomogramOffset](TomogramOffset.md) | The offset of a tomogram in voxels in each dimension relative to the canonica... | direct | +| [authors](authors.md) | 1..*
[Author](Author.md) | Author of a scientific data entity | direct | +| [key_photos](key_photos.md) | 1..1
[PicturePath](PicturePath.md) | A set of paths to representative images of a piece of data | direct | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:Tomogram | +| native | cdp-meta:Tomogram | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: Tomogram +description: Metadata describing a tomogram. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +mixins: +- AuthoredEntity +- PicturedEntity +attributes: + voxel_spacing: + name: voxel_spacing + description: Voxel spacing equal in all three axes in angstroms + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_voxel_spacing + rank: 1000 + alias: voxel_spacing + owner: Tomogram + domain_of: + - Tomogram + range: float + inlined: true + inlined_as_list: true + fiducial_alignment_status: + name: fiducial_alignment_status + description: Whether the tomographic alignment was computed based on fiducial + markers. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_fiducial_alignment_status + rank: 1000 + alias: fiducial_alignment_status + owner: Tomogram + domain_of: + - Tomogram + range: fiducial_alignment_status_enum + inlined: true + inlined_as_list: true + ctf_corrected: + name: ctf_corrected + description: Whether this tomogram is CTF corrected + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_ctf_corrected + rank: 1000 + alias: ctf_corrected + owner: Tomogram + domain_of: + - Tomogram + range: boolean + inlined: true + inlined_as_list: true + reconstruction_method: + name: reconstruction_method + description: Describe reconstruction method (Weighted back-projection, SART, SIRT) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_method + rank: 1000 + alias: reconstruction_method + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + reconstruction_software: + name: reconstruction_software + description: Name of software used for reconstruction + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_software + rank: 1000 + alias: reconstruction_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + processing: + name: processing + description: Describe additional processing used to derive the tomogram + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_processing + rank: 1000 + alias: processing + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + processing_software: + name: processing_software + description: Processing software used to derive the tomogram + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_processing_software + rank: 1000 + alias: processing_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + tomogram_version: + name: tomogram_version + description: Version of tomogram using the same software and post-processing. + Version of tomogram using the same software and post-processing. This will be + presented as the latest version + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_version + rank: 1000 + alias: tomogram_version + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + affine_transformation_matrix: + name: affine_transformation_matrix + description: The flip or rotation transformation of this author submitted tomogram + is indicated here + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_affine_transformation_matrix + rank: 1000 + alias: affine_transformation_matrix + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + size: + name: size + description: The size of a tomogram in voxels in each dimension. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: size + owner: Tomogram + domain_of: + - Tomogram + range: TomogramSize + inlined: true + inlined_as_list: true + offset: + name: offset + description: The offset of a tomogram in voxels in each dimension relative to + the canonical tomogram. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: offset + owner: Tomogram + domain_of: + - Tomogram + range: TomogramOffset + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Tomogram + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Author + required: true + inlined: true + inlined_as_list: true + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: Tomogram + domain_of: + - PicturedEntity + - Dataset + - Tomogram + range: PicturePath + required: true + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: Tomogram +description: Metadata describing a tomogram. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +mixins: +- AuthoredEntity +- PicturedEntity +attributes: + voxel_spacing: + name: voxel_spacing + description: Voxel spacing equal in all three axes in angstroms + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_voxel_spacing + rank: 1000 + alias: voxel_spacing + owner: Tomogram + domain_of: + - Tomogram + range: float + inlined: true + inlined_as_list: true + fiducial_alignment_status: + name: fiducial_alignment_status + description: Whether the tomographic alignment was computed based on fiducial + markers. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_fiducial_alignment_status + rank: 1000 + alias: fiducial_alignment_status + owner: Tomogram + domain_of: + - Tomogram + range: fiducial_alignment_status_enum + inlined: true + inlined_as_list: true + ctf_corrected: + name: ctf_corrected + description: Whether this tomogram is CTF corrected + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_ctf_corrected + rank: 1000 + alias: ctf_corrected + owner: Tomogram + domain_of: + - Tomogram + range: boolean + inlined: true + inlined_as_list: true + reconstruction_method: + name: reconstruction_method + description: Describe reconstruction method (Weighted back-projection, SART, SIRT) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_method + rank: 1000 + alias: reconstruction_method + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + reconstruction_software: + name: reconstruction_software + description: Name of software used for reconstruction + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_software + rank: 1000 + alias: reconstruction_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + processing: + name: processing + description: Describe additional processing used to derive the tomogram + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_processing + rank: 1000 + alias: processing + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + processing_software: + name: processing_software + description: Processing software used to derive the tomogram + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_processing_software + rank: 1000 + alias: processing_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + tomogram_version: + name: tomogram_version + description: Version of tomogram using the same software and post-processing. + Version of tomogram using the same software and post-processing. This will be + presented as the latest version + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_version + rank: 1000 + alias: tomogram_version + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + affine_transformation_matrix: + name: affine_transformation_matrix + description: The flip or rotation transformation of this author submitted tomogram + is indicated here + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_affine_transformation_matrix + rank: 1000 + alias: affine_transformation_matrix + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + size: + name: size + description: The size of a tomogram in voxels in each dimension. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: size + owner: Tomogram + domain_of: + - Tomogram + range: TomogramSize + inlined: true + inlined_as_list: true + offset: + name: offset + description: The offset of a tomogram in voxels in each dimension relative to + the canonical tomogram. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + rank: 1000 + alias: offset + owner: Tomogram + domain_of: + - Tomogram + range: TomogramOffset + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Tomogram + domain_of: + - AuthoredEntity + - AnnotatoredEntity + - Dataset + - Tomogram + - Annotation + range: Author + required: true + inlined: true + inlined_as_list: true + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: Tomogram + domain_of: + - PicturedEntity + - Dataset + - Tomogram + range: PicturePath + required: true + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/TomogramOffset.md b/schema/v1.1.0/metadata-docs/TomogramOffset.md new file mode 100644 index 000000000..a739c7c9e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/TomogramOffset.md @@ -0,0 +1,196 @@ +# Class: TomogramOffset + + +_The offset of a tomogram in voxels in each dimension relative to the canonical tomogram._ + + + + + +URI: [cdp-meta:TomogramOffset](https://cryoetdataportal.czscience.com/schema/metadata/TomogramOffset) + + + + +```mermaid + classDiagram + class TomogramOffset + TomogramOffset : x + + TomogramOffset --> string : x + + TomogramOffset : y + + TomogramOffset --> string : y + + TomogramOffset : z + + TomogramOffset --> string : z + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [x](x.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [y](y.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | +| [z](z.md) | 0..1
[xsd:string](http://www.w3.org/2001/XMLSchema#string) | | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [Tomogram](Tomogram.md) | [offset](offset.md) | range | [TomogramOffset](TomogramOffset.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:TomogramOffset | +| native | cdp-meta:TomogramOffset | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: TomogramOffset +description: The offset of a tomogram in voxels in each dimension relative to the + canonical tomogram. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + x: + name: x + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_x + alias: x + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + y: + name: y + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_y + alias: y + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + z: + name: z + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_z + alias: z + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: TomogramOffset +description: The offset of a tomogram in voxels in each dimension relative to the + canonical tomogram. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + x: + name: x + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_x + alias: x + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + y: + name: y + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_y + alias: y + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + z: + name: z + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_z + alias: z + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/TomogramSize.md b/schema/v1.1.0/metadata-docs/TomogramSize.md new file mode 100644 index 000000000..8ad184076 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/TomogramSize.md @@ -0,0 +1,208 @@ +# Class: TomogramSize + + +_The size of a tomogram in voxels in each dimension._ + + + + + +URI: [cdp-meta:TomogramSize](https://cryoetdataportal.czscience.com/schema/metadata/TomogramSize) + + + + +```mermaid + classDiagram + class TomogramSize + TomogramSize : x + + TomogramSize --> integer : x + + TomogramSize : y + + TomogramSize --> integer : y + + TomogramSize : z + + TomogramSize --> integer : z + + +``` + + + + + + + +## Slots + +| Name | Cardinality and Range | Description | Inheritance | +| --- | --- | --- | --- | +| [x](x.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Number of pixels in the 3D data fast axis | direct | +| [y](y.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Number of pixels in the 3D data medium axis | direct | +| [z](z.md) | 0..1
[xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Number of pixels in the 3D data slow axis | direct | + + + + + +## Usages + +| used by | used in | type | used | +| --- | --- | --- | --- | +| [Tomogram](Tomogram.md) | [size](size.md) | range | [TomogramSize](TomogramSize.md) | + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + + +## Mappings + +| Mapping Type | Mapped Value | +| --- | --- | +| self | cdp-meta:TomogramSize | +| native | cdp-meta:TomogramSize | + + + + + +## LinkML Source + + + +### Direct + +
+```yaml +name: TomogramSize +description: The size of a tomogram in voxels in each dimension. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + x: + name: x + description: Number of pixels in the 3D data fast axis + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_x + rank: 1000 + alias: x + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + y: + name: y + description: Number of pixels in the 3D data medium axis + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_y + rank: 1000 + alias: y + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + z: + name: z + description: Number of pixels in the 3D data slow axis. This is the image projection + direction at zero stage tilt + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_z + rank: 1000 + alias: z + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + +``` +
+ +### Induced + +
+```yaml +name: TomogramSize +description: The size of a tomogram in voxels in each dimension. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +attributes: + x: + name: x + description: Number of pixels in the 3D data fast axis + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_x + rank: 1000 + alias: x + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + y: + name: y + description: Number of pixels in the 3D data medium axis + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_y + rank: 1000 + alias: y + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + z: + name: z + description: Number of pixels in the 3D data slow axis. This is the image projection + direction at zero stage tilt + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_z + rank: 1000 + alias: z + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md b/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md new file mode 100644 index 000000000..09aadb185 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md @@ -0,0 +1,56 @@ +# Enum: TomogramTypeEnum + + + + +_Tomogram type_ + + + +URI: [TomogramTypeEnum](TomogramTypeEnum.md) + +## Permissible Values + +| Value | Meaning | Description | +| --- | --- | --- | +| CANONICAL | None | Canonical tomogram (basis geometry for all annotations) | + + + + + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tomogram_type_enum +description: Tomogram type +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +permissible_values: + CANONICAL: + text: CANONICAL + description: Canonical tomogram (basis geometry for all annotations) + +``` +
diff --git a/schema/v1.1.0/metadata-docs/acceleration_voltage.md b/schema/v1.1.0/metadata-docs/acceleration_voltage.md new file mode 100644 index 000000000..ee3d8cb51 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/acceleration_voltage.md @@ -0,0 +1,72 @@ +# Slot: acceleration_voltage + + +_Electron Microscope Accelerator voltage in volts_ + + + +URI: [cdp-meta:acceleration_voltage](https://cryoetdataportal.czscience.com/schema/metadata/acceleration_voltage) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: acceleration_voltage +description: Electron Microscope Accelerator voltage in volts +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_acceleration_voltage +rank: 1000 +alias: acceleration_voltage +owner: TiltSeries +domain_of: +- TiltSeries +range: integer +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/affiliation_address.md b/schema/v1.1.0/metadata-docs/affiliation_address.md new file mode 100644 index 000000000..5952e5c8a --- /dev/null +++ b/schema/v1.1.0/metadata-docs/affiliation_address.md @@ -0,0 +1,54 @@ +# Slot: affiliation_address + +URI: [cdp-meta:affiliation_address](https://cryoetdataportal.czscience.com/schema/metadata/affiliation_address) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: affiliation_address +alias: affiliation_address +domain_of: +- Author +- Annotator +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/affiliation_identifier.md b/schema/v1.1.0/metadata-docs/affiliation_identifier.md new file mode 100644 index 000000000..e1a8187df --- /dev/null +++ b/schema/v1.1.0/metadata-docs/affiliation_identifier.md @@ -0,0 +1,54 @@ +# Slot: affiliation_identifier + +URI: [cdp-meta:affiliation_identifier](https://cryoetdataportal.czscience.com/schema/metadata/affiliation_identifier) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: affiliation_identifier +alias: affiliation_identifier +domain_of: +- Author +- Annotator +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/affiliation_name.md b/schema/v1.1.0/metadata-docs/affiliation_name.md new file mode 100644 index 000000000..9b711b430 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/affiliation_name.md @@ -0,0 +1,54 @@ +# Slot: affiliation_name + +URI: [cdp-meta:affiliation_name](https://cryoetdataportal.czscience.com/schema/metadata/affiliation_name) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: affiliation_name +alias: affiliation_name +domain_of: +- Author +- Annotator +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md b/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md new file mode 100644 index 000000000..35b10c3d2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md @@ -0,0 +1,73 @@ +# Slot: affine_transformation_matrix + + +_The flip or rotation transformation of this author submitted tomogram is indicated here_ + + + +URI: [cdp-meta:affine_transformation_matrix](https://cryoetdataportal.czscience.com/schema/metadata/affine_transformation_matrix) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: affine_transformation_matrix +description: The flip or rotation transformation of this author submitted tomogram + is indicated here +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_affine_transformation_matrix +rank: 1000 +alias: affine_transformation_matrix +owner: Tomogram +domain_of: +- Tomogram +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md b/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md new file mode 100644 index 000000000..2fc143347 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md @@ -0,0 +1,72 @@ +# Slot: aligned_tiltseries_binning + + +_Binning factor of the aligned tilt series_ + + + +URI: [cdp-meta:aligned_tiltseries_binning](https://cryoetdataportal.czscience.com/schema/metadata/aligned_tiltseries_binning) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: aligned_tiltseries_binning +description: Binning factor of the aligned tilt series +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_aligned_tiltseries_binning +rank: 1000 +alias: aligned_tiltseries_binning +owner: TiltSeries +domain_of: +- TiltSeries +range: integer +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/annotation_method.md b/schema/v1.1.0/metadata-docs/annotation_method.md new file mode 100644 index 000000000..7b3b960ae --- /dev/null +++ b/schema/v1.1.0/metadata-docs/annotation_method.md @@ -0,0 +1,73 @@ +# Slot: annotation_method + + +_Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching)_ + + + +URI: [cdp-meta:annotation_method](https://cryoetdataportal.czscience.com/schema/metadata/annotation_method) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_method +description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled + Learning, template matching) +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_method +rank: 1000 +alias: annotation_method +owner: Annotation +domain_of: +- Annotation +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/annotation_method_type.md b/schema/v1.1.0/metadata-docs/annotation_method_type.md new file mode 100644 index 000000000..a97e87735 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/annotation_method_type.md @@ -0,0 +1,72 @@ +# Slot: annotation_method_type + + +_Classification of the annotation method based on supervision._ + + + +URI: [cdp-meta:annotation_method_type](https://cryoetdataportal.czscience.com/schema/metadata/annotation_method_type) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [AnnotationMethodTypeEnum](AnnotationMethodTypeEnum.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_method_type +description: Classification of the annotation method based on supervision. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_method_type +rank: 1000 +alias: annotation_method_type +owner: Annotation +domain_of: +- Annotation +range: annotation_method_type_enum +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/annotation_object.md b/schema/v1.1.0/metadata-docs/annotation_object.md new file mode 100644 index 000000000..7894a7aef --- /dev/null +++ b/schema/v1.1.0/metadata-docs/annotation_object.md @@ -0,0 +1,70 @@ +# Slot: annotation_object + + +_Metadata describing the object being annotated._ + + + +URI: [cdp-meta:annotation_object](https://cryoetdataportal.czscience.com/schema/metadata/annotation_object) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [AnnotationObject](AnnotationObject.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_object +description: Metadata describing the object being annotated. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: annotation_object +owner: Annotation +domain_of: +- Annotation +range: AnnotationObject +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/annotation_publications.md b/schema/v1.1.0/metadata-docs/annotation_publications.md new file mode 100644 index 000000000..6ae49d083 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/annotation_publications.md @@ -0,0 +1,73 @@ +# Slot: annotation_publications + + +_DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs._ + + + +URI: [cdp-meta:annotation_publications](https://cryoetdataportal.czscience.com/schema/metadata/annotation_publications) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_publications +description: DOIs for publications that describe the dataset. Use a comma to separate + multiple DOIs. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_publication +rank: 1000 +alias: annotation_publications +owner: Annotation +domain_of: +- Annotation +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/annotation_software.md b/schema/v1.1.0/metadata-docs/annotation_software.md new file mode 100644 index 000000000..85eac7fc1 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/annotation_software.md @@ -0,0 +1,72 @@ +# Slot: annotation_software + + +_Software used for generating this annotation_ + + + +URI: [cdp-meta:annotation_software](https://cryoetdataportal.czscience.com/schema/metadata/annotation_software) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: annotation_software +description: Software used for generating this annotation +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_software +rank: 1000 +alias: annotation_software +owner: Annotation +domain_of: +- Annotation +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/authors.md b/schema/v1.1.0/metadata-docs/authors.md new file mode 100644 index 000000000..a9c758be0 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/authors.md @@ -0,0 +1,60 @@ +# Slot: authors + +URI: [cdp-meta:authors](https://cryoetdataportal.czscience.com/schema/metadata/authors) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AuthoredEntity](AuthoredEntity.md) | An entity with associated authors | no | +[AnnotatoredEntity](AnnotatoredEntity.md) | An entity with associated annotation authors | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: authors +alias: authors +domain_of: +- AuthoredEntity +- AnnotatoredEntity +- Dataset +- Tomogram +- Annotation +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/binning_from_frames.md b/schema/v1.1.0/metadata-docs/binning_from_frames.md new file mode 100644 index 000000000..922306895 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/binning_from_frames.md @@ -0,0 +1,72 @@ +# Slot: binning_from_frames + + +_Describes the binning factor from frames to tilt series file_ + + + +URI: [cdp-meta:binning_from_frames](https://cryoetdataportal.czscience.com/schema/metadata/binning_from_frames) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: binning_from_frames +description: Describes the binning factor from frames to tilt series file +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_binning_from_frames +rank: 1000 +alias: binning_from_frames +owner: TiltSeries +domain_of: +- TiltSeries +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/cdp-meta.md b/schema/v1.1.0/metadata-docs/cdp-meta.md new file mode 100644 index 000000000..9f8cb135e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/cdp-meta.md @@ -0,0 +1,6 @@ +# cdp-meta + +None + +URI: https://cryoetdataportal.czscience.com/schema-docs/metadata + diff --git a/schema/v1.1.0/metadata-docs/cell_component.md b/schema/v1.1.0/metadata-docs/cell_component.md new file mode 100644 index 000000000..6573d7fc2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/cell_component.md @@ -0,0 +1,54 @@ +# Slot: cell_component + +URI: [cdp-meta:cell_component](https://cryoetdataportal.czscience.com/schema/metadata/cell_component) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: cell_component +alias: cell_component +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/cell_strain.md b/schema/v1.1.0/metadata-docs/cell_strain.md new file mode 100644 index 000000000..22a518234 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/cell_strain.md @@ -0,0 +1,54 @@ +# Slot: cell_strain + +URI: [cdp-meta:cell_strain](https://cryoetdataportal.czscience.com/schema/metadata/cell_strain) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: cell_strain +alias: cell_strain +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/cell_type.md b/schema/v1.1.0/metadata-docs/cell_type.md new file mode 100644 index 000000000..cbf8dda64 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/cell_type.md @@ -0,0 +1,54 @@ +# Slot: cell_type + +URI: [cdp-meta:cell_type](https://cryoetdataportal.czscience.com/schema/metadata/cell_type) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: cell_type +alias: cell_type +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/confidence.md b/schema/v1.1.0/metadata-docs/confidence.md new file mode 100644 index 000000000..fc2def7a2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/confidence.md @@ -0,0 +1,70 @@ +# Slot: confidence + + +_Metadata describing the confidence of an annotation._ + + + +URI: [cdp-meta:confidence](https://cryoetdataportal.czscience.com/schema/metadata/confidence) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [AnnotationConfidence](AnnotationConfidence.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: confidence +description: Metadata describing the confidence of an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: confidence +owner: Annotation +domain_of: +- Annotation +range: AnnotationConfidence +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/cross_references.md b/schema/v1.1.0/metadata-docs/cross_references.md new file mode 100644 index 000000000..e082729cc --- /dev/null +++ b/schema/v1.1.0/metadata-docs/cross_references.md @@ -0,0 +1,54 @@ +# Slot: cross_references + +URI: [cdp-meta:cross_references](https://cryoetdataportal.czscience.com/schema/metadata/cross_references) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[CrossReferencedEntity](CrossReferencedEntity.md) | An entity with associated cross-references to other databases and publication... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: cross_references +alias: cross_references +domain_of: +- CrossReferencedEntity +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/ctf_corrected.md b/schema/v1.1.0/metadata-docs/ctf_corrected.md new file mode 100644 index 000000000..c967baac5 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/ctf_corrected.md @@ -0,0 +1,72 @@ +# Slot: ctf_corrected + + +_Whether this tomogram is CTF corrected_ + + + +URI: [cdp-meta:ctf_corrected](https://cryoetdataportal.czscience.com/schema/metadata/ctf_corrected) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: ctf_corrected +description: Whether this tomogram is CTF corrected +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_ctf_corrected +rank: 1000 +alias: ctf_corrected +owner: Tomogram +domain_of: +- Tomogram +range: boolean +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/data_acquisition_software.md b/schema/v1.1.0/metadata-docs/data_acquisition_software.md new file mode 100644 index 000000000..54ec77ae1 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/data_acquisition_software.md @@ -0,0 +1,72 @@ +# Slot: data_acquisition_software + + +_Software used to collect data_ + + + +URI: [cdp-meta:data_acquisition_software](https://cryoetdataportal.czscience.com/schema/metadata/data_acquisition_software) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: data_acquisition_software +description: Software used to collect data +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_data_acquisition_software +rank: 1000 +alias: data_acquisition_software +owner: TiltSeries +domain_of: +- TiltSeries +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/dataset_citations.md b/schema/v1.1.0/metadata-docs/dataset_citations.md new file mode 100644 index 000000000..4b98fc247 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/dataset_citations.md @@ -0,0 +1,70 @@ +# Slot: dataset_citations + + +_Comma-separated list of DOIs for publications citing the dataset._ + + + +URI: [cdp-meta:dataset_citations](https://cryoetdataportal.czscience.com/schema/metadata/dataset_citations) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: dataset_citations +description: Comma-separated list of DOIs for publications citing the dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: dataset_citations +owner: CrossReferences +domain_of: +- CrossReferences +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/dataset_description.md b/schema/v1.1.0/metadata-docs/dataset_description.md new file mode 100644 index 000000000..0c1263647 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/dataset_description.md @@ -0,0 +1,73 @@ +# Slot: dataset_description + + +_A short description of a CryoET dataset, similar to an abstract for a journal article or dataset._ + + + +URI: [cdp-meta:dataset_description](https://cryoetdataportal.czscience.com/schema/metadata/dataset_description) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: dataset_description +description: A short description of a CryoET dataset, similar to an abstract for a + journal article or dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:dataset_description +rank: 1000 +alias: dataset_description +owner: Dataset +domain_of: +- Dataset +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/dataset_identifier.md b/schema/v1.1.0/metadata-docs/dataset_identifier.md new file mode 100644 index 000000000..94dd88ebc --- /dev/null +++ b/schema/v1.1.0/metadata-docs/dataset_identifier.md @@ -0,0 +1,73 @@ +# Slot: dataset_identifier + + +_An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree._ + + + +URI: [cdp-meta:dataset_identifier](https://cryoetdataportal.czscience.com/schema/metadata/dataset_identifier) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: dataset_identifier +description: An identifier for a CryoET dataset, assigned by the Data Portal. Used + to identify the dataset as the directory name in data tree. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:dataset_identifier +rank: 1000 +alias: dataset_identifier +owner: Dataset +domain_of: +- Dataset +range: integer +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/dataset_publications.md b/schema/v1.1.0/metadata-docs/dataset_publications.md new file mode 100644 index 000000000..3729b4464 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/dataset_publications.md @@ -0,0 +1,73 @@ +# Slot: dataset_publications + + +_Comma-separated list of DOIs for publications associated with the dataset._ + + + +URI: [cdp-meta:dataset_publications](https://cryoetdataportal.czscience.com/schema/metadata/dataset_publications) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + +* Recommended: True + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: dataset_publications +description: Comma-separated list of DOIs for publications associated with the dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: dataset_publications +owner: CrossReferences +domain_of: +- CrossReferences +range: string +recommended: true +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/dataset_title.md b/schema/v1.1.0/metadata-docs/dataset_title.md new file mode 100644 index 000000000..8536705f4 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/dataset_title.md @@ -0,0 +1,72 @@ +# Slot: dataset_title + + +_Title of a CryoET dataset._ + + + +URI: [cdp-meta:dataset_title](https://cryoetdataportal.czscience.com/schema/metadata/dataset_title) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: dataset_title +description: Title of a CryoET dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:dataset_title +rank: 1000 +alias: dataset_title +owner: Dataset +domain_of: +- Dataset +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/dates.md b/schema/v1.1.0/metadata-docs/dates.md new file mode 100644 index 000000000..ce8f19d38 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/dates.md @@ -0,0 +1,56 @@ +# Slot: dates + +URI: [cdp-meta:dates](https://cryoetdataportal.czscience.com/schema/metadata/dates) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[DatestampedEntity](DatestampedEntity.md) | An entity with associated deposition, release and last modified dates | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: dates +alias: dates +domain_of: +- DatestampedEntity +- Dataset +- Annotation +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/deposition_date.md b/schema/v1.1.0/metadata-docs/deposition_date.md new file mode 100644 index 000000000..78b5c466b --- /dev/null +++ b/schema/v1.1.0/metadata-docs/deposition_date.md @@ -0,0 +1,73 @@ +# Slot: deposition_date + + +_The date a data item was received by the cryoET data portal._ + + + +URI: [cdp-meta:deposition_date](https://cryoetdataportal.czscience.com/schema/metadata/deposition_date) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modifie... | yes | + + + + + + + +## Properties + +* Range: [xsd:date](http://www.w3.org/2001/XMLSchema#date) + +* Required: True + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: deposition_date +description: The date a data item was received by the cryoET data portal. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: deposition_date +owner: DateStamp +domain_of: +- DateStamp +range: date +required: true +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/description.md b/schema/v1.1.0/metadata-docs/description.md new file mode 100644 index 000000000..c29b0af67 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/description.md @@ -0,0 +1,74 @@ +# Slot: description + + +_A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state._ + + + +URI: [cdp-meta:description](https://cryoetdataportal.czscience.com/schema/metadata/description) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationObject](AnnotationObject.md) | Metadata describing the object being annotated | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: description +description: A textual description of the annotation object, can be a longer description + to include additional information not covered by the Annotation object name and + state. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_object_description +rank: 1000 +alias: description +owner: AnnotationObject +domain_of: +- AnnotationObject +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/email.md b/schema/v1.1.0/metadata-docs/email.md new file mode 100644 index 000000000..82d876da2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/email.md @@ -0,0 +1,54 @@ +# Slot: email + +URI: [cdp-meta:email](https://cryoetdataportal.czscience.com/schema/metadata/email) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: email +alias: email +domain_of: +- Author +- Annotator +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/energy_filter.md b/schema/v1.1.0/metadata-docs/energy_filter.md new file mode 100644 index 000000000..d6bfa5229 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/energy_filter.md @@ -0,0 +1,72 @@ +# Slot: energy_filter + + +_Energy filter setup used_ + + + +URI: [cdp-meta:energy_filter](https://cryoetdataportal.czscience.com/schema/metadata/energy_filter) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) | The optical setup of the microscope used to collect the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: energy_filter +description: Energy filter setup used +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_microscope_energy_filter +rank: 1000 +alias: energy_filter +owner: MicroscopeOpticalSetup +domain_of: +- MicroscopeOpticalSetup +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md b/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md new file mode 100644 index 000000000..209612612 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md @@ -0,0 +1,72 @@ +# Slot: fiducial_alignment_status + + +_Whether the tomographic alignment was computed based on fiducial markers._ + + + +URI: [cdp-meta:fiducial_alignment_status](https://cryoetdataportal.czscience.com/schema/metadata/fiducial_alignment_status) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [FiducialAlignmentStatusEnum](FiducialAlignmentStatusEnum.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: fiducial_alignment_status +description: Whether the tomographic alignment was computed based on fiducial markers. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_fiducial_alignment_status +rank: 1000 +alias: fiducial_alignment_status +owner: Tomogram +domain_of: +- Tomogram +range: fiducial_alignment_status_enum +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/files.md b/schema/v1.1.0/metadata-docs/files.md new file mode 100644 index 000000000..250fdbba0 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/files.md @@ -0,0 +1,74 @@ +# Slot: files + + +_Metadata describing a file containing an annotation._ + + + +URI: [cdp-meta:files](https://cryoetdataportal.czscience.com/schema/metadata/files) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [AnnotationFile](AnnotationFile.md) + +* Multivalued: True + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: files +description: Metadata describing a file containing an annotation. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +multivalued: true +list_elements_ordered: true +alias: files +owner: Annotation +domain_of: +- Annotation +range: AnnotationFile +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/format.md b/schema/v1.1.0/metadata-docs/format.md new file mode 100644 index 000000000..5c62c3b89 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/format.md @@ -0,0 +1,72 @@ +# Slot: format + + +_File format for this file_ + + + +URI: [cdp-meta:format](https://cryoetdataportal.czscience.com/schema/metadata/format) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationFile](AnnotationFile.md) | Metadata describing a file containing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: format +description: File format for this file +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_file_format +rank: 1000 +alias: format +owner: AnnotationFile +domain_of: +- AnnotationFile +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/frames_count.md b/schema/v1.1.0/metadata-docs/frames_count.md new file mode 100644 index 000000000..82535ce19 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/frames_count.md @@ -0,0 +1,72 @@ +# Slot: frames_count + + +_Number of frames associated with this tiltseries_ + + + +URI: [cdp-meta:frames_count](https://cryoetdataportal.czscience.com/schema/metadata/frames_count) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: frames_count +description: Number of frames associated with this tiltseries +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_frames_count +rank: 1000 +alias: frames_count +owner: TiltSeries +domain_of: +- TiltSeries +range: integer +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/funding_agency_name.md b/schema/v1.1.0/metadata-docs/funding_agency_name.md new file mode 100644 index 000000000..4b44ab802 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/funding_agency_name.md @@ -0,0 +1,72 @@ +# Slot: funding_agency_name + + +_The name of the funding source._ + + + +URI: [cdp-meta:funding_agency_name](https://cryoetdataportal.czscience.com/schema/metadata/funding_agency_name) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Funding](Funding.md) | A funding source for a scientific data entity (base for JSON and DB represent... | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: funding_agency_name +description: The name of the funding source. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:funding_agency_name +rank: 1000 +alias: funding_agency_name +owner: Funding +domain_of: +- Funding +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/grant_id.md b/schema/v1.1.0/metadata-docs/grant_id.md new file mode 100644 index 000000000..77622aea6 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/grant_id.md @@ -0,0 +1,72 @@ +# Slot: grant_id + + +_Grant identifier provided by the funding agency_ + + + +URI: [cdp-meta:grant_id](https://cryoetdataportal.czscience.com/schema/metadata/grant_id) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Funding](Funding.md) | A funding source for a scientific data entity (base for JSON and DB represent... | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: grant_id +description: Grant identifier provided by the funding agency +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:funding_grant_id +rank: 1000 +alias: grant_id +owner: Funding +domain_of: +- Funding +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/grid_preparation.md b/schema/v1.1.0/metadata-docs/grid_preparation.md new file mode 100644 index 000000000..cd741089d --- /dev/null +++ b/schema/v1.1.0/metadata-docs/grid_preparation.md @@ -0,0 +1,54 @@ +# Slot: grid_preparation + +URI: [cdp-meta:grid_preparation](https://cryoetdataportal.czscience.com/schema/metadata/grid_preparation) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: grid_preparation +alias: grid_preparation +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/ground_truth_status.md b/schema/v1.1.0/metadata-docs/ground_truth_status.md new file mode 100644 index 000000000..d9ce70fbf --- /dev/null +++ b/schema/v1.1.0/metadata-docs/ground_truth_status.md @@ -0,0 +1,73 @@ +# Slot: ground_truth_status + + +_Whether an annotation is considered ground truth, as determined by the annotator._ + + + +URI: [cdp-meta:ground_truth_status](https://cryoetdataportal.czscience.com/schema/metadata/ground_truth_status) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: ground_truth_status +description: Whether an annotation is considered ground truth, as determined by the + annotator. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_ground_truth_status +rank: 1000 +alias: ground_truth_status +owner: Annotation +domain_of: +- Annotation +range: boolean +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/ground_truth_used.md b/schema/v1.1.0/metadata-docs/ground_truth_used.md new file mode 100644 index 000000000..fe00c1727 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/ground_truth_used.md @@ -0,0 +1,72 @@ +# Slot: ground_truth_used + + +_Annotation filename used as ground truth for precision and recall_ + + + +URI: [cdp-meta:ground_truth_used](https://cryoetdataportal.czscience.com/schema/metadata/ground_truth_used) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationConfidence](AnnotationConfidence.md) | Metadata describing the confidence of an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: ground_truth_used +description: Annotation filename used as ground truth for precision and recall +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_ground_truth_used +rank: 1000 +alias: ground_truth_used +owner: AnnotationConfidence +domain_of: +- AnnotationConfidence +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/id.md b/schema/v1.1.0/metadata-docs/id.md new file mode 100644 index 000000000..3e2e5bad5 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/id.md @@ -0,0 +1,60 @@ +# Slot: id + +URI: [cdp-meta:id](https://cryoetdataportal.czscience.com/schema/metadata/id) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tissue](Tissue.md) | The type of tissue from which the sample was derived | no | +[CellType](CellType.md) | The cell type from which the sample was derived | no | +[CellStrain](CellStrain.md) | The strain or cell line from which the sample was derived | no | +[CellComponent](CellComponent.md) | The cellular component from which the sample was derived | no | +[AnnotationObject](AnnotationObject.md) | Metadata describing the object being annotated | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: id +alias: id +domain_of: +- Tissue +- CellType +- CellStrain +- CellComponent +- AnnotationObject +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/image_corrector.md b/schema/v1.1.0/metadata-docs/image_corrector.md new file mode 100644 index 000000000..90797f8e1 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/image_corrector.md @@ -0,0 +1,72 @@ +# Slot: image_corrector + + +_Image corrector setup_ + + + +URI: [cdp-meta:image_corrector](https://cryoetdataportal.czscience.com/schema/metadata/image_corrector) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) | The optical setup of the microscope used to collect the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: image_corrector +description: Image corrector setup +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_microscope_image_corrector +rank: 1000 +alias: image_corrector +owner: MicroscopeOpticalSetup +domain_of: +- MicroscopeOpticalSetup +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/index.md b/schema/v1.1.0/metadata-docs/index.md new file mode 100644 index 000000000..e9c1ddc62 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/index.md @@ -0,0 +1,171 @@ +# cdp-meta + + + +URI: https://cryoetdataportal.czscience.com/schema-docs/metadata + +Name: cdp-meta + + + +## Classes + +| Class | Description | +| --- | --- | +| [Annotation](Annotation.md) | Metadata describing an annotation. | +| [AnnotationConfidence](AnnotationConfidence.md) | Metadata describing the confidence of an annotation. | +| [AnnotationFile](AnnotationFile.md) | Metadata describing a file containing an annotation. | +| [AnnotationObject](AnnotationObject.md) | Metadata describing the object being annotated. | +| [Annotator](Annotator.md) | Annotator of a scientific data entity. | +| [AnnotatoredEntity](AnnotatoredEntity.md) | An entity with associated annotation authors. | +| [Author](Author.md) | Author of a scientific data entity. | +| [AuthoredEntity](AuthoredEntity.md) | An entity with associated authors. | +| [Camera](Camera.md) | The camera used to collect the tilt series. | +| [CellComponent](CellComponent.md) | The cellular component from which the sample was derived. | +| [CellStrain](CellStrain.md) | The strain or cell line from which the sample was derived. | +| [CellType](CellType.md) | The cell type from which the sample was derived. | +| [CrossReferencedEntity](CrossReferencedEntity.md) | An entity with associated cross-references to other databases and publications. | +| [CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications. | +| [Dataset](Dataset.md) | High-level description of a cryoET dataset. | +| [DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modified. | +| [DatestampedEntity](DatestampedEntity.md) | An entity with associated deposition, release and last modified dates. | +| [ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET dataset. | +| [FundedEntity](FundedEntity.md) | An entity with associated funding sources. | +| [Funding](Funding.md) | A funding source for a scientific data entity (base for JSON and DB representation). | +| [Microscope](Microscope.md) | The microscope used to collect the tilt series. | +| [MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) | The optical setup of the microscope used to collect the tilt series. | +| [Organism](Organism.md) | The species from which the sample was derived. | +| [PicturedEntity](PicturedEntity.md) | An entity with associated preview images. | +| [PicturePath](PicturePath.md) | A set of paths to representative images of a piece of data. | +| [TiltRange](TiltRange.md) | The range of tilt angles in the tilt series. | +| [TiltSeries](TiltSeries.md) | Metadata describing a tilt series. | +| [Tissue](Tissue.md) | The type of tissue from which the sample was derived. | +| [Tomogram](Tomogram.md) | Metadata describing a tomogram. | +| [TomogramOffset](TomogramOffset.md) | The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. | +| [TomogramSize](TomogramSize.md) | The size of a tomogram in voxels in each dimension. | + + + +## Slots + +| Slot | Description | +| --- | --- | +| [acceleration_voltage](acceleration_voltage.md) | Electron Microscope Accelerator voltage in volts | +| [affiliation_address](affiliation_address.md) | The address of the author's affiliation | +| [affiliation_identifier](affiliation_identifier.md) | A Research Organization Registry (ROR) identifier | +| [affiliation_name](affiliation_name.md) | The name of the author's affiliation | +| [affine_transformation_matrix](affine_transformation_matrix.md) | The flip or rotation transformation of this author submitted tomogram is indi... | +| [aligned_tiltseries_binning](aligned_tiltseries_binning.md) | Binning factor of the aligned tilt series | +| [annotation_method](annotation_method.md) | Describe how the annotation is made (e | +| [annotation_method_type](annotation_method_type.md) | Classification of the annotation method based on supervision | +| [annotation_object](annotation_object.md) | Metadata describing the object being annotated | +| [annotation_publications](annotation_publications.md) | DOIs for publications that describe the dataset | +| [annotation_software](annotation_software.md) | Software used for generating this annotation | +| [authors](authors.md) | Author of a scientific data entity | +| [binning_from_frames](binning_from_frames.md) | Describes the binning factor from frames to tilt series file | +| [camera](camera.md) | The camera used to collect the tilt series | +| [cell_component](cell_component.md) | The cellular component from which the sample was derived | +| [cell_strain](cell_strain.md) | The strain or cell line from which the sample was derived | +| [cell_type](cell_type.md) | The cell type from which the sample was derived | +| [confidence](confidence.md) | Metadata describing the confidence of an annotation | +| [cross_references](cross_references.md) | A set of cross-references to other databases and publications | +| [ctf_corrected](ctf_corrected.md) | Whether this tomogram is CTF corrected | +| [data_acquisition_software](data_acquisition_software.md) | Software used to collect data | +| [dataset_citations](dataset_citations.md) | Comma-separated list of DOIs for publications citing the dataset | +| [dataset_description](dataset_description.md) | A short description of a CryoET dataset, similar to an abstract for a journal... | +| [dataset_identifier](dataset_identifier.md) | An identifier for a CryoET dataset, assigned by the Data Portal | +| [dataset_publications](dataset_publications.md) | Comma-separated list of DOIs for publications associated with the dataset | +| [dataset_title](dataset_title.md) | Title of a CryoET dataset | +| [dates](dates.md) | A set of dates at which a data item was deposited, published and last modifie... | +| [deposition_date](deposition_date.md) | The date a data item was received by the cryoET data portal | +| [description](description.md) | A textual description of the annotation object, can be a longer description t... | +| [email](email.md) | The email address of the author | +| [energy_filter](energy_filter.md) | Energy filter setup used | +| [fiducial_alignment_status](fiducial_alignment_status.md) | Whether the tomographic alignment was computed based on fiducial markers | +| [files](files.md) | Metadata describing a file containing an annotation | +| [format](format.md) | File format for this file | +| [frames_count](frames_count.md) | Number of frames associated with this tiltseries | +| [funding](funding.md) | A funding source for a scientific data entity (base for JSON and DB represent... | +| [funding_agency_name](funding_agency_name.md) | The name of the funding source | +| [grant_id](grant_id.md) | Grant identifier provided by the funding agency | +| [grid_preparation](grid_preparation.md) | Describes Cryo-ET grid preparation | +| [ground_truth_status](ground_truth_status.md) | Whether an annotation is considered ground truth, as determined by the annota... | +| [ground_truth_used](ground_truth_used.md) | Annotation filename used as ground truth for precision and recall | +| [id](id.md) | The UBERON identifier for the tissue | +| [image_corrector](image_corrector.md) | Image corrector setup | +| [is_corresponding](is_corresponding.md) | Whether the author is a corresponding author | +| [is_curator_recommended](is_curator_recommended.md) | This annotation is recommended by the curator to be preferred for this object... | +| [is_primary_annotator](is_primary_annotator.md) | Whether the author is a primary author | +| [is_primary_author](is_primary_author.md) | Whether the author is a primary author | +| [is_visualization_default](is_visualization_default.md) | This annotation will be rendered in neuroglancer by default | +| [key_photos](key_photos.md) | A set of paths to representative images of a piece of data | +| [last_modified_date](last_modified_date.md) | The date a piece of data was last modified on the cryoET data portal | +| [manufacturer](manufacturer.md) | Name of the camera manufacturer | +| [max](max.md) | Maximal tilt angle in degrees | +| [microscope](microscope.md) | The microscope used to collect the tilt series | +| [microscope_additional_info](microscope_additional_info.md) | Other microscope optical setup information, in addition to energy filter, pha... | +| [microscope_optical_setup](microscope_optical_setup.md) | The optical setup of the microscope used to collect the tilt series | +| [min](min.md) | Minimal tilt angle in degrees | +| [model](model.md) | Camera model name | +| [name](name.md) | The full name of the author | +| [object_count](object_count.md) | Number of objects identified | +| [offset](offset.md) | The offset of a tomogram in voxels in each dimension relative to the canonica... | +| [ORCID](ORCID.md) | A unique, persistent identifier for researchers, provided by ORCID | +| [organism](organism.md) | The species from which the sample was derived | +| [other_setup](other_setup.md) | Describes other setup not covered by sample preparation or grid preparation t... | +| [path](path.md) | Path to the annotation file relative to the dataset root | +| [phase_plate](phase_plate.md) | Phase plate configuration | +| [pixel_spacing](pixel_spacing.md) | Pixel spacing for the tilt series | +| [precision](precision.md) | Describe the confidence level of the annotation | +| [processing](processing.md) | Describe additional processing used to derive the tomogram | +| [processing_software](processing_software.md) | Processing software used to derive the tomogram | +| [recall](recall.md) | Describe the confidence level of the annotation | +| [reconstruction_method](reconstruction_method.md) | Describe reconstruction method (Weighted back-projection, SART, SIRT) | +| [reconstruction_software](reconstruction_software.md) | Name of software used for reconstruction | +| [related_database_entries](related_database_entries.md) | Comma-separated list of related database entries for the dataset | +| [related_database_links](related_database_links.md) | Comma-separated list of related database links for the dataset | +| [release_date](release_date.md) | The date a data item was received by the cryoET data portal | +| [sample_preparation](sample_preparation.md) | Describes how the sample was prepared | +| [sample_type](sample_type.md) | Type of sample imaged in a CryoET study | +| [shape](shape.md) | Describe whether this is a Point, OrientedPoint, or SegmentationMask file | +| [size](size.md) | The size of a tomogram in voxels in each dimension | +| [snapshot](snapshot.md) | Path to the dataset preview image relative to the dataset directory root | +| [spherical_aberration_constant](spherical_aberration_constant.md) | Spherical Aberration Constant of the objective lens in millimeters | +| [state](state.md) | Molecule state annotated (e | +| [taxonomy_id](taxonomy_id.md) | NCBI taxonomy identifier for the organism, e | +| [thumbnail](thumbnail.md) | Path to the thumbnail of preview image relative to the dataset directory root | +| [tilt_axis](tilt_axis.md) | Rotation angle in degrees | +| [tilt_range](tilt_range.md) | The range of tilt angles in the tilt series | +| [tilt_series_quality](tilt_series_quality.md) | Author assessment of tilt series quality within the dataset (1-5, 5 is best) | +| [tilt_step](tilt_step.md) | Tilt step in degrees | +| [tilting_scheme](tilting_scheme.md) | The order of stage tilting during acquisition of the data | +| [tissue](tissue.md) | The type of tissue from which the sample was derived | +| [tomogram_version](tomogram_version.md) | Version of tomogram using the same software and post-processing | +| [total_flux](total_flux.md) | Number of Electrons reaching the specimen in a square Angstrom area for the e... | +| [voxel_spacing](voxel_spacing.md) | Voxel spacing equal in all three axes in angstroms | +| [x](x.md) | Number of pixels in the 3D data fast axis | +| [y](y.md) | Number of pixels in the 3D data medium axis | +| [z](z.md) | Number of pixels in the 3D data slow axis | + + +## Enumerations + +| Enumeration | Description | +| --- | --- | +| [AnnotationMethodTypeEnum](AnnotationMethodTypeEnum.md) | Describes how the annotations were generated | +| [AnnotationShapeEnum](AnnotationShapeEnum.md) | Annotation shape types available on the data portal | +| [FiducialAlignmentStatusEnum](FiducialAlignmentStatusEnum.md) | Fiducial Alignment method | +| [SampleTypeEnum](SampleTypeEnum.md) | Type of sample imaged in a CryoET study | +| [TomogramTypeEnum](TomogramTypeEnum.md) | Tomogram type | + + +## Types + +| Type | Description | +| --- | --- | + + +## Subsets + +| Subset | Description | +| --- | --- | diff --git a/schema/v1.1.0/metadata-docs/is_corresponding.md b/schema/v1.1.0/metadata-docs/is_corresponding.md new file mode 100644 index 000000000..67226abb2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/is_corresponding.md @@ -0,0 +1,54 @@ +# Slot: is_corresponding + +URI: [cdp-meta:is_corresponding](https://cryoetdataportal.czscience.com/schema/metadata/is_corresponding) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: is_corresponding +alias: is_corresponding +domain_of: +- Author +- Annotator +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/is_curator_recommended.md b/schema/v1.1.0/metadata-docs/is_curator_recommended.md new file mode 100644 index 000000000..dcea34198 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/is_curator_recommended.md @@ -0,0 +1,73 @@ +# Slot: is_curator_recommended + + +_This annotation is recommended by the curator to be preferred for this object type._ + + + +URI: [cdp-meta:is_curator_recommended](https://cryoetdataportal.czscience.com/schema/metadata/is_curator_recommended) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: is_curator_recommended +description: This annotation is recommended by the curator to be preferred for this + object type. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_is_curator_recommended +rank: 1000 +alias: is_curator_recommended +owner: Annotation +domain_of: +- Annotation +range: boolean +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/is_primary_annotator.md b/schema/v1.1.0/metadata-docs/is_primary_annotator.md new file mode 100644 index 000000000..6dc61da38 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/is_primary_annotator.md @@ -0,0 +1,72 @@ +# Slot: is_primary_annotator + + +_Whether the author is a primary author._ + + + +URI: [cdp-meta:is_primary_annotator](https://cryoetdataportal.czscience.com/schema/metadata/is_primary_annotator) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: is_primary_annotator +description: Whether the author is a primary author. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:author_primary_author_status +rank: 1000 +alias: is_primary_annotator +owner: Annotator +domain_of: +- Annotator +range: boolean +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/is_primary_author.md b/schema/v1.1.0/metadata-docs/is_primary_author.md new file mode 100644 index 000000000..8d832acb9 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/is_primary_author.md @@ -0,0 +1,72 @@ +# Slot: is_primary_author + + +_Whether the author is a primary author._ + + + +URI: [cdp-meta:is_primary_author](https://cryoetdataportal.czscience.com/schema/metadata/is_primary_author) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | + + + + + + + +## Properties + +* Range: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: is_primary_author +description: Whether the author is a primary author. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:author_primary_author_status +rank: 1000 +alias: is_primary_author +owner: Author +domain_of: +- Author +range: boolean +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/is_visualization_default.md b/schema/v1.1.0/metadata-docs/is_visualization_default.md new file mode 100644 index 000000000..c3eaf1159 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/is_visualization_default.md @@ -0,0 +1,72 @@ +# Slot: is_visualization_default + + +_This annotation will be rendered in neuroglancer by default._ + + + +URI: [cdp-meta:is_visualization_default](https://cryoetdataportal.czscience.com/schema/metadata/is_visualization_default) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationFile](AnnotationFile.md) | Metadata describing a file containing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: is_visualization_default +description: This annotation will be rendered in neuroglancer by default. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_file_is_visualization_default +rank: 1000 +alias: is_visualization_default +owner: AnnotationFile +domain_of: +- AnnotationFile +range: boolean +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/key_photos.md b/schema/v1.1.0/metadata-docs/key_photos.md new file mode 100644 index 000000000..d3d3ae8cf --- /dev/null +++ b/schema/v1.1.0/metadata-docs/key_photos.md @@ -0,0 +1,56 @@ +# Slot: key_photos + +URI: [cdp-meta:key_photos](https://cryoetdataportal.czscience.com/schema/metadata/key_photos) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[PicturedEntity](PicturedEntity.md) | An entity with associated preview images | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: key_photos +alias: key_photos +domain_of: +- PicturedEntity +- Dataset +- Tomogram +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/last_modified_date.md b/schema/v1.1.0/metadata-docs/last_modified_date.md new file mode 100644 index 000000000..6e7c8a5c2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/last_modified_date.md @@ -0,0 +1,74 @@ +# Slot: last_modified_date + + +_The date a piece of data was last modified on the cryoET data portal._ + + + +URI: [cdp-meta:last_modified_date](https://cryoetdataportal.czscience.com/schema/metadata/last_modified_date) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modifie... | yes | + + + + + + + +## Properties + +* Range: [xsd:date](http://www.w3.org/2001/XMLSchema#date) + +* Required: True + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: last_modified_date +description: The date a piece of data was last modified on the cryoET data portal. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: last_modified_date +owner: DateStamp +domain_of: +- DateStamp +range: date +required: true +recommended: true +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/manufacturer.md b/schema/v1.1.0/metadata-docs/manufacturer.md new file mode 100644 index 000000000..fd08619bf --- /dev/null +++ b/schema/v1.1.0/metadata-docs/manufacturer.md @@ -0,0 +1,54 @@ +# Slot: manufacturer + +URI: [cdp-meta:manufacturer](https://cryoetdataportal.czscience.com/schema/metadata/manufacturer) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Camera](Camera.md) | The camera used to collect the tilt series | no | +[Microscope](Microscope.md) | The microscope used to collect the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: manufacturer +alias: manufacturer +domain_of: +- Camera +- Microscope +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/max.md b/schema/v1.1.0/metadata-docs/max.md new file mode 100644 index 000000000..ae462b631 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/max.md @@ -0,0 +1,72 @@ +# Slot: max + + +_Maximal tilt angle in degrees_ + + + +URI: [cdp-meta:max](https://cryoetdataportal.czscience.com/schema/metadata/max) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltRange](TiltRange.md) | The range of tilt angles in the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: max +description: Maximal tilt angle in degrees +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_tilt_max +rank: 1000 +alias: max +owner: TiltRange +domain_of: +- TiltRange +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/microscope_additional_info.md b/schema/v1.1.0/metadata-docs/microscope_additional_info.md new file mode 100644 index 000000000..d9440aee4 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/microscope_additional_info.md @@ -0,0 +1,73 @@ +# Slot: microscope_additional_info + + +_Other microscope optical setup information, in addition to energy filter, phase plate and image corrector_ + + + +URI: [cdp-meta:microscope_additional_info](https://cryoetdataportal.czscience.com/schema/metadata/microscope_additional_info) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: microscope_additional_info +description: Other microscope optical setup information, in addition to energy filter, + phase plate and image corrector +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_microscope_additional_info +rank: 1000 +alias: microscope_additional_info +owner: TiltSeries +domain_of: +- TiltSeries +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/microscope_optical_setup.md b/schema/v1.1.0/metadata-docs/microscope_optical_setup.md new file mode 100644 index 000000000..6087adc4e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/microscope_optical_setup.md @@ -0,0 +1,70 @@ +# Slot: microscope_optical_setup + + +_The optical setup of the microscope used to collect the tilt series._ + + + +URI: [cdp-meta:microscope_optical_setup](https://cryoetdataportal.czscience.com/schema/metadata/microscope_optical_setup) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: microscope_optical_setup +description: The optical setup of the microscope used to collect the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: microscope_optical_setup +owner: TiltSeries +domain_of: +- TiltSeries +range: MicroscopeOpticalSetup +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/min.md b/schema/v1.1.0/metadata-docs/min.md new file mode 100644 index 000000000..a1b6a4fa1 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/min.md @@ -0,0 +1,72 @@ +# Slot: min + + +_Minimal tilt angle in degrees_ + + + +URI: [cdp-meta:min](https://cryoetdataportal.czscience.com/schema/metadata/min) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltRange](TiltRange.md) | The range of tilt angles in the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: min +description: Minimal tilt angle in degrees +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_tilt_min +rank: 1000 +alias: min +owner: TiltRange +domain_of: +- TiltRange +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/model.md b/schema/v1.1.0/metadata-docs/model.md new file mode 100644 index 000000000..18d976904 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/model.md @@ -0,0 +1,54 @@ +# Slot: model + +URI: [cdp-meta:model](https://cryoetdataportal.czscience.com/schema/metadata/model) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Camera](Camera.md) | The camera used to collect the tilt series | no | +[Microscope](Microscope.md) | The microscope used to collect the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: model +alias: model +domain_of: +- Camera +- Microscope +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/name.md b/schema/v1.1.0/metadata-docs/name.md new file mode 100644 index 000000000..90e8901fc --- /dev/null +++ b/schema/v1.1.0/metadata-docs/name.md @@ -0,0 +1,66 @@ +# Slot: name + +URI: [cdp-meta:name](https://cryoetdataportal.czscience.com/schema/metadata/name) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Author](Author.md) | Author of a scientific data entity | no | +[Annotator](Annotator.md) | Annotator of a scientific data entity | no | +[Organism](Organism.md) | The species from which the sample was derived | no | +[Tissue](Tissue.md) | The type of tissue from which the sample was derived | no | +[CellType](CellType.md) | The cell type from which the sample was derived | no | +[CellStrain](CellStrain.md) | The strain or cell line from which the sample was derived | no | +[CellComponent](CellComponent.md) | The cellular component from which the sample was derived | no | +[AnnotationObject](AnnotationObject.md) | Metadata describing the object being annotated | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: name +alias: name +domain_of: +- Author +- Annotator +- Organism +- Tissue +- CellType +- CellStrain +- CellComponent +- AnnotationObject +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/object_count.md b/schema/v1.1.0/metadata-docs/object_count.md new file mode 100644 index 000000000..27db3f5a1 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/object_count.md @@ -0,0 +1,72 @@ +# Slot: object_count + + +_Number of objects identified_ + + + +URI: [cdp-meta:object_count](https://cryoetdataportal.czscience.com/schema/metadata/object_count) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Annotation](Annotation.md) | Metadata describing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: object_count +description: Number of objects identified +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_object_count +rank: 1000 +alias: object_count +owner: Annotation +domain_of: +- Annotation +range: integer +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/offset.md b/schema/v1.1.0/metadata-docs/offset.md new file mode 100644 index 000000000..c03694aae --- /dev/null +++ b/schema/v1.1.0/metadata-docs/offset.md @@ -0,0 +1,71 @@ +# Slot: offset + + +_The offset of a tomogram in voxels in each dimension relative to the canonical tomogram._ + + + +URI: [cdp-meta:offset](https://cryoetdataportal.czscience.com/schema/metadata/offset) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [TomogramOffset](TomogramOffset.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: offset +description: The offset of a tomogram in voxels in each dimension relative to the + canonical tomogram. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: offset +owner: Tomogram +domain_of: +- Tomogram +range: TomogramOffset +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/other_setup.md b/schema/v1.1.0/metadata-docs/other_setup.md new file mode 100644 index 000000000..14664c5b4 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/other_setup.md @@ -0,0 +1,54 @@ +# Slot: other_setup + +URI: [cdp-meta:other_setup](https://cryoetdataportal.czscience.com/schema/metadata/other_setup) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: other_setup +alias: other_setup +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/path.md b/schema/v1.1.0/metadata-docs/path.md new file mode 100644 index 000000000..483c7425c --- /dev/null +++ b/schema/v1.1.0/metadata-docs/path.md @@ -0,0 +1,72 @@ +# Slot: path + + +_Path to the annotation file relative to the dataset root._ + + + +URI: [cdp-meta:path](https://cryoetdataportal.czscience.com/schema/metadata/path) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationFile](AnnotationFile.md) | Metadata describing a file containing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: path +description: Path to the annotation file relative to the dataset root. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_file_path +rank: 1000 +alias: path +owner: AnnotationFile +domain_of: +- AnnotationFile +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/phase_plate.md b/schema/v1.1.0/metadata-docs/phase_plate.md new file mode 100644 index 000000000..d1271287f --- /dev/null +++ b/schema/v1.1.0/metadata-docs/phase_plate.md @@ -0,0 +1,72 @@ +# Slot: phase_plate + + +_Phase plate configuration_ + + + +URI: [cdp-meta:phase_plate](https://cryoetdataportal.czscience.com/schema/metadata/phase_plate) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[MicroscopeOpticalSetup](MicroscopeOpticalSetup.md) | The optical setup of the microscope used to collect the tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: phase_plate +description: Phase plate configuration +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_microscope_phase_plate +rank: 1000 +alias: phase_plate +owner: MicroscopeOpticalSetup +domain_of: +- MicroscopeOpticalSetup +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/pixel_spacing.md b/schema/v1.1.0/metadata-docs/pixel_spacing.md new file mode 100644 index 000000000..5bb126e57 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/pixel_spacing.md @@ -0,0 +1,72 @@ +# Slot: pixel_spacing + + +_Pixel spacing for the tilt series_ + + + +URI: [cdp-meta:pixel_spacing](https://cryoetdataportal.czscience.com/schema/metadata/pixel_spacing) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: pixel_spacing +description: Pixel spacing for the tilt series +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_pixel_spacing +rank: 1000 +alias: pixel_spacing +owner: TiltSeries +domain_of: +- TiltSeries +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/precision.md b/schema/v1.1.0/metadata-docs/precision.md new file mode 100644 index 000000000..1ac0b5301 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/precision.md @@ -0,0 +1,73 @@ +# Slot: precision + + +_Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive_ + + + +URI: [cdp-meta:precision](https://cryoetdataportal.czscience.com/schema/metadata/precision) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationConfidence](AnnotationConfidence.md) | Metadata describing the confidence of an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: precision +description: Describe the confidence level of the annotation. Precision is defined + as the % of annotation objects being true positive +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_confidence_precision +rank: 1000 +alias: precision +owner: AnnotationConfidence +domain_of: +- AnnotationConfidence +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/processing.md b/schema/v1.1.0/metadata-docs/processing.md new file mode 100644 index 000000000..7e7f70f76 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/processing.md @@ -0,0 +1,72 @@ +# Slot: processing + + +_Describe additional processing used to derive the tomogram_ + + + +URI: [cdp-meta:processing](https://cryoetdataportal.czscience.com/schema/metadata/processing) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: processing +description: Describe additional processing used to derive the tomogram +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_processing +rank: 1000 +alias: processing +owner: Tomogram +domain_of: +- Tomogram +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/processing_software.md b/schema/v1.1.0/metadata-docs/processing_software.md new file mode 100644 index 000000000..315182f18 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/processing_software.md @@ -0,0 +1,72 @@ +# Slot: processing_software + + +_Processing software used to derive the tomogram_ + + + +URI: [cdp-meta:processing_software](https://cryoetdataportal.czscience.com/schema/metadata/processing_software) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: processing_software +description: Processing software used to derive the tomogram +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_processing_software +rank: 1000 +alias: processing_software +owner: Tomogram +domain_of: +- Tomogram +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/recall.md b/schema/v1.1.0/metadata-docs/recall.md new file mode 100644 index 000000000..0be0f3a3d --- /dev/null +++ b/schema/v1.1.0/metadata-docs/recall.md @@ -0,0 +1,73 @@ +# Slot: recall + + +_Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly_ + + + +URI: [cdp-meta:recall](https://cryoetdataportal.czscience.com/schema/metadata/recall) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationConfidence](AnnotationConfidence.md) | Metadata describing the confidence of an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: recall +description: Describe the confidence level of the annotation. Recall is defined as + the % of true positives being annotated correctly +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_confidence_recall +rank: 1000 +alias: recall +owner: AnnotationConfidence +domain_of: +- AnnotationConfidence +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/reconstruction_method.md b/schema/v1.1.0/metadata-docs/reconstruction_method.md new file mode 100644 index 000000000..515d881d9 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/reconstruction_method.md @@ -0,0 +1,72 @@ +# Slot: reconstruction_method + + +_Describe reconstruction method (Weighted back-projection, SART, SIRT)_ + + + +URI: [cdp-meta:reconstruction_method](https://cryoetdataportal.czscience.com/schema/metadata/reconstruction_method) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: reconstruction_method +description: Describe reconstruction method (Weighted back-projection, SART, SIRT) +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_reconstruction_method +rank: 1000 +alias: reconstruction_method +owner: Tomogram +domain_of: +- Tomogram +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/reconstruction_software.md b/schema/v1.1.0/metadata-docs/reconstruction_software.md new file mode 100644 index 000000000..698a347ab --- /dev/null +++ b/schema/v1.1.0/metadata-docs/reconstruction_software.md @@ -0,0 +1,72 @@ +# Slot: reconstruction_software + + +_Name of software used for reconstruction_ + + + +URI: [cdp-meta:reconstruction_software](https://cryoetdataportal.czscience.com/schema/metadata/reconstruction_software) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: reconstruction_software +description: Name of software used for reconstruction +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_reconstruction_software +rank: 1000 +alias: reconstruction_software +owner: Tomogram +domain_of: +- Tomogram +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/related_database_entries.md b/schema/v1.1.0/metadata-docs/related_database_entries.md new file mode 100644 index 000000000..fce85dc73 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/related_database_entries.md @@ -0,0 +1,73 @@ +# Slot: related_database_entries + + +_Comma-separated list of related database entries for the dataset._ + + + +URI: [cdp-meta:related_database_entries](https://cryoetdataportal.czscience.com/schema/metadata/related_database_entries) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + +* Recommended: True + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: related_database_entries +description: Comma-separated list of related database entries for the dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: related_database_entries +owner: CrossReferences +domain_of: +- CrossReferences +range: string +recommended: true +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/related_database_links.md b/schema/v1.1.0/metadata-docs/related_database_links.md new file mode 100644 index 000000000..6bd0922c4 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/related_database_links.md @@ -0,0 +1,70 @@ +# Slot: related_database_links + + +_Comma-separated list of related database links for the dataset._ + + + +URI: [cdp-meta:related_database_links](https://cryoetdataportal.czscience.com/schema/metadata/related_database_links) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[CrossReferences](CrossReferences.md) | A set of cross-references to other databases and publications | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: related_database_links +description: Comma-separated list of related database links for the dataset. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: related_database_links +owner: CrossReferences +domain_of: +- CrossReferences +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/release_date.md b/schema/v1.1.0/metadata-docs/release_date.md new file mode 100644 index 000000000..7539c4ea5 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/release_date.md @@ -0,0 +1,74 @@ +# Slot: release_date + + +_The date a data item was received by the cryoET data portal._ + + + +URI: [cdp-meta:release_date](https://cryoetdataportal.czscience.com/schema/metadata/release_date) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[DateStamp](DateStamp.md) | A set of dates at which a data item was deposited, published and last modifie... | yes | + + + + + + + +## Properties + +* Range: [xsd:date](http://www.w3.org/2001/XMLSchema#date) + +* Required: True + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: release_date +description: The date a data item was received by the cryoET data portal. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: release_date +owner: DateStamp +domain_of: +- DateStamp +range: date +required: true +recommended: true +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/sample_preparation.md b/schema/v1.1.0/metadata-docs/sample_preparation.md new file mode 100644 index 000000000..4458c6da0 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/sample_preparation.md @@ -0,0 +1,54 @@ +# Slot: sample_preparation + +URI: [cdp-meta:sample_preparation](https://cryoetdataportal.czscience.com/schema/metadata/sample_preparation) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: sample_preparation +alias: sample_preparation +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/sample_type.md b/schema/v1.1.0/metadata-docs/sample_type.md new file mode 100644 index 000000000..357a9aadc --- /dev/null +++ b/schema/v1.1.0/metadata-docs/sample_type.md @@ -0,0 +1,54 @@ +# Slot: sample_type + +URI: [cdp-meta:sample_type](https://cryoetdataportal.czscience.com/schema/metadata/sample_type) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[ExperimentalMetadata](ExperimentalMetadata.md) | Metadata describing sample and sample preparation methods used in a cryoET da... | no | +[Dataset](Dataset.md) | High-level description of a cryoET dataset | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: sample_type +alias: sample_type +domain_of: +- ExperimentalMetadata +- Dataset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/shape.md b/schema/v1.1.0/metadata-docs/shape.md new file mode 100644 index 000000000..0256d25c2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/shape.md @@ -0,0 +1,73 @@ +# Slot: shape + + +_Describe whether this is a Point, OrientedPoint, or SegmentationMask file_ + + + +URI: [cdp-meta:shape](https://cryoetdataportal.czscience.com/schema/metadata/shape) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationFile](AnnotationFile.md) | Metadata describing a file containing an annotation | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: shape +description: Describe whether this is a Point, OrientedPoint, or SegmentationMask + file +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_file_shape_type +rank: 1000 +alias: shape +owner: AnnotationFile +domain_of: +- AnnotationFile +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/size.md b/schema/v1.1.0/metadata-docs/size.md new file mode 100644 index 000000000..8fe80ba4e --- /dev/null +++ b/schema/v1.1.0/metadata-docs/size.md @@ -0,0 +1,70 @@ +# Slot: size + + +_The size of a tomogram in voxels in each dimension._ + + + +URI: [cdp-meta:size](https://cryoetdataportal.czscience.com/schema/metadata/size) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [TomogramSize](TomogramSize.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: size +description: The size of a tomogram in voxels in each dimension. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: size +owner: Tomogram +domain_of: +- Tomogram +range: TomogramSize +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/snapshot.md b/schema/v1.1.0/metadata-docs/snapshot.md new file mode 100644 index 000000000..cbde5245f --- /dev/null +++ b/schema/v1.1.0/metadata-docs/snapshot.md @@ -0,0 +1,70 @@ +# Slot: snapshot + + +_Path to the dataset preview image relative to the dataset directory root._ + + + +URI: [cdp-meta:snapshot](https://cryoetdataportal.czscience.com/schema/metadata/snapshot) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[PicturePath](PicturePath.md) | A set of paths to representative images of a piece of data | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: snapshot +description: Path to the dataset preview image relative to the dataset directory root. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: snapshot +owner: PicturePath +domain_of: +- PicturePath +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md b/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md new file mode 100644 index 000000000..8272e12c2 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md @@ -0,0 +1,72 @@ +# Slot: spherical_aberration_constant + + +_Spherical Aberration Constant of the objective lens in millimeters_ + + + +URI: [cdp-meta:spherical_aberration_constant](https://cryoetdataportal.czscience.com/schema/metadata/spherical_aberration_constant) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: spherical_aberration_constant +description: Spherical Aberration Constant of the objective lens in millimeters +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_spherical_aberration_constant +rank: 1000 +alias: spherical_aberration_constant +owner: TiltSeries +domain_of: +- TiltSeries +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/state.md b/schema/v1.1.0/metadata-docs/state.md new file mode 100644 index 000000000..180cc88e7 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/state.md @@ -0,0 +1,72 @@ +# Slot: state + + +_Molecule state annotated (e.g. open, closed)_ + + + +URI: [cdp-meta:state](https://cryoetdataportal.czscience.com/schema/metadata/state) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[AnnotationObject](AnnotationObject.md) | Metadata describing the object being annotated | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: state +description: Molecule state annotated (e.g. open, closed) +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:annotation_object_state +rank: 1000 +alias: state +owner: AnnotationObject +domain_of: +- AnnotationObject +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/taxonomy_id.md b/schema/v1.1.0/metadata-docs/taxonomy_id.md new file mode 100644 index 000000000..b4bc7262a --- /dev/null +++ b/schema/v1.1.0/metadata-docs/taxonomy_id.md @@ -0,0 +1,72 @@ +# Slot: taxonomy_id + + +_NCBI taxonomy identifier for the organism, e.g. 9606_ + + + +URI: [cdp-meta:taxonomy_id](https://cryoetdataportal.czscience.com/schema/metadata/taxonomy_id) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Organism](Organism.md) | The species from which the sample was derived | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: taxonomy_id +description: NCBI taxonomy identifier for the organism, e.g. 9606 +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:organism_taxid +rank: 1000 +alias: taxonomy_id +owner: Organism +domain_of: +- Organism +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/thumbnail.md b/schema/v1.1.0/metadata-docs/thumbnail.md new file mode 100644 index 000000000..5763ed6fd --- /dev/null +++ b/schema/v1.1.0/metadata-docs/thumbnail.md @@ -0,0 +1,71 @@ +# Slot: thumbnail + + +_Path to the thumbnail of preview image relative to the dataset directory root._ + + + +URI: [cdp-meta:thumbnail](https://cryoetdataportal.czscience.com/schema/metadata/thumbnail) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[PicturePath](PicturePath.md) | A set of paths to representative images of a piece of data | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: thumbnail +description: Path to the thumbnail of preview image relative to the dataset directory + root. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: thumbnail +owner: PicturePath +domain_of: +- PicturePath +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/tilt_axis.md b/schema/v1.1.0/metadata-docs/tilt_axis.md new file mode 100644 index 000000000..b8c721d98 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/tilt_axis.md @@ -0,0 +1,72 @@ +# Slot: tilt_axis + + +_Rotation angle in degrees_ + + + +URI: [cdp-meta:tilt_axis](https://cryoetdataportal.czscience.com/schema/metadata/tilt_axis) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tilt_axis +description: Rotation angle in degrees +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_tilt_axis +rank: 1000 +alias: tilt_axis +owner: TiltSeries +domain_of: +- TiltSeries +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/tilt_range.md b/schema/v1.1.0/metadata-docs/tilt_range.md new file mode 100644 index 000000000..851388156 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/tilt_range.md @@ -0,0 +1,70 @@ +# Slot: tilt_range + + +_The range of tilt angles in the tilt series._ + + + +URI: [cdp-meta:tilt_range](https://cryoetdataportal.czscience.com/schema/metadata/tilt_range) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [TiltRange](TiltRange.md) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tilt_range +description: The range of tilt angles in the tilt series. +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +rank: 1000 +alias: tilt_range +owner: TiltSeries +domain_of: +- TiltSeries +range: TiltRange +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/tilt_series_quality.md b/schema/v1.1.0/metadata-docs/tilt_series_quality.md new file mode 100644 index 000000000..2284fe3fa --- /dev/null +++ b/schema/v1.1.0/metadata-docs/tilt_series_quality.md @@ -0,0 +1,73 @@ +# Slot: tilt_series_quality + + +_Author assessment of tilt series quality within the dataset (1-5, 5 is best)_ + + + +URI: [cdp-meta:tilt_series_quality](https://cryoetdataportal.czscience.com/schema/metadata/tilt_series_quality) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tilt_series_quality +description: Author assessment of tilt series quality within the dataset (1-5, 5 is + best) +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_tilt_series_quality +rank: 1000 +alias: tilt_series_quality +owner: TiltSeries +domain_of: +- TiltSeries +range: integer +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/tilt_step.md b/schema/v1.1.0/metadata-docs/tilt_step.md new file mode 100644 index 000000000..24ba20963 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/tilt_step.md @@ -0,0 +1,72 @@ +# Slot: tilt_step + + +_Tilt step in degrees_ + + + +URI: [cdp-meta:tilt_step](https://cryoetdataportal.czscience.com/schema/metadata/tilt_step) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tilt_step +description: Tilt step in degrees +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_tilt_step +rank: 1000 +alias: tilt_step +owner: TiltSeries +domain_of: +- TiltSeries +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/tilting_scheme.md b/schema/v1.1.0/metadata-docs/tilting_scheme.md new file mode 100644 index 000000000..b09425d62 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/tilting_scheme.md @@ -0,0 +1,72 @@ +# Slot: tilting_scheme + + +_The order of stage tilting during acquisition of the data_ + + + +URI: [cdp-meta:tilting_scheme](https://cryoetdataportal.czscience.com/schema/metadata/tilting_scheme) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tilting_scheme +description: The order of stage tilting during acquisition of the data +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_tilting_scheme +rank: 1000 +alias: tilting_scheme +owner: TiltSeries +domain_of: +- TiltSeries +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/tomogram_version.md b/schema/v1.1.0/metadata-docs/tomogram_version.md new file mode 100644 index 000000000..b817bc549 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/tomogram_version.md @@ -0,0 +1,74 @@ +# Slot: tomogram_version + + +_Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version_ + + + +URI: [cdp-meta:tomogram_version](https://cryoetdataportal.czscience.com/schema/metadata/tomogram_version) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: tomogram_version +description: Version of tomogram using the same software and post-processing. Version + of tomogram using the same software and post-processing. This will be presented + as the latest version +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_version +rank: 1000 +alias: tomogram_version +owner: Tomogram +domain_of: +- Tomogram +range: string +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/total_flux.md b/schema/v1.1.0/metadata-docs/total_flux.md new file mode 100644 index 000000000..be3067c1c --- /dev/null +++ b/schema/v1.1.0/metadata-docs/total_flux.md @@ -0,0 +1,73 @@ +# Slot: total_flux + + +_Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series_ + + + +URI: [cdp-meta:total_flux](https://cryoetdataportal.czscience.com/schema/metadata/total_flux) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TiltSeries](TiltSeries.md) | Metadata describing a tilt series | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: total_flux +description: Number of Electrons reaching the specimen in a square Angstrom area for + the entire tilt series +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tiltseries_total_flux +rank: 1000 +alias: total_flux +owner: TiltSeries +domain_of: +- TiltSeries +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/types.md b/schema/v1.1.0/metadata-docs/types.md new file mode 100644 index 000000000..557e79b16 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/types.md @@ -0,0 +1,6 @@ +# types + +Shared type definitions for the core LinkML mode and metamodel + +URI: https://w3id.org/linkml/types + diff --git a/schema/v1.1.0/metadata-docs/voxel_spacing.md b/schema/v1.1.0/metadata-docs/voxel_spacing.md new file mode 100644 index 000000000..96683715d --- /dev/null +++ b/schema/v1.1.0/metadata-docs/voxel_spacing.md @@ -0,0 +1,72 @@ +# Slot: voxel_spacing + + +_Voxel spacing equal in all three axes in angstroms_ + + + +URI: [cdp-meta:voxel_spacing](https://cryoetdataportal.czscience.com/schema/metadata/voxel_spacing) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[Tomogram](Tomogram.md) | Metadata describing a tomogram | no | + + + + + + + +## Properties + +* Range: [xsd:float](http://www.w3.org/2001/XMLSchema#float) + + + + + +## Identifier and Mapping Information + + + + + + + +### Schema Source + + +* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + + + + +## LinkML Source + +
+```yaml +name: voxel_spacing +description: Voxel spacing equal in all three axes in angstroms +from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +exact_mappings: +- cdp-common:tomogram_voxel_spacing +rank: 1000 +alias: voxel_spacing +owner: Tomogram +domain_of: +- Tomogram +range: float +inlined: true +inlined_as_list: true + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/x.md b/schema/v1.1.0/metadata-docs/x.md new file mode 100644 index 000000000..89107b370 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/x.md @@ -0,0 +1,54 @@ +# Slot: x + +URI: [cdp-meta:x](https://cryoetdataportal.czscience.com/schema/metadata/x) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TomogramSize](TomogramSize.md) | The size of a tomogram in voxels in each dimension | no | +[TomogramOffset](TomogramOffset.md) | The offset of a tomogram in voxels in each dimension relative to the canonica... | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: x +alias: x +domain_of: +- TomogramSize +- TomogramOffset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/y.md b/schema/v1.1.0/metadata-docs/y.md new file mode 100644 index 000000000..a54ae633f --- /dev/null +++ b/schema/v1.1.0/metadata-docs/y.md @@ -0,0 +1,54 @@ +# Slot: y + +URI: [cdp-meta:y](https://cryoetdataportal.czscience.com/schema/metadata/y) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TomogramSize](TomogramSize.md) | The size of a tomogram in voxels in each dimension | no | +[TomogramOffset](TomogramOffset.md) | The offset of a tomogram in voxels in each dimension relative to the canonica... | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: y +alias: y +domain_of: +- TomogramSize +- TomogramOffset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata-docs/z.md b/schema/v1.1.0/metadata-docs/z.md new file mode 100644 index 000000000..656be1293 --- /dev/null +++ b/schema/v1.1.0/metadata-docs/z.md @@ -0,0 +1,54 @@ +# Slot: z + +URI: [cdp-meta:z](https://cryoetdataportal.czscience.com/schema/metadata/z) + + + + + + + + +## Applicable Classes + +| Name | Description | Modifies Slot | +| --- | --- | --- | +[TomogramSize](TomogramSize.md) | The size of a tomogram in voxels in each dimension | no | +[TomogramOffset](TomogramOffset.md) | The offset of a tomogram in voxels in each dimension relative to the canonica... | no | + + + + + + + +## Properties + +* Range: [xsd:string](http://www.w3.org/2001/XMLSchema#string) + + + + + +## Identifier and Mapping Information + + + + + + + + +## LinkML Source + +
+```yaml +name: z +alias: z +domain_of: +- TomogramSize +- TomogramOffset +range: string + +``` +
\ No newline at end of file diff --git a/schema/v1.1.0/metadata.yaml b/schema/v1.1.0/metadata.yaml index 3a9368d7b..404bd08c3 100644 --- a/schema/v1.1.0/metadata.yaml +++ b/schema/v1.1.0/metadata.yaml @@ -1,329 +1,588 @@ -id: https://cryoetdataportal.czscience.com/cetdp +id: https://cryoetdataportal.czscience.com/schema-docs/metadata name: cdp-meta +version: 1.1.0 prefixes: linkml: https://w3id.org/linkml/ + cdp-meta: https://cryoetdataportal.czscience.com/schema/metadata/ ORCID: https://orcid.org/ ROR: https://ror.org/ UBERON: http://purl.obolibrary.org/obo/UBERON_ CL: http://purl.obolibrary.org/obo/CL_ GO: http://purl.obolibrary.org/obo/GO_ + #cdp-common: common imports: - linkml:types default_range: string +default_prefix: cdp-meta -slots: +classes: # ============================================================================ - # Common slots + # Snapshot / Thumbnail # ============================================================================ - ORCID: - description: An ORCID identifier. - range: string - pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' - affiliation_identifier: - description: A research organization registry identifier. - range: string - pattern: '^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$' + PicturePath: + description: A set of paths to representative images of a piece of data. -enums: - # ============================================================================ - # Controlled vocabularies - # ============================================================================ + attributes: + snapshot: + range: string + description: Path to the dataset preview image relative to the dataset directory root. + thumbnail: + range: string + description: Path to the thumbnail of preview image relative to the dataset directory root. - sample_type: - description: Type of sample imaged in a CryoET study. - permissible_values: - cell: - description: Tomographic data of whole cells or cell sections. - tissue: - description: Tomographic data of tissue sections. - organism: - description: Tomographic data of sections through multicellular organisms. - organelle: - description: Tomographic data of purified organelles. - virus: - description: Tomographic data of purified viruses or VLPs. - in vitro: - description: Tomographic data of in vitro reconstituted systems or mixtures of proteins. - in silico: - description: Simulated tomographic data. - other: - description: Other type of sample. + # ============================================================================ -classes: # ============================================================================ - # Author and Annotator information + # Author / Annotator # ============================================================================ - Author: - description: An author of a scientific data entity. + description: >- + Author of a scientific data entity. attributes: name: - range: string - required: true - description: The full name of the author. + exact_mappings: + - cdp-common:author_name email: - range: string - description: The email of the author. + exact_mappings: + - cdp-common:author_email affiliation_name: - range: string - description: The name of the author's affiliation. + exact_mappings: + - cdp-common:author_affiliation_name affiliation_address: - range: string - description: The address of the author's affiliation. + exact_mappings: + - cdp-common:author_affiliation_address + affiliation_identifier: + exact_mappings: + - cdp-common:affiliation_identifier + recommended: true is_corresponding: - range: boolean - description: Whether the author is the corresponding author. + exact_mappings: + - cdp-common:author_corresponding_author_status is_primary_author: - range: boolean - description: Whether the author is the primary author. - alias: is_primary_annotator - - slots: - - ORCID - - affiliation_identifier - slot_usage: - orcid: + exact_mappings: + - cdp-common:author_primary_author_status + ORCID: + exact_mappings: + - cdp-common:orcid recommended: true + + Annotator: + description: >- + Annotator of a scientific data entity. + attributes: + name: + exact_mappings: + - cdp-common:author_name + email: + exact_mappings: + - cdp-common:author_email + affiliation_name: + exact_mappings: + - cdp-common:author_affiliation_name + affiliation_address: + exact_mappings: + - cdp-common:author_affiliation_address affiliation_identifier: + exact_mappings: + - cdp-common:affiliation_identifier recommended: true + is_corresponding: + exact_mappings: + - cdp-common:author_corresponding_author_status + is_primary_annotator: + exact_mappings: + - cdp-common:author_primary_author_status + ORCID: + exact_mappings: + - cdp-common:orcid + recommended: true + # ============================================================================ + + # ============================================================================ # Funding source information # ============================================================================ - Funding: - description: A funding source for a scientific data entity. + description: A funding source for a scientific data entity (base for JSON and DB representation). attributes: funding_agency_name: - range: string - recommended: true - description: The name of the funding source. + exact_mappings: + - cdp-common:funding_agency_name grant_id: - range: string - recommended: true - description: Grant identifier provided by the funding agency + exact_mappings: + - cdp-common:funding_grant_id + # ============================================================================ # ============================================================================ # Deposition, release and last modified dates # ============================================================================ - - Dates: - description: A set of dates. + DateStamp: + abstract: true + description: A set of dates at which a data item was deposited, published and last modified. attributes: deposition_date: - range: date required: true - description: The date a piece of data was deposited to the cryoET data portal. + exact_mappings: + - cdp-common:deposition_date release_date: - range: date - required: true - description: The date a piece of data was made public on the cryoET data portal. + recommended: true + exact_mappings: + - cdp-common:release_date last_modified_date: - range: date - required: true - description: The date a piece of data was last modified on the cryoET data portal. + recommended: true + exact_mappings: + - cdp-common:last_modified_date # ============================================================================ - # Snapshot / Thumbnail + # Meta-Mixins # ============================================================================ + DatestampedEntity: + abstract: true + description: An entity with associated deposition, release and last modified dates. + attributes: + dates: + range: DateStamp + required: true - PictureLocations: - description: A set of paths to representative images of a piece of data. + AuthoredEntity: + abstract: true + description: An entity with associated authors. attributes: - snapshot: - range: string - description: Path to an associated (larger) snapshot image relative to the dataset directory root. - thumbnail: - range: string - description: Path to an associated (smaller) thumbnail image relative to the dataset directory root. + authors: + range: Author + required: true + description: An ordered list of authors of the entity. + multivalued: true + inlined_as_list: true + list_elements_ordered: true + + AnnotatoredEntity: + abstract: true + description: An entity with associated annotation authors. + attributes: + authors: + range: Annotator + required: true + description: An ordered list of annotation authors of the entity. + multivalued: true + inlined_as_list: true + list_elements_ordered: true + + FundedEntity: + abstract: true + description: An entity with associated funding sources. + attributes: + funding: + range: Funding + recommended: true + description: An ordered list of funding sources for the entity. + multivalued: true + inlined_as_list: true + list_elements_ordered: true + CrossReferencedEntity: + abstract: true + description: An entity with associated cross-references to other databases and publications. + attributes: + cross_references: + range: CrossReferences + + PicturedEntity: + abstract: true + description: An entity with associated preview images. + attributes: + key_photos: + range: PicturePath + description: A set of paths to representative images of the entity. + required: true + # ============================================================================ # ============================================================================ # Experimental metadata # ============================================================================ - - Species: - description: The species from which the sample was derived. + Organism: + description: &desc_Organism The species from which the sample was derived. attributes: name: - range: string - recommended: true - description: The name of the species. + exact_mappings: + - cdp-common:organism_name taxonomy_id: - range: integer - recommended: true - description: The NCBI taxonomy identifier for the species. + exact_mappings: + - cdp-common:organism_taxid Tissue: - description: The type of tissue from which the sample was derived. + description: &desc_Tissue The type of tissue from which the sample was derived. attributes: name: - range: string - recommended: true - description: The name of the tissue. + exact_mappings: + - cdp-common:tissue_name id: - range: string - recommended: true - description: The UBERON identifier for the tissue. + exact_mappings: + - cdp-common:tissue_id CellType: - description: The cell type from which the sample was derived. + description: &desc_CellType The cell type from which the sample was derived. attributes: name: - range: string - recommended: true - description: The name of the cell type. + exact_mappings: + - cdp-common:cell_name id: - range: string - recommended: true - description: The CL identifier for the cell type. + exact_mappings: + - cdp-common:cell_type_id CellStrain: - description: The strain or cell line from which the sample was derived. + description: &desc_CellStrain The strain or cell line from which the sample was derived. attributes: name: - range: string - recommended: true - description: The name of the cell line or strain. + exact_mappings: + - cdp-common:cell_strain_name id: - range: string - recommended: true - description: The CL identifier for the cell line or strain. + exact_mappings: + - cdp-common:cell_strain_id CellComponent: - description: The cellular component from which the sample was derived. + description: &desc_CellComponent The cellular component from which the sample was derived. attributes: name: - range: string - recommended: true - description: The name of the cellular component. + exact_mappings: + - cdp-common:cell_component_name id: - range: string - recommended: true - description: The GO identifier for the cellular component. + exact_mappings: + - cdp-common:cell_component_id ExperimentalMetadata: + abstract: true description: Metadata describing sample and sample preparation methods used in a cryoET dataset. attributes: sample_type: - range: sample_type - required: true - description: The type of sample imaged in a CryoET study. + exact_mappings: + - cdp-common:preparation_sample_type + sample_preparation: + exact_mappings: + - cdp-common:sample_preparation + grid_preparation: + exact_mappings: + - cdp-common:grid_preparation + other_setup: + exact_mappings: + - cdp-common:preparation_other_setup organism: - range: Species - description: The species from which the sample was derived. + description: *desc_Organism + range: Organism tissue: + description: *desc_Tissue range: Tissue - description: The type of tissue from which the sample was derived. cell_type: + description: *desc_CellType range: CellType - description: The cell type from which the sample was derived. cell_strain: + description: *desc_CellStrain range: CellStrain - description: The strain or cell line from which the sample was derived. cell_component: + description: *desc_CellComponent range: CellComponent - description: The cellular component from which the sample was derived. - sample_preparation: - range: string - description: A description of the sample preparation. - grid_preparation: - range: string - description: A description of the grid preparation. - other_setup: - range: string - description: Any other experimental setup information not covered by the other fields. - + # ============================================================================ # ============================================================================ - # Dataset + # dataset_metadata.json # ============================================================================ - - CrossReferences: - description: A set of cross-references to other databases. - attributes: - dataset_publications: - range: string - description: Comma-separated list of DOIs for publications associated with the dataset. - related_database_entries: - range: string - description: Comma-separated list of related database entries for the dataset. - related_database_links: - range: string - description: Comma-separated list of related database links for the dataset. - dataset_citations: - range: string - description: Comma-separated list of DOIs for publications citing the dataset. - Dataset: description: High-level description of a cryoET dataset. mixins: - - TimestampedEntity + - DatestampedEntity - AuthoredEntity - FundedEntity - - PreviewableEntity + - PicturedEntity + - CrossReferencedEntity - ExperimentalMetadata + attributes: dataset_identifier: - range: integer - required: true - description: The unique identifier of the dataset on the cryoET data portal. + exact_mappings: + - cdp-common:dataset_identifier dataset_title: - range: string - required: true - description: The title of the dataset. + exact_mappings: + - cdp-common:dataset_title dataset_description: - range: string - required: true - description: A short description of the CryoET dataset. - cross_references: - range: CrossReferences - description: A set of cross-references to other databases and publications. - snapshot: - range: string - description: Path to an associated snapshot image relative to the dataset directory root. - thumbnail: - range: string - description: Path to an associated thumbnail image relative to the dataset directory root. + exact_mappings: + - cdp-common:dataset_description + # ============================================================================ # ============================================================================ - # Meta-Mixins + # TiltSeries metadata # ============================================================================ + Camera: + description: &desc_camera The camera used to collect the tilt series. + attributes: + manufacturer: + exact_mappings: + - cdp-common:tiltseries_camera_manufacturer + model: + exact_mappings: + - cdp-common:tiltseries_camera_model - TimestampedEntity: - description: An entity with associated deposition, release and last modified dates. + Microscope: + description: &desc_microscope The microscope used to collect the tilt series. attributes: - dates: - range: Dates - required: true - description: The dates at which the entity was deposited, released and last modified. + manufacturer: + exact_mappings: + - cdp-common:tiltseries_microscope_manufacturer + model: + exact_mappings: + - cdp-common:tiltseries_microscope_model - AuthoredEntity: - description: An entity with associated authors. + MicroscopeOpticalSetup: + description: &desc_microscope_optical_setup The optical setup of the microscope used to collect the tilt series. attributes: - authors: - range: Author - required: true - description: An ordered list of authors of the entity. - multivalued: true - inlined_as_list : true + energy_filter: + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + phase_plate: + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + image_corrector: + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector - FundedEntity: - description: An entity with associated funding sources. + TiltRange: + description: &desc_tilt_range The range of tilt angles in the tilt series. attributes: - funding: - range: Funding - recommended: true - description: An ordered list of funding sources for the entity. - multivalued: true - inlined_as_list : true + min: + exact_mappings: + - cdp-common:tiltseries_tilt_min + max: + exact_mappings: + - cdp-common:tiltseries_tilt_max + # ============================================================================ + + # ============================================================================ + # tiltseries_metadata.json + # ============================================================================ + TiltSeries: + description: Metadata describing a tilt series. - PreviewableEntity: - description: An entity with associated preview images. attributes: - key_photos: - range: PictureLocations - description: A set of paths to representative images of the entity. - multivalued: false \ No newline at end of file + acceleration_voltage: + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + spherical_aberration_constant: + exact_mappings: + - cdp-common:tiltseries_spherical_aberration_constant + microscope_additional_info: + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + tilt_axis: + exact_mappings: + - cdp-common:tiltseries_tilt_axis + tilt_step: + exact_mappings: + - cdp-common:tiltseries_tilt_step + tilting_scheme: + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + total_flux: + exact_mappings: + - cdp-common:tiltseries_total_flux + data_acquisition_software: + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + binning_from_frames: + exact_mappings: + - cdp-common:tiltseries_binning_from_frames + tilt_series_quality: + exact_mappings: + - cdp-common:tiltseries_tilt_series_quality + pixel_spacing: + exact_mappings: + - cdp-common:tiltseries_pixel_spacing + aligned_tiltseries_binning: + exact_mappings: + - cdp-common:tiltseries_aligned_tiltseries_binning + frames_count: + exact_mappings: + - cdp-common:tiltseries_frames_count + camera: + description: *desc_camera + range: Camera + microscope: + description: *desc_microscope + range: Microscope + microscope_optical_setup: + description: *desc_microscope_optical_setup + range: MicroscopeOpticalSetup + tilt_range: + description: *desc_tilt_range + range: TiltRange + # ============================================================================ + + # ============================================================================ + # Tomogram metadata + # ============================================================================ + TomogramSize: + description: &desc_tomogram_size The size of a tomogram in voxels in each dimension. + attributes: + x: + exact_mappings: + - cdp-common:tomogram_size_x + y: + exact_mappings: + - cdp-common:tomogram_size_y + z: + exact_mappings: + - cdp-common:tomogram_size_z + + TomogramOffset: + description: &desc_tomogram_offset The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. + attributes: + x: + exact_mappings: + - cdp-common:tomogram_offset_x + y: + exact_mappings: + - cdp-common:tomogram_offset_y + z: + exact_mappings: + - cdp-common:tomogram_offset_z + # ============================================================================ + + # ============================================================================ + # tomogram_metadata.json + # ============================================================================ + Tomogram: + description: Metadata describing a tomogram. + mixins: + - AuthoredEntity + - PicturedEntity + + attributes: + voxel_spacing: + exact_mappings: + - cdp-common:tomogram_voxel_spacing + fiducial_alignment_status: + exact_mappings: + - cdp-common:tomogram_fiducial_alignment_status + ctf_corrected: + exact_mappings: + - cdp-common:tomogram_ctf_corrected + reconstruction_method: + exact_mappings: + - cdp-common:tomogram_reconstruction_method + reconstruction_software: + exact_mappings: + - cdp-common:tomogram_reconstruction_software + processing: + exact_mappings: + - cdp-common:tomogram_processing + processing_software: + exact_mappings: + - cdp-common:tomogram_processing_software + tomogram_version: + exact_mappings: + - cdp-common:tomogram_version + affine_transformation_matrix: + exact_mappings: + - cdp-common:tomogram_affine_transformation_matrix + size: + description: *desc_tomogram_size + range: TomogramSize + offset: + description: *desc_tomogram_offset + range: TomogramOffset + # ============================================================================ + + # ============================================================================ + # Annotation metadata + # ============================================================================ + AnnotationFile: + description: &desc_annotation_file Metadata describing a file containing an annotation. + attributes: + format: + exact_mappings: + - cdp-common:annotation_file_format + shape: + exact_mappings: + - cdp-common:annotation_file_shape_type + path: + exact_mappings: + - cdp-common:annotation_file_path + is_visualization_default: + exact_mappings: + - cdp-common:annotation_file_is_visualization_default + + AnnotationConfidence: + description: &desc_annotation_confidence Metadata describing the confidence of an annotation. + attributes: + precision: + exact_mappings: + - cdp-common:annotation_confidence_precision + recall: + exact_mappings: + - cdp-common:annotation_confidence_recall + ground_truth_used: + exact_mappings: + - cdp-common:annotation_ground_truth_used + + AnnotationObject: + description: &desc_annotation_object Metadata describing the object being annotated. + attributes: + id: + exact_mappings: + - cdp-common:annotation_object_id + name: + exact_mappings: + - cdp-common:annotation_object_name + description: + exact_mappings: + - cdp-common:annotation_object_description + state: + exact_mappings: + - cdp-common:annotation_object_state + # ============================================================================ + + # ============================================================================ + # annotation_metadata.json + # ============================================================================ + Annotation: + description: Metadata describing an annotation. + mixins: + - DatestampedEntity + - AnnotatoredEntity + + attributes: + annotation_method: + exact_mappings: + - cdp-common:annotation_method + annotation_method_type: + exact_mappings: + - cdp-common:annotation_method_type + annotation_publications: + exact_mappings: + - cdp-common:annotation_publication + annotation_software: + exact_mappings: + - cdp-common:annotation_software + ground_truth_status: + exact_mappings: + - cdp-common:annotation_ground_truth_status + object_count: + exact_mappings: + - cdp-common:annotation_object_count + is_curator_recommended: + exact_mappings: + - cdp-common:annotation_is_curator_recommended + files: + description: *desc_annotation_file + range: AnnotationFile + multivalued: true + inlined_as_list: true + list_elements_ordered: true + confidence: + description: *desc_annotation_confidence + range: AnnotationConfidence + annotation_object: + description: *desc_annotation_object + range: AnnotationObject + # ============================================================================ diff --git a/schema/v1.1.0/metadata_materialized.yaml b/schema/v1.1.0/metadata_materialized.yaml new file mode 100644 index 000000000..4e79821e6 --- /dev/null +++ b/schema/v1.1.0/metadata_materialized.yaml @@ -0,0 +1,2162 @@ +name: cdp-meta +id: https://cryoetdataportal.czscience.com/schema-docs/metadata +version: 1.1.0 +imports: +- linkml:types +prefixes: + linkml: + prefix_prefix: linkml + prefix_reference: https://w3id.org/linkml/ + cdp-meta: + prefix_prefix: cdp-meta + prefix_reference: https://cryoetdataportal.czscience.com/schema/metadata/ + ORCID: + prefix_prefix: ORCID + prefix_reference: https://orcid.org/ + ROR: + prefix_prefix: ROR + prefix_reference: https://ror.org/ + UBERON: + prefix_prefix: UBERON + prefix_reference: http://purl.obolibrary.org/obo/UBERON_ + CL: + prefix_prefix: CL + prefix_reference: http://purl.obolibrary.org/obo/CL_ + GO: + prefix_prefix: GO + prefix_reference: http://purl.obolibrary.org/obo/GO_ +default_prefix: cdp-meta +default_range: string +enums: + sample_type_enum: + name: sample_type_enum + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + permissible_values: + cell: + text: cell + description: Tomographic data of whole cells or cell sections. + tissue: + text: tissue + description: Tomographic data of tissue sections. + organism: + text: organism + description: Tomographic data of sections through multicellular organisms. + organelle: + text: organelle + description: Tomographic data of purified organelles. + virus: + text: virus + description: Tomographic data of purified viruses or VLPs. + in_vitro: + text: in_vitro + description: Tomographic data of in vitro reconstituted systems or mixtures + of proteins. + in_silico: + text: in_silico + description: Simulated tomographic data. + other: + text: other + description: Other type of sample. + fiducial_alignment_status_enum: + name: fiducial_alignment_status_enum + description: Fiducial Alignment method + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + permissible_values: + FIDUCIAL: + text: FIDUCIAL + description: Alignment computed based on fiducial markers + NON_FIDUCIAL: + text: NON_FIDUCIAL + description: Alignment computed without fiducial markers + tomogram_type_enum: + name: tomogram_type_enum + description: Tomogram type + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + permissible_values: + CANONICAL: + text: CANONICAL + description: Canonical tomogram (basis geometry for all annotations) + annotation_method_type_enum: + name: annotation_method_type_enum + description: Describes how the annotations were generated. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + permissible_values: + manual: + text: manual + description: Annotations were generated manually. + automated: + text: automated + description: Annotations were generated semi-automatically. + hybrid: + text: hybrid + description: Annotations were generated automatically. + annotation_shape_enum: + name: annotation_shape_enum + description: Annotation shape types available on the data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + permissible_values: + Point: + text: Point + description: Annotations were generated manually. + OrientedPoint: + text: OrientedPoint + description: Annotations were generated semi-automatically. + SegmentationMask: + text: SegmentationMask + description: Annotations were generated automatically. +classes: + PicturePath: + name: PicturePath + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + snapshot: + name: snapshot + description: Path to the dataset preview image relative to the dataset directory + root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: snapshot + owner: PicturePath + domain_of: + - PicturePath + range: string + inlined: true + inlined_as_list: true + thumbnail: + name: thumbnail + description: Path to the thumbnail of preview image relative to the dataset + directory root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: thumbnail + owner: PicturePath + domain_of: + - PicturePath + range: string + inlined: true + inlined_as_list: true + Author: + name: Author + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + description: The full name of the author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_name + alias: name + owner: Author + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_email + alias: email + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: Author + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:affiliation_identifier + alias: affiliation_identifier + owner: Author + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$ + is_corresponding: + name: is_corresponding + description: Whether the author is a corresponding author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + alias: is_corresponding + owner: Author + domain_of: + - Author + - Annotator + range: boolean + inlined: true + inlined_as_list: true + is_primary_author: + name: is_primary_author + description: Whether the author is a primary author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_primary_author_status + alias: is_primary_author + owner: Author + domain_of: + - Author + range: boolean + inlined: true + inlined_as_list: true + ORCID: + name: ORCID + description: A unique, persistent identifier for researchers, provided by + ORCID. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:orcid + alias: ORCID + owner: Author + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + Annotator: + name: Annotator + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_name + alias: name + owner: Annotator + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + email: + name: email + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_email + alias: email + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:affiliation_identifier + alias: affiliation_identifier + owner: Annotator + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + is_corresponding: + name: is_corresponding + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + alias: is_corresponding + owner: Annotator + domain_of: + - Author + - Annotator + range: string + inlined: true + inlined_as_list: true + is_primary_annotator: + name: is_primary_annotator + description: Whether the author is a primary author. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:author_primary_author_status + alias: is_primary_annotator + owner: Annotator + domain_of: + - Annotator + range: boolean + inlined: true + inlined_as_list: true + ORCID: + name: ORCID + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:orcid + alias: ORCID + owner: Annotator + domain_of: + - Author + - Annotator + range: string + recommended: true + inlined: true + inlined_as_list: true + Funding: + name: Funding + description: A funding source for a scientific data entity (base for JSON and + DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + funding_agency_name: + name: funding_agency_name + description: The name of the funding source. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:funding_agency_name + alias: funding_agency_name + owner: Funding + domain_of: + - Funding + range: string + inlined: true + inlined_as_list: true + grant_id: + name: grant_id + description: Grant identifier provided by the funding agency + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:funding_grant_id + alias: grant_id + owner: Funding + domain_of: + - Funding + range: string + inlined: true + inlined_as_list: true + DateStamp: + name: DateStamp + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + slots: + - deposition_date + - release_date + - last_modified_date + slot_usage: + deposition_date: + name: deposition_date + domain_of: + - DateStamp + required: true + release_date: + name: release_date + domain_of: + - DateStamp + recommended: true + last_modified_date: + name: last_modified_date + domain_of: + - DateStamp + recommended: true + attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: deposition_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: release_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + recommended: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: last_modified_date + owner: DateStamp + domain_of: + - DateStamp + range: date + required: true + recommended: true + inlined: true + inlined_as_list: true + DatestampedEntity: + name: DatestampedEntity + description: An entity with associated deposition, release and last modified dates. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: DatestampedEntity + domain_of: + - DatestampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + AuthoredEntity: + name: AuthoredEntity + description: An entity with associated authors. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: AuthoredEntity + domain_of: + - AuthoredEntity + - AnnotatoredEntity + range: Author + required: true + inlined: true + inlined_as_list: true + AnnotatoredEntity: + name: AnnotatoredEntity + description: An entity with associated annotation authors. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + authors: + name: authors + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: AnnotatoredEntity + domain_of: + - AuthoredEntity + - AnnotatoredEntity + range: Annotator + required: true + inlined: true + inlined_as_list: true + FundedEntity: + name: FundedEntity + description: An entity with associated funding sources. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON + and DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: funding + owner: FundedEntity + domain_of: + - FundedEntity + range: Funding + recommended: true + inlined: true + inlined_as_list: true + CrossReferencedEntity: + name: CrossReferencedEntity + description: An entity with associated cross-references to other databases and + publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cross_references + owner: CrossReferencedEntity + domain_of: + - CrossReferencedEntity + range: CrossReferences + inlined: true + inlined_as_list: true + PicturedEntity: + name: PicturedEntity + description: An entity with associated preview images. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: PicturedEntity + domain_of: + - PicturedEntity + range: PicturePath + required: true + inlined: true + inlined_as_list: true + Organism: + name: Organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:organism_name + alias: name + owner: Organism + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + taxonomy_id: + name: taxonomy_id + description: NCBI taxonomy identifier for the organism, e.g. 9606 + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:organism_taxid + alias: taxonomy_id + owner: Organism + domain_of: + - Organism + range: string + inlined: true + inlined_as_list: true + Tissue: + name: Tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tissue_name + alias: name + owner: Tissue + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + description: The UBERON identifier for the tissue. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tissue_id + alias: id + owner: Tissue + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + CellType: + name: CellType + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_name + alias: name + owner: CellType + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_type_id + alias: id + owner: CellType + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + CellStrain: + name: CellStrain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_strain_name + alias: name + owner: CellStrain + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_strain_id + alias: id + owner: CellStrain + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + CellComponent: + name: CellComponent + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_component_name + alias: name + owner: CellComponent + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:cell_component_id + alias: id + owner: CellComponent + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + ExperimentalMetadata: + name: ExperimentalMetadata + description: Metadata describing sample and sample preparation methods used in + a cryoET dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + abstract: true + attributes: + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: sample_type_enum + inlined: true + inlined_as_list: true + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid + preparation that may make this dataset unique in the same publication. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: organism + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: Organism + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: tissue + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: Tissue + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_type + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_strain + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_component + owner: ExperimentalMetadata + domain_of: + - ExperimentalMetadata + range: CellComponent + inlined: true + inlined_as_list: true + Dataset: + name: Dataset + description: High-level description of a cryoET dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + mixins: + - DatestampedEntity + - AuthoredEntity + - FundedEntity + - PicturedEntity + - CrossReferencedEntity + - ExperimentalMetadata + attributes: + dataset_identifier: + name: dataset_identifier + description: An identifier for a CryoET dataset, assigned by the Data Portal. + Used to identify the dataset as the directory name in data tree. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_identifier + alias: dataset_identifier + owner: Dataset + domain_of: + - Dataset + range: integer + inlined: true + inlined_as_list: true + dataset_title: + name: dataset_title + description: Title of a CryoET dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_title + alias: dataset_title + owner: Dataset + domain_of: + - Dataset + range: string + inlined: true + inlined_as_list: true + dataset_description: + name: dataset_description + description: A short description of a CryoET dataset, similar to an abstract + for a journal article or dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:dataset_description + alias: dataset_description + owner: Dataset + domain_of: + - Dataset + range: string + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: Dataset + domain_of: + - DatestampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Dataset + domain_of: + - AuthoredEntity + - AnnotatoredEntity + range: Author + required: true + inlined: true + inlined_as_list: true + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON + and DB representation). + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: funding + owner: Dataset + domain_of: + - FundedEntity + range: Funding + recommended: true + inlined: true + inlined_as_list: true + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: Dataset + domain_of: + - PicturedEntity + range: PicturePath + required: true + inlined: true + inlined_as_list: true + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cross_references + owner: Dataset + domain_of: + - CrossReferencedEntity + range: CrossReferences + inlined: true + inlined_as_list: true + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: Dataset + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: Dataset + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: Dataset + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid + preparation that may make this dataset unique in the same publication. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: Dataset + domain_of: + - ExperimentalMetadata + range: string + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: organism + owner: Dataset + domain_of: + - ExperimentalMetadata + range: Organism + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: tissue + owner: Dataset + domain_of: + - ExperimentalMetadata + range: Tissue + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_type + owner: Dataset + domain_of: + - ExperimentalMetadata + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_strain + owner: Dataset + domain_of: + - ExperimentalMetadata + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: cell_component + owner: Dataset + domain_of: + - ExperimentalMetadata + range: CellComponent + inlined: true + inlined_as_list: true + Camera: + name: Camera + description: The camera used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + manufacturer: + name: manufacturer + description: Name of the camera manufacturer + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_camera_manufacturer + alias: manufacturer + owner: Camera + domain_of: + - Camera + - Microscope + range: string + inlined: true + inlined_as_list: true + model: + name: model + description: Camera model name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_camera_model + alias: model + owner: Camera + domain_of: + - Camera + - Microscope + range: string + inlined: true + inlined_as_list: true + Microscope: + name: Microscope + description: The microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + manufacturer: + name: manufacturer + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_manufacturer + alias: manufacturer + owner: Microscope + domain_of: + - Camera + - Microscope + range: string + inlined: true + inlined_as_list: true + model: + name: model + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_model + alias: model + owner: Microscope + domain_of: + - Camera + - Microscope + range: string + inlined: true + inlined_as_list: true + MicroscopeOpticalSetup: + name: MicroscopeOpticalSetup + description: The optical setup of the microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + energy_filter: + name: energy_filter + description: Energy filter setup used + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + alias: energy_filter + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + phase_plate: + name: phase_plate + description: Phase plate configuration + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + alias: phase_plate + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + image_corrector: + name: image_corrector + description: Image corrector setup + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + alias: image_corrector + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + TiltRange: + name: TiltRange + description: The range of tilt angles in the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + min: + name: min + description: Minimal tilt angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_min + alias: min + owner: TiltRange + domain_of: + - TiltRange + range: float + inlined: true + inlined_as_list: true + max: + name: max + description: Maximal tilt angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_max + alias: max + owner: TiltRange + domain_of: + - TiltRange + range: float + inlined: true + inlined_as_list: true + TiltSeries: + name: TiltSeries + description: Metadata describing a tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + acceleration_voltage: + name: acceleration_voltage + description: Electron Microscope Accelerator voltage in volts + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + alias: acceleration_voltage + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + spherical_aberration_constant: + name: spherical_aberration_constant + description: Spherical Aberration Constant of the objective lens in millimeters + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_spherical_aberration_constant + alias: spherical_aberration_constant + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + microscope_additional_info: + name: microscope_additional_info + description: Other microscope optical setup information, in addition to energy + filter, phase plate and image corrector + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + alias: microscope_additional_info + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + tilt_axis: + name: tilt_axis + description: Rotation angle in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_axis + alias: tilt_axis + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilt_step: + name: tilt_step + description: Tilt step in degrees + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_step + alias: tilt_step + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilting_scheme: + name: tilting_scheme + description: The order of stage tilting during acquisition of the data + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + alias: tilting_scheme + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + total_flux: + name: total_flux + description: Number of Electrons reaching the specimen in a square Angstrom + area for the entire tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_total_flux + alias: total_flux + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + data_acquisition_software: + name: data_acquisition_software + description: Software used to collect data + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + alias: data_acquisition_software + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + binning_from_frames: + name: binning_from_frames + description: Describes the binning factor from frames to tilt series file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_binning_from_frames + alias: binning_from_frames + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + tilt_series_quality: + name: tilt_series_quality + description: Author assessment of tilt series quality within the dataset (1-5, + 5 is best) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_tilt_series_quality + alias: tilt_series_quality + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + pixel_spacing: + name: pixel_spacing + description: Pixel spacing for the tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_pixel_spacing + alias: pixel_spacing + owner: TiltSeries + domain_of: + - TiltSeries + range: float + inlined: true + inlined_as_list: true + aligned_tiltseries_binning: + name: aligned_tiltseries_binning + description: Binning factor of the aligned tilt series + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_aligned_tiltseries_binning + alias: aligned_tiltseries_binning + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + frames_count: + name: frames_count + description: Number of frames associated with this tiltseries + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tiltseries_frames_count + alias: frames_count + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + camera: + name: camera + description: The camera used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: camera + owner: TiltSeries + domain_of: + - TiltSeries + range: Camera + inlined: true + inlined_as_list: true + microscope: + name: microscope + description: The microscope used to collect the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: microscope + owner: TiltSeries + domain_of: + - TiltSeries + range: Microscope + inlined: true + inlined_as_list: true + microscope_optical_setup: + name: microscope_optical_setup + description: The optical setup of the microscope used to collect the tilt + series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: microscope_optical_setup + owner: TiltSeries + domain_of: + - TiltSeries + range: MicroscopeOpticalSetup + inlined: true + inlined_as_list: true + tilt_range: + name: tilt_range + description: The range of tilt angles in the tilt series. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: tilt_range + owner: TiltSeries + domain_of: + - TiltSeries + range: TiltRange + inlined: true + inlined_as_list: true + TomogramSize: + name: TomogramSize + description: The size of a tomogram in voxels in each dimension. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + x: + name: x + description: Number of pixels in the 3D data fast axis + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_x + alias: x + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + y: + name: y + description: Number of pixels in the 3D data medium axis + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_y + alias: y + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + z: + name: z + description: Number of pixels in the 3D data slow axis. This is the image + projection direction at zero stage tilt + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_size_z + alias: z + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + inlined: true + inlined_as_list: true + TomogramOffset: + name: TomogramOffset + description: The offset of a tomogram in voxels in each dimension relative to + the canonical tomogram. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + x: + name: x + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_x + alias: x + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + y: + name: y + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_y + alias: y + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + z: + name: z + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_offset_z + alias: z + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: string + inlined: true + inlined_as_list: true + Tomogram: + name: Tomogram + description: Metadata describing a tomogram. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + mixins: + - AuthoredEntity + - PicturedEntity + attributes: + voxel_spacing: + name: voxel_spacing + description: Voxel spacing equal in all three axes in angstroms + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_voxel_spacing + alias: voxel_spacing + owner: Tomogram + domain_of: + - Tomogram + range: float + inlined: true + inlined_as_list: true + fiducial_alignment_status: + name: fiducial_alignment_status + description: Whether the tomographic alignment was computed based on fiducial + markers. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_fiducial_alignment_status + alias: fiducial_alignment_status + owner: Tomogram + domain_of: + - Tomogram + range: fiducial_alignment_status_enum + inlined: true + inlined_as_list: true + ctf_corrected: + name: ctf_corrected + description: Whether this tomogram is CTF corrected + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_ctf_corrected + alias: ctf_corrected + owner: Tomogram + domain_of: + - Tomogram + range: boolean + inlined: true + inlined_as_list: true + reconstruction_method: + name: reconstruction_method + description: Describe reconstruction method (Weighted back-projection, SART, + SIRT) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_method + alias: reconstruction_method + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + reconstruction_software: + name: reconstruction_software + description: Name of software used for reconstruction + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_software + alias: reconstruction_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + processing: + name: processing + description: Describe additional processing used to derive the tomogram + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_processing + alias: processing + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + processing_software: + name: processing_software + description: Processing software used to derive the tomogram + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_processing_software + alias: processing_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + tomogram_version: + name: tomogram_version + description: Version of tomogram using the same software and post-processing. + Version of tomogram using the same software and post-processing. This will + be presented as the latest version + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_version + alias: tomogram_version + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + affine_transformation_matrix: + name: affine_transformation_matrix + description: The flip or rotation transformation of this author submitted + tomogram is indicated here + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:tomogram_affine_transformation_matrix + alias: affine_transformation_matrix + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + size: + name: size + description: The size of a tomogram in voxels in each dimension. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: size + owner: Tomogram + domain_of: + - Tomogram + range: TomogramSize + inlined: true + inlined_as_list: true + offset: + name: offset + description: The offset of a tomogram in voxels in each dimension relative + to the canonical tomogram. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: offset + owner: Tomogram + domain_of: + - Tomogram + range: TomogramOffset + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Tomogram + domain_of: + - AuthoredEntity + - AnnotatoredEntity + range: Author + required: true + inlined: true + inlined_as_list: true + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: key_photos + owner: Tomogram + domain_of: + - PicturedEntity + range: PicturePath + required: true + inlined: true + inlined_as_list: true + AnnotationFile: + name: AnnotationFile + description: Metadata describing a file containing an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + format: + name: format + description: File format for this file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_format + alias: format + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + shape: + name: shape + description: Describe whether this is a Point, OrientedPoint, or SegmentationMask + file + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_shape_type + alias: shape + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + path: + name: path + description: Path to the annotation file relative to the dataset root. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_path + alias: path + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_file_is_visualization_default + alias: is_visualization_default + owner: AnnotationFile + domain_of: + - AnnotationFile + range: boolean + inlined: true + inlined_as_list: true + AnnotationConfidence: + name: AnnotationConfidence + description: Metadata describing the confidence of an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + precision: + name: precision + description: Describe the confidence level of the annotation. Precision is + defined as the % of annotation objects being true positive + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_confidence_precision + alias: precision + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + recall: + name: recall + description: Describe the confidence level of the annotation. Recall is defined + as the % of true positives being annotated correctly + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_confidence_recall + alias: recall + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + ground_truth_used: + name: ground_truth_used + description: Annotation filename used as ground truth for precision and recall + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_ground_truth_used + alias: ground_truth_used + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: string + inlined: true + inlined_as_list: true + AnnotationObject: + name: AnnotationObject + description: Metadata describing the object being annotated. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + id: + name: id + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_id + alias: id + owner: AnnotationObject + domain_of: + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + name: + name: name + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_name + alias: name + owner: AnnotationObject + domain_of: + - Author + - Annotator + - Organism + - Tissue + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + description: + name: description + description: A textual description of the annotation object, can be a longer + description to include additional information not covered by the Annotation + object name and state. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_description + alias: description + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + state: + name: state + description: Molecule state annotated (e.g. open, closed) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_state + alias: state + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + Annotation: + name: Annotation + description: Metadata describing an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + mixins: + - DatestampedEntity + - AnnotatoredEntity + attributes: + annotation_method: + name: annotation_method + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive + Unlabeled Learning, template matching) + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_method + alias: annotation_method + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_method_type: + name: annotation_method_type + description: Classification of the annotation method based on supervision. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_method_type + alias: annotation_method_type + owner: Annotation + domain_of: + - Annotation + range: annotation_method_type_enum + inlined: true + inlined_as_list: true + annotation_publications: + name: annotation_publications + description: DOIs for publications that describe the dataset. Use a comma + to separate multiple DOIs. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_publication + alias: annotation_publications + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_software: + name: annotation_software + description: Software used for generating this annotation + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_software + alias: annotation_software + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + ground_truth_status: + name: ground_truth_status + description: Whether an annotation is considered ground truth, as determined + by the annotator. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_ground_truth_status + alias: ground_truth_status + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + object_count: + name: object_count + description: Number of objects identified + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_object_count + alias: object_count + owner: Annotation + domain_of: + - Annotation + range: integer + inlined: true + inlined_as_list: true + is_curator_recommended: + name: is_curator_recommended + description: This annotation is recommended by the curator to be preferred + for this object type. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + exact_mappings: + - cdp-common:annotation_is_curator_recommended + alias: is_curator_recommended + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + files: + name: files + description: Metadata describing a file containing an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: files + owner: Annotation + domain_of: + - Annotation + range: AnnotationFile + inlined: true + inlined_as_list: true + confidence: + name: confidence + description: Metadata describing the confidence of an annotation. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: confidence + owner: Annotation + domain_of: + - Annotation + range: AnnotationConfidence + inlined: true + inlined_as_list: true + annotation_object: + name: annotation_object + description: Metadata describing the object being annotated. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: annotation_object + owner: Annotation + domain_of: + - Annotation + range: AnnotationObject + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dates + owner: Annotation + domain_of: + - DatestampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Annotator of a scientific data entity. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + multivalued: true + list_elements_ordered: true + alias: authors + owner: Annotation + domain_of: + - AuthoredEntity + - AnnotatoredEntity + range: Annotator + required: true + inlined: true + inlined_as_list: true + CrossReferences: + name: CrossReferences + description: A set of cross-references to other databases and publications. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + attributes: + dataset_publications: + name: dataset_publications + description: Comma-separated list of DOIs for publications associated with + the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dataset_publications + owner: CrossReferences + domain_of: + - CrossReferences + range: string + recommended: true + inlined: true + inlined_as_list: true + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: related_database_entries + owner: CrossReferences + domain_of: + - CrossReferences + range: string + recommended: true + inlined: true + inlined_as_list: true + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: related_database_links + owner: CrossReferences + domain_of: + - CrossReferences + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + alias: dataset_citations + owner: CrossReferences + domain_of: + - CrossReferences + range: string + inlined: true + inlined_as_list: true +source_file: metadata.yaml diff --git a/schema/v1.1.0/metadata_models.py b/schema/v1.1.0/metadata_models.py new file mode 100644 index 000000000..925b9db02 --- /dev/null +++ b/schema/v1.1.0/metadata_models.py @@ -0,0 +1,512 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum + +from decimal import Decimal +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator +import re +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +metamodel_version = "None" +version = "1.1.0" + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment=True, + validate_default=True, + extra = 'forbid', + arbitrary_types_allowed=True, + use_enum_values = True) + + pass + + + +class SampleTypeEnum(str, Enum): + """ + Type of sample imaged in a CryoET study. + """ + # Tomographic data of whole cells or cell sections. + cell = "cell" + # Tomographic data of tissue sections. + tissue = "tissue" + # Tomographic data of sections through multicellular organisms. + organism = "organism" + # Tomographic data of purified organelles. + organelle = "organelle" + # Tomographic data of purified viruses or VLPs. + virus = "virus" + # Tomographic data of in vitro reconstituted systems or mixtures of proteins. + in_vitro = "in_vitro" + # Simulated tomographic data. + in_silico = "in_silico" + # Other type of sample. + other = "other" + + + +class FiducialAlignmentStatusEnum(str, Enum): + """ + Fiducial Alignment method + """ + # Alignment computed based on fiducial markers + FIDUCIAL = "FIDUCIAL" + # Alignment computed without fiducial markers + NON_FIDUCIAL = "NON_FIDUCIAL" + + + +class TomogramTypeEnum(str, Enum): + """ + Tomogram type + """ + # Canonical tomogram (basis geometry for all annotations) + CANONICAL = "CANONICAL" + + + +class AnnotationMethodTypeEnum(str, Enum): + """ + Describes how the annotations were generated. + """ + # Annotations were generated manually. + manual = "manual" + # Annotations were generated semi-automatically. + automated = "automated" + # Annotations were generated automatically. + hybrid = "hybrid" + + + +class AnnotationShapeEnum(str, Enum): + """ + Annotation shape types available on the data portal. + """ + # Annotations were generated manually. + Point = "Point" + # Annotations were generated semi-automatically. + OrientedPoint = "OrientedPoint" + # Annotations were generated automatically. + SegmentationMask = "SegmentationMask" + + + +class PicturePath(ConfiguredBaseModel): + """ + A set of paths to representative images of a piece of data. + """ + snapshot: Optional[str] = Field(None, description="""Path to the dataset preview image relative to the dataset directory root.""") + thumbnail: Optional[str] = Field(None, description="""Path to the thumbnail of preview image relative to the dataset directory root.""") + + + +class Author(ConfiguredBaseModel): + """ + Author of a scientific data entity. + """ + name: Optional[str] = Field(None, description="""The full name of the author.""") + email: Optional[str] = Field(None, description="""The email address of the author.""") + affiliation_name: Optional[str] = Field(None, description="""The name of the author's affiliation.""") + affiliation_address: Optional[str] = Field(None, description="""The address of the author's affiliation.""") + affiliation_identifier: Optional[str] = Field(None, description="""A Research Organization Registry (ROR) identifier.""") + is_corresponding: Optional[bool] = Field(None, description="""Whether the author is a corresponding author.""") + is_primary_author: Optional[bool] = Field(None, description="""Whether the author is a primary author.""") + ORCID: Optional[str] = Field(None, description="""A unique, persistent identifier for researchers, provided by ORCID.""") + + + @field_validator('affiliation_identifier') + def pattern_affiliation_identifier(cls, v): + pattern=re.compile(r"^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$") + if isinstance(v,list): + for element in v: + if not pattern.match(element): + raise ValueError(f"Invalid affiliation_identifier format: {element}") + elif isinstance(v,str): + if not pattern.match(v): + raise ValueError(f"Invalid affiliation_identifier format: {v}") + return v + + @field_validator('ORCID') + def pattern_ORCID(cls, v): + pattern=re.compile(r"[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$") + if isinstance(v,list): + for element in v: + if not pattern.match(element): + raise ValueError(f"Invalid ORCID format: {element}") + elif isinstance(v,str): + if not pattern.match(v): + raise ValueError(f"Invalid ORCID format: {v}") + return v + + +class Annotator(ConfiguredBaseModel): + """ + Annotator of a scientific data entity. + """ + name: Optional[str] = Field(None) + email: Optional[str] = Field(None) + affiliation_name: Optional[str] = Field(None) + affiliation_address: Optional[str] = Field(None) + affiliation_identifier: Optional[str] = Field(None) + is_corresponding: Optional[str] = Field(None) + is_primary_annotator: Optional[bool] = Field(None, description="""Whether the author is a primary author.""") + ORCID: Optional[str] = Field(None) + + + +class Funding(ConfiguredBaseModel): + """ + A funding source for a scientific data entity (base for JSON and DB representation). + """ + funding_agency_name: Optional[str] = Field(None, description="""The name of the funding source.""") + grant_id: Optional[str] = Field(None, description="""Grant identifier provided by the funding agency""") + + + +class DateStamp(ConfiguredBaseModel): + """ + A set of dates at which a data item was deposited, published and last modified. + """ + deposition_date: date = Field(..., description="""The date a data item was received by the cryoET data portal.""") + release_date: date = Field(..., description="""The date a data item was received by the cryoET data portal.""") + last_modified_date: date = Field(..., description="""The date a piece of data was last modified on the cryoET data portal.""") + + + +class DatestampedEntity(ConfiguredBaseModel): + """ + An entity with associated deposition, release and last modified dates. + """ + dates: DateStamp = Field(..., description="""A set of dates at which a data item was deposited, published and last modified.""") + + + +class AuthoredEntity(ConfiguredBaseModel): + """ + An entity with associated authors. + """ + authors: List[Author] = Field(default_factory=list, description="""Author of a scientific data entity.""") + + + +class AnnotatoredEntity(ConfiguredBaseModel): + """ + An entity with associated annotation authors. + """ + authors: List[Annotator] = Field(default_factory=list, description="""Annotator of a scientific data entity.""") + + + +class FundedEntity(ConfiguredBaseModel): + """ + An entity with associated funding sources. + """ + funding: Optional[List[Funding]] = Field(default_factory=list, description="""A funding source for a scientific data entity (base for JSON and DB representation).""") + + + +class CrossReferencedEntity(ConfiguredBaseModel): + """ + An entity with associated cross-references to other databases and publications. + """ + cross_references: Optional[CrossReferences] = Field(None, description="""A set of cross-references to other databases and publications.""") + + + +class PicturedEntity(ConfiguredBaseModel): + """ + An entity with associated preview images. + """ + key_photos: PicturePath = Field(..., description="""A set of paths to representative images of a piece of data.""") + + + +class Organism(ConfiguredBaseModel): + """ + The species from which the sample was derived. + """ + name: Optional[str] = Field(None) + taxonomy_id: Optional[str] = Field(None, description="""NCBI taxonomy identifier for the organism, e.g. 9606""") + + + +class Tissue(ConfiguredBaseModel): + """ + The type of tissue from which the sample was derived. + """ + name: Optional[str] = Field(None) + id: Optional[str] = Field(None, description="""The UBERON identifier for the tissue.""") + + + +class CellType(ConfiguredBaseModel): + """ + The cell type from which the sample was derived. + """ + name: Optional[str] = Field(None) + id: Optional[str] = Field(None) + + + +class CellStrain(ConfiguredBaseModel): + """ + The strain or cell line from which the sample was derived. + """ + name: Optional[str] = Field(None) + id: Optional[str] = Field(None) + + + +class CellComponent(ConfiguredBaseModel): + """ + The cellular component from which the sample was derived. + """ + name: Optional[str] = Field(None) + id: Optional[str] = Field(None) + + + +class ExperimentalMetadata(ConfiguredBaseModel): + """ + Metadata describing sample and sample preparation methods used in a cryoET dataset. + """ + sample_type: Optional[SampleTypeEnum] = Field(None, description="""Type of sample imaged in a CryoET study.""") + sample_preparation: Optional[str] = Field(None, description="""Describes how the sample was prepared.""") + grid_preparation: Optional[str] = Field(None, description="""Describes Cryo-ET grid preparation.""") + other_setup: Optional[str] = Field(None, description="""Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication.""") + organism: Optional[Organism] = Field(None, description="""The species from which the sample was derived.""") + tissue: Optional[Tissue] = Field(None, description="""The type of tissue from which the sample was derived.""") + cell_type: Optional[CellType] = Field(None, description="""The cell type from which the sample was derived.""") + cell_strain: Optional[CellStrain] = Field(None, description="""The strain or cell line from which the sample was derived.""") + cell_component: Optional[CellComponent] = Field(None, description="""The cellular component from which the sample was derived.""") + + + +class Dataset(ExperimentalMetadata, PicturedEntity, CrossReferencedEntity, FundedEntity, AuthoredEntity, DatestampedEntity): + """ + High-level description of a cryoET dataset. + """ + dataset_identifier: Optional[int] = Field(None, description="""An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree.""") + dataset_title: Optional[str] = Field(None, description="""Title of a CryoET dataset.""") + dataset_description: Optional[str] = Field(None, description="""A short description of a CryoET dataset, similar to an abstract for a journal article or dataset.""") + dates: DateStamp = Field(..., description="""A set of dates at which a data item was deposited, published and last modified.""") + authors: List[Author] = Field(default_factory=list, description="""Author of a scientific data entity.""") + funding: Optional[List[Funding]] = Field(default_factory=list, description="""A funding source for a scientific data entity (base for JSON and DB representation).""") + key_photos: PicturePath = Field(..., description="""A set of paths to representative images of a piece of data.""") + cross_references: Optional[CrossReferences] = Field(None, description="""A set of cross-references to other databases and publications.""") + sample_type: Optional[str] = Field(None, description="""Type of sample imaged in a CryoET study.""") + sample_preparation: Optional[str] = Field(None, description="""Describes how the sample was prepared.""") + grid_preparation: Optional[str] = Field(None, description="""Describes Cryo-ET grid preparation.""") + other_setup: Optional[str] = Field(None, description="""Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication.""") + organism: Optional[Organism] = Field(None, description="""The species from which the sample was derived.""") + tissue: Optional[Tissue] = Field(None, description="""The type of tissue from which the sample was derived.""") + cell_type: Optional[CellType] = Field(None, description="""The cell type from which the sample was derived.""") + cell_strain: Optional[CellStrain] = Field(None, description="""The strain or cell line from which the sample was derived.""") + cell_component: Optional[CellComponent] = Field(None, description="""The cellular component from which the sample was derived.""") + + + +class Camera(ConfiguredBaseModel): + """ + The camera used to collect the tilt series. + """ + manufacturer: Optional[str] = Field(None, description="""Name of the camera manufacturer""") + model: Optional[str] = Field(None, description="""Camera model name""") + + + +class Microscope(ConfiguredBaseModel): + """ + The microscope used to collect the tilt series. + """ + manufacturer: Optional[str] = Field(None) + model: Optional[str] = Field(None) + + + +class MicroscopeOpticalSetup(ConfiguredBaseModel): + """ + The optical setup of the microscope used to collect the tilt series. + """ + energy_filter: Optional[str] = Field(None, description="""Energy filter setup used""") + phase_plate: Optional[str] = Field(None, description="""Phase plate configuration""") + image_corrector: Optional[str] = Field(None, description="""Image corrector setup""") + + + +class TiltRange(ConfiguredBaseModel): + """ + The range of tilt angles in the tilt series. + """ + min: Optional[float] = Field(None, description="""Minimal tilt angle in degrees""") + max: Optional[float] = Field(None, description="""Maximal tilt angle in degrees""") + + + +class TiltSeries(ConfiguredBaseModel): + """ + Metadata describing a tilt series. + """ + acceleration_voltage: Optional[int] = Field(None, description="""Electron Microscope Accelerator voltage in volts""") + spherical_aberration_constant: Optional[float] = Field(None, description="""Spherical Aberration Constant of the objective lens in millimeters""") + microscope_additional_info: Optional[str] = Field(None, description="""Other microscope optical setup information, in addition to energy filter, phase plate and image corrector""") + tilt_axis: Optional[float] = Field(None, description="""Rotation angle in degrees""") + tilt_step: Optional[float] = Field(None, description="""Tilt step in degrees""") + tilting_scheme: Optional[str] = Field(None, description="""The order of stage tilting during acquisition of the data""") + total_flux: Optional[float] = Field(None, description="""Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series""") + data_acquisition_software: Optional[str] = Field(None, description="""Software used to collect data""") + binning_from_frames: Optional[float] = Field(None, description="""Describes the binning factor from frames to tilt series file""") + tilt_series_quality: Optional[int] = Field(None, description="""Author assessment of tilt series quality within the dataset (1-5, 5 is best)""") + pixel_spacing: Optional[float] = Field(None, description="""Pixel spacing for the tilt series""") + aligned_tiltseries_binning: Optional[int] = Field(None, description="""Binning factor of the aligned tilt series""") + frames_count: Optional[int] = Field(None, description="""Number of frames associated with this tiltseries""") + camera: Optional[Camera] = Field(None, description="""The camera used to collect the tilt series.""") + microscope: Optional[Microscope] = Field(None, description="""The microscope used to collect the tilt series.""") + microscope_optical_setup: Optional[MicroscopeOpticalSetup] = Field(None, description="""The optical setup of the microscope used to collect the tilt series.""") + tilt_range: Optional[TiltRange] = Field(None, description="""The range of tilt angles in the tilt series.""") + + + +class TomogramSize(ConfiguredBaseModel): + """ + The size of a tomogram in voxels in each dimension. + """ + x: Optional[int] = Field(None, description="""Number of pixels in the 3D data fast axis""") + y: Optional[int] = Field(None, description="""Number of pixels in the 3D data medium axis""") + z: Optional[int] = Field(None, description="""Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt""") + + + +class TomogramOffset(ConfiguredBaseModel): + """ + The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. + """ + x: Optional[str] = Field(None) + y: Optional[str] = Field(None) + z: Optional[str] = Field(None) + + + +class Tomogram(PicturedEntity, AuthoredEntity): + """ + Metadata describing a tomogram. + """ + voxel_spacing: Optional[float] = Field(None, description="""Voxel spacing equal in all three axes in angstroms""") + fiducial_alignment_status: Optional[FiducialAlignmentStatusEnum] = Field(None, description="""Whether the tomographic alignment was computed based on fiducial markers.""") + ctf_corrected: Optional[bool] = Field(None, description="""Whether this tomogram is CTF corrected""") + reconstruction_method: Optional[str] = Field(None, description="""Describe reconstruction method (Weighted back-projection, SART, SIRT)""") + reconstruction_software: Optional[str] = Field(None, description="""Name of software used for reconstruction""") + processing: Optional[str] = Field(None, description="""Describe additional processing used to derive the tomogram""") + processing_software: Optional[str] = Field(None, description="""Processing software used to derive the tomogram""") + tomogram_version: Optional[str] = Field(None, description="""Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version""") + affine_transformation_matrix: Optional[str] = Field(None, description="""The flip or rotation transformation of this author submitted tomogram is indicated here""") + size: Optional[TomogramSize] = Field(None, description="""The size of a tomogram in voxels in each dimension.""") + offset: Optional[TomogramOffset] = Field(None, description="""The offset of a tomogram in voxels in each dimension relative to the canonical tomogram.""") + authors: List[Author] = Field(default_factory=list, description="""Author of a scientific data entity.""") + key_photos: PicturePath = Field(..., description="""A set of paths to representative images of a piece of data.""") + + + +class AnnotationFile(ConfiguredBaseModel): + """ + Metadata describing a file containing an annotation. + """ + format: Optional[str] = Field(None, description="""File format for this file""") + shape: Optional[str] = Field(None, description="""Describe whether this is a Point, OrientedPoint, or SegmentationMask file""") + path: Optional[str] = Field(None, description="""Path to the annotation file relative to the dataset root.""") + is_visualization_default: Optional[bool] = Field(None, description="""This annotation will be rendered in neuroglancer by default.""") + + + +class AnnotationConfidence(ConfiguredBaseModel): + """ + Metadata describing the confidence of an annotation. + """ + precision: Optional[float] = Field(None, description="""Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive""") + recall: Optional[float] = Field(None, description="""Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly""") + ground_truth_used: Optional[str] = Field(None, description="""Annotation filename used as ground truth for precision and recall""") + + + +class AnnotationObject(ConfiguredBaseModel): + """ + Metadata describing the object being annotated. + """ + id: Optional[str] = Field(None) + name: Optional[str] = Field(None) + description: Optional[str] = Field(None, description="""A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.""") + state: Optional[str] = Field(None, description="""Molecule state annotated (e.g. open, closed)""") + + + +class Annotation(AnnotatoredEntity, DatestampedEntity): + """ + Metadata describing an annotation. + """ + annotation_method: Optional[str] = Field(None, description="""Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching)""") + annotation_method_type: Optional[AnnotationMethodTypeEnum] = Field(None, description="""Classification of the annotation method based on supervision.""") + annotation_publications: Optional[str] = Field(None, description="""DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs.""") + annotation_software: Optional[str] = Field(None, description="""Software used for generating this annotation""") + ground_truth_status: Optional[bool] = Field(None, description="""Whether an annotation is considered ground truth, as determined by the annotator.""") + object_count: Optional[int] = Field(None, description="""Number of objects identified""") + is_curator_recommended: Optional[bool] = Field(None, description="""This annotation is recommended by the curator to be preferred for this object type.""") + files: Optional[List[AnnotationFile]] = Field(default_factory=list, description="""Metadata describing a file containing an annotation.""") + confidence: Optional[AnnotationConfidence] = Field(None, description="""Metadata describing the confidence of an annotation.""") + annotation_object: Optional[AnnotationObject] = Field(None, description="""Metadata describing the object being annotated.""") + dates: DateStamp = Field(..., description="""A set of dates at which a data item was deposited, published and last modified.""") + authors: List[Annotator] = Field(default_factory=list, description="""Annotator of a scientific data entity.""") + + + +class CrossReferences(ConfiguredBaseModel): + """ + A set of cross-references to other databases and publications. + """ + dataset_publications: Optional[str] = Field(None, description="""Comma-separated list of DOIs for publications associated with the dataset.""") + related_database_entries: Optional[str] = Field(None, description="""Comma-separated list of related database entries for the dataset.""") + related_database_links: Optional[str] = Field(None, description="""Comma-separated list of related database links for the dataset.""") + dataset_citations: Optional[str] = Field(None, description="""Comma-separated list of DOIs for publications citing the dataset.""") + + + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +PicturePath.model_rebuild() +Author.model_rebuild() +Annotator.model_rebuild() +Funding.model_rebuild() +DateStamp.model_rebuild() +DatestampedEntity.model_rebuild() +AuthoredEntity.model_rebuild() +AnnotatoredEntity.model_rebuild() +FundedEntity.model_rebuild() +CrossReferencedEntity.model_rebuild() +PicturedEntity.model_rebuild() +Organism.model_rebuild() +Tissue.model_rebuild() +CellType.model_rebuild() +CellStrain.model_rebuild() +CellComponent.model_rebuild() +ExperimentalMetadata.model_rebuild() +Dataset.model_rebuild() +Camera.model_rebuild() +Microscope.model_rebuild() +MicroscopeOpticalSetup.model_rebuild() +TiltRange.model_rebuild() +TiltSeries.model_rebuild() +TomogramSize.model_rebuild() +TomogramOffset.model_rebuild() +Tomogram.model_rebuild() +AnnotationFile.model_rebuild() +AnnotationConfidence.model_rebuild() +AnnotationObject.model_rebuild() +Annotation.model_rebuild() +CrossReferences.model_rebuild() + diff --git a/schema/v1.1.0/schema.py b/schema/v1.1.0/schema.py new file mode 100644 index 000000000..5e5176ea8 --- /dev/null +++ b/schema/v1.1.0/schema.py @@ -0,0 +1,103 @@ +from linkml_runtime.utils.schemaview import SchemaView +from linkml_runtime.dumpers import json_dumper, yaml_dumper +from linkml.utils.helpers import write_to_file + +import click + + +def _materialize_classes(schema: SchemaView) -> None: + all_classes = schema.all_classes() + + for c_name, c_def in all_classes.items(): + attrs = schema.class_induced_slots(c_name) + for attr in attrs: + c_def.attributes[attr.name] = attr + + +def _materialize_schema(schema: SchemaView, common_schema: SchemaView) -> SchemaView: + """ + Copy range, descriptions and patterns from exact_mappings to common_schema. + """ + # Make all slots attributes of their classes + _materialize_classes(schema) + + # Copy descriptions and ranges from common_schema + input_slots = schema.all_slots() + common_slots = common_schema.all_slots() + + for s in input_slots: + slot = input_slots.get(s) + mappings = slot["exact_mappings"] + if mappings: + mappings = [ + m.replace("cdp-common:", "") for m in mappings if "cdp-common:" in m + ] + + if len(mappings) > 1: + raise ValueError( + f"Slot {slot['name']} has multiple mappings to common schema" + ) + + common_slot = common_slots.get(mappings[0]) + + if not common_slot: + raise ValueError( + f"Slot {mappings[0]} does not exist in common schema. Check the exact_mappings for {slot['name']}." + ) + + slot["range"] = common_slot["range"] + slot["description"] = common_slot["description"] + slot["pattern"] = common_slot["pattern"] + + # Make sure the descriptions from mixin classes are carried over + for c in schema.all_classes(): + clz = schema.get_class(c) + for m in clz.mixins: + mixin = schema.get_class(m) + for name, attr in mixin.attributes.items(): + clz.attributes[name].description = attr.description + + # Make sure the attributes that have classes as range have their descriptions set + for c in schema.all_classes(): + clz = schema.get_class(c) + for name, attr in clz.attributes.items(): + if attr.range in schema.all_classes(): + attr.description = schema.get_class(attr.range).description + + return schema + + +@click.group() +@click.pass_context +def cli(ctx): + pass + + +@cli.command() +@click.argument("schema_file", required=True, type=str) +@click.argument("common_schema_file", required=True, type=str) +@click.argument("output_path", required=True, type=str) +@click.pass_context +def materialize(ctx, schema_file: str, common_schema_file: str, output_path: str): + # Load + schema = SchemaView(schema_file) + common_schema = SchemaView(common_schema_file) + + # Copy common elements from common definitions to schema + _materialize_classes(common_schema) + for c in common_schema.all_classes(): + schema.add_class(common_schema.get_class(c)) + + for e in common_schema.all_enums(): + schema.add_enum(common_schema.get_enum(e)) + + # Materialize output schema from common schema + schema.materialize_derived_schema() + output_schema = _materialize_schema(schema, common_schema) + + output = yaml_dumper.dumps(output_schema.schema) + write_to_file(output_path, output) + + +if __name__ == "__main__": + cli() diff --git a/test_infra/seed_moto.sh b/test_infra/seed_moto.sh index 8af9da40f..b6dfda83c 100755 --- a/test_infra/seed_moto.sh +++ b/test_infra/seed_moto.sh @@ -2,7 +2,7 @@ # Script to seed moto server; runs outside the motoserver container for development -aws="aws --endpoint-url=http://localhost:4000" +aws="aws --endpoint-url=http://localhost:4001" export AWS_ACCESS_KEY_ID=test export AWS_SECRET_ACCESS_KEY=test export AWS_REGION=us-west-2 From 5fc2111f9144736a062a4cf8919a6856a4898306 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 5 Mar 2024 17:45:35 -0800 Subject: [PATCH 4/7] LinkML schema, documentation and codegen. revert local change --- test_infra/seed_moto.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test_infra/seed_moto.sh b/test_infra/seed_moto.sh index b6dfda83c..8af9da40f 100755 --- a/test_infra/seed_moto.sh +++ b/test_infra/seed_moto.sh @@ -2,7 +2,7 @@ # Script to seed moto server; runs outside the motoserver container for development -aws="aws --endpoint-url=http://localhost:4001" +aws="aws --endpoint-url=http://localhost:4000" export AWS_ACCESS_KEY_ID=test export AWS_SECRET_ACCESS_KEY=test export AWS_REGION=us-west-2 From e89032d677d9ee39d5251f3f64e346ef71a57c28 Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 5 Mar 2024 17:49:56 -0800 Subject: [PATCH 5/7] remove phony links --- schema/v1.1.0/common.yaml | 4 +- schema/v1.1.0/metadata-docs/Annotation.md | 56 +-- .../metadata-docs/AnnotationConfidence.md | 20 +- schema/v1.1.0/metadata-docs/AnnotationFile.md | 24 +- .../metadata-docs/AnnotationMethodTypeEnum.md | 4 +- .../v1.1.0/metadata-docs/AnnotationObject.md | 24 +- .../metadata-docs/AnnotationShapeEnum.md | 4 +- schema/v1.1.0/metadata-docs/Annotator.md | 40 +- .../v1.1.0/metadata-docs/AnnotatoredEntity.md | 12 +- schema/v1.1.0/metadata-docs/Author.md | 40 +- schema/v1.1.0/metadata-docs/AuthoredEntity.md | 12 +- schema/v1.1.0/metadata-docs/Camera.md | 6 +- schema/v1.1.0/metadata-docs/CellComponent.md | 16 +- schema/v1.1.0/metadata-docs/CellStrain.md | 16 +- schema/v1.1.0/metadata-docs/CellType.md | 16 +- .../metadata-docs/CrossReferencedEntity.md | 12 +- .../v1.1.0/metadata-docs/CrossReferences.md | 24 +- schema/v1.1.0/metadata-docs/Dataset.md | 76 ++-- schema/v1.1.0/metadata-docs/DateStamp.md | 20 +- .../v1.1.0/metadata-docs/DatestampedEntity.md | 12 +- .../metadata-docs/ExperimentalMetadata.md | 44 +-- .../FiducialAlignmentStatusEnum.md | 4 +- schema/v1.1.0/metadata-docs/FundedEntity.md | 12 +- schema/v1.1.0/metadata-docs/Funding.md | 2 +- schema/v1.1.0/metadata-docs/Microscope.md | 6 +- .../metadata-docs/MicroscopeOpticalSetup.md | 20 +- schema/v1.1.0/metadata-docs/ORCID.md | 2 +- schema/v1.1.0/metadata-docs/Organism.md | 2 +- schema/v1.1.0/metadata-docs/PicturePath.md | 16 +- schema/v1.1.0/metadata-docs/PicturedEntity.md | 12 +- schema/v1.1.0/metadata-docs/SampleTypeEnum.md | 4 +- schema/v1.1.0/metadata-docs/TiltRange.md | 16 +- schema/v1.1.0/metadata-docs/TiltSeries.md | 76 ++-- schema/v1.1.0/metadata-docs/Tissue.md | 2 +- schema/v1.1.0/metadata-docs/Tomogram.md | 60 +-- schema/v1.1.0/metadata-docs/TomogramOffset.md | 20 +- schema/v1.1.0/metadata-docs/TomogramSize.md | 20 +- .../v1.1.0/metadata-docs/TomogramTypeEnum.md | 4 +- .../metadata-docs/acceleration_voltage.md | 6 +- .../metadata-docs/affiliation_address.md | 2 +- .../metadata-docs/affiliation_identifier.md | 2 +- .../v1.1.0/metadata-docs/affiliation_name.md | 2 +- .../affine_transformation_matrix.md | 6 +- .../aligned_tiltseries_binning.md | 6 +- .../v1.1.0/metadata-docs/annotation_method.md | 6 +- .../metadata-docs/annotation_method_type.md | 6 +- .../v1.1.0/metadata-docs/annotation_object.md | 6 +- .../metadata-docs/annotation_publications.md | 6 +- .../metadata-docs/annotation_software.md | 6 +- schema/v1.1.0/metadata-docs/authors.md | 2 +- .../metadata-docs/binning_from_frames.md | 6 +- schema/v1.1.0/metadata-docs/cdp-meta.md | 2 +- schema/v1.1.0/metadata-docs/cell_component.md | 2 +- schema/v1.1.0/metadata-docs/cell_strain.md | 2 +- schema/v1.1.0/metadata-docs/cell_type.md | 2 +- schema/v1.1.0/metadata-docs/confidence.md | 6 +- .../v1.1.0/metadata-docs/cross_references.md | 2 +- schema/v1.1.0/metadata-docs/ctf_corrected.md | 6 +- .../data_acquisition_software.md | 6 +- .../v1.1.0/metadata-docs/dataset_citations.md | 6 +- .../metadata-docs/dataset_description.md | 6 +- .../metadata-docs/dataset_identifier.md | 6 +- .../metadata-docs/dataset_publications.md | 6 +- schema/v1.1.0/metadata-docs/dataset_title.md | 6 +- schema/v1.1.0/metadata-docs/dates.md | 2 +- .../v1.1.0/metadata-docs/deposition_date.md | 6 +- schema/v1.1.0/metadata-docs/description.md | 6 +- schema/v1.1.0/metadata-docs/email.md | 2 +- schema/v1.1.0/metadata-docs/energy_filter.md | 6 +- .../fiducial_alignment_status.md | 6 +- schema/v1.1.0/metadata-docs/files.md | 6 +- schema/v1.1.0/metadata-docs/format.md | 6 +- schema/v1.1.0/metadata-docs/frames_count.md | 6 +- .../metadata-docs/funding_agency_name.md | 6 +- schema/v1.1.0/metadata-docs/grant_id.md | 6 +- .../v1.1.0/metadata-docs/grid_preparation.md | 2 +- .../metadata-docs/ground_truth_status.md | 6 +- .../v1.1.0/metadata-docs/ground_truth_used.md | 6 +- schema/v1.1.0/metadata-docs/id.md | 2 +- .../v1.1.0/metadata-docs/image_corrector.md | 6 +- schema/v1.1.0/metadata-docs/index.md | 2 +- .../v1.1.0/metadata-docs/is_corresponding.md | 2 +- .../metadata-docs/is_curator_recommended.md | 6 +- .../metadata-docs/is_primary_annotator.md | 6 +- .../v1.1.0/metadata-docs/is_primary_author.md | 6 +- .../metadata-docs/is_visualization_default.md | 6 +- schema/v1.1.0/metadata-docs/key_photos.md | 2 +- .../metadata-docs/last_modified_date.md | 6 +- schema/v1.1.0/metadata-docs/manufacturer.md | 2 +- schema/v1.1.0/metadata-docs/max.md | 6 +- .../microscope_additional_info.md | 6 +- .../metadata-docs/microscope_optical_setup.md | 6 +- schema/v1.1.0/metadata-docs/min.md | 6 +- schema/v1.1.0/metadata-docs/model.md | 2 +- schema/v1.1.0/metadata-docs/name.md | 2 +- schema/v1.1.0/metadata-docs/object_count.md | 6 +- schema/v1.1.0/metadata-docs/offset.md | 6 +- schema/v1.1.0/metadata-docs/other_setup.md | 2 +- schema/v1.1.0/metadata-docs/path.md | 6 +- schema/v1.1.0/metadata-docs/phase_plate.md | 6 +- schema/v1.1.0/metadata-docs/pixel_spacing.md | 6 +- schema/v1.1.0/metadata-docs/precision.md | 6 +- schema/v1.1.0/metadata-docs/processing.md | 6 +- .../metadata-docs/processing_software.md | 6 +- schema/v1.1.0/metadata-docs/recall.md | 6 +- .../metadata-docs/reconstruction_method.md | 6 +- .../metadata-docs/reconstruction_software.md | 6 +- .../metadata-docs/related_database_entries.md | 6 +- .../metadata-docs/related_database_links.md | 6 +- schema/v1.1.0/metadata-docs/release_date.md | 6 +- .../metadata-docs/sample_preparation.md | 2 +- schema/v1.1.0/metadata-docs/sample_type.md | 2 +- schema/v1.1.0/metadata-docs/shape.md | 6 +- schema/v1.1.0/metadata-docs/size.md | 6 +- schema/v1.1.0/metadata-docs/snapshot.md | 6 +- .../spherical_aberration_constant.md | 6 +- schema/v1.1.0/metadata-docs/state.md | 6 +- schema/v1.1.0/metadata-docs/taxonomy_id.md | 6 +- schema/v1.1.0/metadata-docs/thumbnail.md | 6 +- schema/v1.1.0/metadata-docs/tilt_axis.md | 6 +- schema/v1.1.0/metadata-docs/tilt_range.md | 6 +- .../metadata-docs/tilt_series_quality.md | 6 +- schema/v1.1.0/metadata-docs/tilt_step.md | 6 +- schema/v1.1.0/metadata-docs/tilting_scheme.md | 6 +- .../v1.1.0/metadata-docs/tomogram_version.md | 6 +- schema/v1.1.0/metadata-docs/total_flux.md | 6 +- schema/v1.1.0/metadata-docs/voxel_spacing.md | 6 +- schema/v1.1.0/metadata-docs/x.md | 2 +- schema/v1.1.0/metadata-docs/y.md | 2 +- schema/v1.1.0/metadata-docs/z.md | 2 +- schema/v1.1.0/metadata.yaml | 4 +- schema/v1.1.0/metadata_materialized.yaml | 350 +++++++++--------- 132 files changed, 783 insertions(+), 783 deletions(-) diff --git a/schema/v1.1.0/common.yaml b/schema/v1.1.0/common.yaml index c99bb37fe..1b0c59179 100644 --- a/schema/v1.1.0/common.yaml +++ b/schema/v1.1.0/common.yaml @@ -1,9 +1,9 @@ -id: https://cryoetdataportal.czscience.com/schema-docs/common +id: common name: cdp-common version: 1.1.0 prefixes: linkml: https://w3id.org/linkml/ - cdp-common: https://cryoetdataportal.czscience.com/schema/common/ + cdp-common: common ROR: https://ror.org/ UBERON: http://purl.obolibrary.org/obo/UBERON_ CL: http://purl.obolibrary.org/obo/CL_ diff --git a/schema/v1.1.0/metadata-docs/Annotation.md b/schema/v1.1.0/metadata-docs/Annotation.md index 28d3fe09a..971a3f580 100644 --- a/schema/v1.1.0/metadata-docs/Annotation.md +++ b/schema/v1.1.0/metadata-docs/Annotation.md @@ -7,7 +7,7 @@ _Metadata describing an annotation._ -URI: [cdp-meta:Annotation](https://cryoetdataportal.czscience.com/schema/metadata/Annotation) +URI: [cdp-meta:Annotation](metadataAnnotation) @@ -114,7 +114,7 @@ URI: [cdp-meta:Annotation](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -141,7 +141,7 @@ URI: [cdp-meta:Annotation](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: Annotation description: Metadata describing an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata mixins: - DatestampedEntity - AnnotatoredEntity @@ -150,7 +150,7 @@ attributes: name: annotation_method description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_method rank: 1000 @@ -164,7 +164,7 @@ attributes: annotation_method_type: name: annotation_method_type description: Classification of the annotation method based on supervision. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_method_type rank: 1000 @@ -179,7 +179,7 @@ attributes: name: annotation_publications description: DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_publication rank: 1000 @@ -193,7 +193,7 @@ attributes: annotation_software: name: annotation_software description: Software used for generating this annotation - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_software rank: 1000 @@ -208,7 +208,7 @@ attributes: name: ground_truth_status description: Whether an annotation is considered ground truth, as determined by the annotator. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_status rank: 1000 @@ -222,7 +222,7 @@ attributes: object_count: name: object_count description: Number of objects identified - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_count rank: 1000 @@ -237,7 +237,7 @@ attributes: name: is_curator_recommended description: This annotation is recommended by the curator to be preferred for this object type. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_is_curator_recommended rank: 1000 @@ -251,7 +251,7 @@ attributes: files: name: files description: Metadata describing a file containing an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true @@ -265,7 +265,7 @@ attributes: confidence: name: confidence description: Metadata describing the confidence of an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: confidence owner: Annotation @@ -277,7 +277,7 @@ attributes: annotation_object: name: annotation_object description: Metadata describing the object being annotated. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: annotation_object owner: Annotation @@ -290,7 +290,7 @@ attributes: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: Annotation domain_of: @@ -304,7 +304,7 @@ attributes: authors: name: authors description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -329,7 +329,7 @@ attributes: ```yaml name: Annotation description: Metadata describing an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata mixins: - DatestampedEntity - AnnotatoredEntity @@ -338,7 +338,7 @@ attributes: name: annotation_method description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_method rank: 1000 @@ -352,7 +352,7 @@ attributes: annotation_method_type: name: annotation_method_type description: Classification of the annotation method based on supervision. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_method_type rank: 1000 @@ -367,7 +367,7 @@ attributes: name: annotation_publications description: DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_publication rank: 1000 @@ -381,7 +381,7 @@ attributes: annotation_software: name: annotation_software description: Software used for generating this annotation - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_software rank: 1000 @@ -396,7 +396,7 @@ attributes: name: ground_truth_status description: Whether an annotation is considered ground truth, as determined by the annotator. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_status rank: 1000 @@ -410,7 +410,7 @@ attributes: object_count: name: object_count description: Number of objects identified - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_count rank: 1000 @@ -425,7 +425,7 @@ attributes: name: is_curator_recommended description: This annotation is recommended by the curator to be preferred for this object type. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_is_curator_recommended rank: 1000 @@ -439,7 +439,7 @@ attributes: files: name: files description: Metadata describing a file containing an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true @@ -453,7 +453,7 @@ attributes: confidence: name: confidence description: Metadata describing the confidence of an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: confidence owner: Annotation @@ -465,7 +465,7 @@ attributes: annotation_object: name: annotation_object description: Metadata describing the object being annotated. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: annotation_object owner: Annotation @@ -478,7 +478,7 @@ attributes: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: Annotation domain_of: @@ -492,7 +492,7 @@ attributes: authors: name: authors description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors diff --git a/schema/v1.1.0/metadata-docs/AnnotationConfidence.md b/schema/v1.1.0/metadata-docs/AnnotationConfidence.md index a06ff2574..b46414d29 100644 --- a/schema/v1.1.0/metadata-docs/AnnotationConfidence.md +++ b/schema/v1.1.0/metadata-docs/AnnotationConfidence.md @@ -7,7 +7,7 @@ _Metadata describing the confidence of an annotation._ -URI: [cdp-meta:AnnotationConfidence](https://cryoetdataportal.czscience.com/schema/metadata/AnnotationConfidence) +URI: [cdp-meta:AnnotationConfidence](metadataAnnotationConfidence) @@ -70,7 +70,7 @@ URI: [cdp-meta:AnnotationConfidence](https://cryoetdataportal.czscience.com/sche ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -97,13 +97,13 @@ URI: [cdp-meta:AnnotationConfidence](https://cryoetdataportal.czscience.com/sche ```yaml name: AnnotationConfidence description: Metadata describing the confidence of an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: precision: name: precision description: Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_precision rank: 1000 @@ -118,7 +118,7 @@ attributes: name: recall description: Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_recall rank: 1000 @@ -132,7 +132,7 @@ attributes: ground_truth_used: name: ground_truth_used description: Annotation filename used as ground truth for precision and recall - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_used rank: 1000 @@ -153,13 +153,13 @@ attributes: ```yaml name: AnnotationConfidence description: Metadata describing the confidence of an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: precision: name: precision description: Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_precision rank: 1000 @@ -174,7 +174,7 @@ attributes: name: recall description: Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_recall rank: 1000 @@ -188,7 +188,7 @@ attributes: ground_truth_used: name: ground_truth_used description: Annotation filename used as ground truth for precision and recall - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_used rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/AnnotationFile.md b/schema/v1.1.0/metadata-docs/AnnotationFile.md index 2007ccde5..138d236a4 100644 --- a/schema/v1.1.0/metadata-docs/AnnotationFile.md +++ b/schema/v1.1.0/metadata-docs/AnnotationFile.md @@ -7,7 +7,7 @@ _Metadata describing a file containing an annotation._ -URI: [cdp-meta:AnnotationFile](https://cryoetdataportal.czscience.com/schema/metadata/AnnotationFile) +URI: [cdp-meta:AnnotationFile](metadataAnnotationFile) @@ -75,7 +75,7 @@ URI: [cdp-meta:AnnotationFile](https://cryoetdataportal.czscience.com/schema/met ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -102,12 +102,12 @@ URI: [cdp-meta:AnnotationFile](https://cryoetdataportal.czscience.com/schema/met ```yaml name: AnnotationFile description: Metadata describing a file containing an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: format: name: format description: File format for this file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_format rank: 1000 @@ -122,7 +122,7 @@ attributes: name: shape description: Describe whether this is a Point, OrientedPoint, or SegmentationMask file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_shape_type rank: 1000 @@ -136,7 +136,7 @@ attributes: path: name: path description: Path to the annotation file relative to the dataset root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_path rank: 1000 @@ -150,7 +150,7 @@ attributes: is_visualization_default: name: is_visualization_default description: This annotation will be rendered in neuroglancer by default. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_is_visualization_default rank: 1000 @@ -171,12 +171,12 @@ attributes: ```yaml name: AnnotationFile description: Metadata describing a file containing an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: format: name: format description: File format for this file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_format rank: 1000 @@ -191,7 +191,7 @@ attributes: name: shape description: Describe whether this is a Point, OrientedPoint, or SegmentationMask file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_shape_type rank: 1000 @@ -205,7 +205,7 @@ attributes: path: name: path description: Path to the annotation file relative to the dataset root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_path rank: 1000 @@ -219,7 +219,7 @@ attributes: is_visualization_default: name: is_visualization_default description: This annotation will be rendered in neuroglancer by default. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_is_visualization_default rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md b/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md index 6a669921e..7482f15fc 100644 --- a/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md +++ b/schema/v1.1.0/metadata-docs/AnnotationMethodTypeEnum.md @@ -42,7 +42,7 @@ URI: [AnnotationMethodTypeEnum](AnnotationMethodTypeEnum.md) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -53,7 +53,7 @@ URI: [AnnotationMethodTypeEnum](AnnotationMethodTypeEnum.md) ```yaml name: annotation_method_type_enum description: Describes how the annotations were generated. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 permissible_values: manual: diff --git a/schema/v1.1.0/metadata-docs/AnnotationObject.md b/schema/v1.1.0/metadata-docs/AnnotationObject.md index 65fa57d2e..bcbfb175f 100644 --- a/schema/v1.1.0/metadata-docs/AnnotationObject.md +++ b/schema/v1.1.0/metadata-docs/AnnotationObject.md @@ -7,7 +7,7 @@ _Metadata describing the object being annotated._ -URI: [cdp-meta:AnnotationObject](https://cryoetdataportal.czscience.com/schema/metadata/AnnotationObject) +URI: [cdp-meta:AnnotationObject](metadataAnnotationObject) @@ -75,7 +75,7 @@ URI: [cdp-meta:AnnotationObject](https://cryoetdataportal.czscience.com/schema/m ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -102,11 +102,11 @@ URI: [cdp-meta:AnnotationObject](https://cryoetdataportal.czscience.com/schema/m ```yaml name: AnnotationObject description: Metadata describing the object being annotated. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_id alias: id @@ -122,7 +122,7 @@ attributes: inlined_as_list: true name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_name alias: name @@ -144,7 +144,7 @@ attributes: description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_description rank: 1000 @@ -158,7 +158,7 @@ attributes: state: name: state description: Molecule state annotated (e.g. open, closed) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_state rank: 1000 @@ -179,11 +179,11 @@ attributes: ```yaml name: AnnotationObject description: Metadata describing the object being annotated. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_id alias: id @@ -199,7 +199,7 @@ attributes: inlined_as_list: true name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_name alias: name @@ -221,7 +221,7 @@ attributes: description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_description rank: 1000 @@ -235,7 +235,7 @@ attributes: state: name: state description: Molecule state annotated (e.g. open, closed) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_state rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md b/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md index 40882de1d..1dbf852b4 100644 --- a/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md +++ b/schema/v1.1.0/metadata-docs/AnnotationShapeEnum.md @@ -36,7 +36,7 @@ URI: [AnnotationShapeEnum](AnnotationShapeEnum.md) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -47,7 +47,7 @@ URI: [AnnotationShapeEnum](AnnotationShapeEnum.md) ```yaml name: annotation_shape_enum description: Annotation shape types available on the data portal. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 permissible_values: Point: diff --git a/schema/v1.1.0/metadata-docs/Annotator.md b/schema/v1.1.0/metadata-docs/Annotator.md index c832469f5..728ba44d7 100644 --- a/schema/v1.1.0/metadata-docs/Annotator.md +++ b/schema/v1.1.0/metadata-docs/Annotator.md @@ -7,7 +7,7 @@ _Annotator of a scientific data entity._ -URI: [cdp-meta:Annotator](https://cryoetdataportal.czscience.com/schema/metadata/Annotator) +URI: [cdp-meta:Annotator](metadataAnnotator) @@ -96,7 +96,7 @@ URI: [cdp-meta:Annotator](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -123,11 +123,11 @@ URI: [cdp-meta:Annotator](https://cryoetdataportal.czscience.com/schema/metadata ```yaml name: Annotator description: Annotator of a scientific data entity. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_name alias: name @@ -146,7 +146,7 @@ attributes: inlined_as_list: true email: name: email - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_email alias: email @@ -159,7 +159,7 @@ attributes: inlined_as_list: true affiliation_name: name: affiliation_name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_name alias: affiliation_name @@ -172,7 +172,7 @@ attributes: inlined_as_list: true affiliation_address: name: affiliation_address - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_address alias: affiliation_address @@ -185,7 +185,7 @@ attributes: inlined_as_list: true affiliation_identifier: name: affiliation_identifier - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:affiliation_identifier alias: affiliation_identifier @@ -199,7 +199,7 @@ attributes: inlined_as_list: true is_corresponding: name: is_corresponding - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_corresponding_author_status alias: is_corresponding @@ -213,7 +213,7 @@ attributes: is_primary_annotator: name: is_primary_annotator description: Whether the author is a primary author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status rank: 1000 @@ -226,7 +226,7 @@ attributes: inlined_as_list: true ORCID: name: ORCID - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:orcid alias: ORCID @@ -248,11 +248,11 @@ attributes: ```yaml name: Annotator description: Annotator of a scientific data entity. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_name alias: name @@ -271,7 +271,7 @@ attributes: inlined_as_list: true email: name: email - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_email alias: email @@ -284,7 +284,7 @@ attributes: inlined_as_list: true affiliation_name: name: affiliation_name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_name alias: affiliation_name @@ -297,7 +297,7 @@ attributes: inlined_as_list: true affiliation_address: name: affiliation_address - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_address alias: affiliation_address @@ -310,7 +310,7 @@ attributes: inlined_as_list: true affiliation_identifier: name: affiliation_identifier - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:affiliation_identifier alias: affiliation_identifier @@ -324,7 +324,7 @@ attributes: inlined_as_list: true is_corresponding: name: is_corresponding - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_corresponding_author_status alias: is_corresponding @@ -338,7 +338,7 @@ attributes: is_primary_annotator: name: is_primary_annotator description: Whether the author is a primary author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status rank: 1000 @@ -351,7 +351,7 @@ attributes: inlined_as_list: true ORCID: name: ORCID - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:orcid alias: ORCID diff --git a/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md b/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md index a09931ec9..43590ae95 100644 --- a/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md +++ b/schema/v1.1.0/metadata-docs/AnnotatoredEntity.md @@ -9,7 +9,7 @@ _An entity with associated annotation authors._ * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:AnnotatoredEntity](https://cryoetdataportal.czscience.com/schema/metadata/AnnotatoredEntity) +URI: [cdp-meta:AnnotatoredEntity](metadataAnnotatoredEntity) @@ -57,7 +57,7 @@ URI: [cdp-meta:AnnotatoredEntity](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -84,13 +84,13 @@ URI: [cdp-meta:AnnotatoredEntity](https://cryoetdataportal.czscience.com/schema/ ```yaml name: AnnotatoredEntity description: An entity with associated annotation authors. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: authors: name: authors description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -115,13 +115,13 @@ attributes: ```yaml name: AnnotatoredEntity description: An entity with associated annotation authors. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: authors: name: authors description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors diff --git a/schema/v1.1.0/metadata-docs/Author.md b/schema/v1.1.0/metadata-docs/Author.md index 52d7a85e3..865e881d2 100644 --- a/schema/v1.1.0/metadata-docs/Author.md +++ b/schema/v1.1.0/metadata-docs/Author.md @@ -7,7 +7,7 @@ _Author of a scientific data entity._ -URI: [cdp-meta:Author](https://cryoetdataportal.czscience.com/schema/metadata/Author) +URI: [cdp-meta:Author](metadataAuthor) @@ -97,7 +97,7 @@ URI: [cdp-meta:Author](https://cryoetdataportal.czscience.com/schema/metadata/Au ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -124,12 +124,12 @@ URI: [cdp-meta:Author](https://cryoetdataportal.czscience.com/schema/metadata/Au ```yaml name: Author description: Author of a scientific data entity. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name description: The full name of the author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_name rank: 1000 @@ -150,7 +150,7 @@ attributes: email: name: email description: The email address of the author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_email rank: 1000 @@ -165,7 +165,7 @@ attributes: affiliation_name: name: affiliation_name description: The name of the author's affiliation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_name rank: 1000 @@ -180,7 +180,7 @@ attributes: affiliation_address: name: affiliation_address description: The address of the author's affiliation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_address rank: 1000 @@ -195,7 +195,7 @@ attributes: affiliation_identifier: name: affiliation_identifier description: A Research Organization Registry (ROR) identifier. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:affiliation_identifier rank: 1000 @@ -212,7 +212,7 @@ attributes: is_corresponding: name: is_corresponding description: Whether the author is a corresponding author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_corresponding_author_status rank: 1000 @@ -227,7 +227,7 @@ attributes: is_primary_author: name: is_primary_author description: Whether the author is a primary author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status rank: 1000 @@ -241,7 +241,7 @@ attributes: ORCID: name: ORCID description: A unique, persistent identifier for researchers, provided by ORCID. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:orcid rank: 1000 @@ -265,12 +265,12 @@ attributes: ```yaml name: Author description: Author of a scientific data entity. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name description: The full name of the author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_name rank: 1000 @@ -291,7 +291,7 @@ attributes: email: name: email description: The email address of the author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_email rank: 1000 @@ -306,7 +306,7 @@ attributes: affiliation_name: name: affiliation_name description: The name of the author's affiliation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_name rank: 1000 @@ -321,7 +321,7 @@ attributes: affiliation_address: name: affiliation_address description: The address of the author's affiliation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_address rank: 1000 @@ -336,7 +336,7 @@ attributes: affiliation_identifier: name: affiliation_identifier description: A Research Organization Registry (ROR) identifier. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:affiliation_identifier rank: 1000 @@ -353,7 +353,7 @@ attributes: is_corresponding: name: is_corresponding description: Whether the author is a corresponding author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_corresponding_author_status rank: 1000 @@ -368,7 +368,7 @@ attributes: is_primary_author: name: is_primary_author description: Whether the author is a primary author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status rank: 1000 @@ -382,7 +382,7 @@ attributes: ORCID: name: ORCID description: A unique, persistent identifier for researchers, provided by ORCID. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:orcid rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/AuthoredEntity.md b/schema/v1.1.0/metadata-docs/AuthoredEntity.md index ed2db70d6..d195d76bb 100644 --- a/schema/v1.1.0/metadata-docs/AuthoredEntity.md +++ b/schema/v1.1.0/metadata-docs/AuthoredEntity.md @@ -9,7 +9,7 @@ _An entity with associated authors._ * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:AuthoredEntity](https://cryoetdataportal.czscience.com/schema/metadata/AuthoredEntity) +URI: [cdp-meta:AuthoredEntity](metadataAuthoredEntity) @@ -58,7 +58,7 @@ URI: [cdp-meta:AuthoredEntity](https://cryoetdataportal.czscience.com/schema/met ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -85,13 +85,13 @@ URI: [cdp-meta:AuthoredEntity](https://cryoetdataportal.czscience.com/schema/met ```yaml name: AuthoredEntity description: An entity with associated authors. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true @@ -117,13 +117,13 @@ attributes: ```yaml name: AuthoredEntity description: An entity with associated authors. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true diff --git a/schema/v1.1.0/metadata-docs/Camera.md b/schema/v1.1.0/metadata-docs/Camera.md index 1977fdff5..3ed425315 100644 --- a/schema/v1.1.0/metadata-docs/Camera.md +++ b/schema/v1.1.0/metadata-docs/Camera.md @@ -5,7 +5,7 @@ _The camera used to collect the tilt series._ -URI: [cdp-meta:camera](https://cryoetdataportal.czscience.com/schema/metadata/camera) +URI: [cdp-meta:camera](metadatacamera) @@ -45,7 +45,7 @@ URI: [cdp-meta:camera](https://cryoetdataportal.czscience.com/schema/metadata/ca ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:camera](https://cryoetdataportal.czscience.com/schema/metadata/ca ```yaml name: camera description: The camera used to collect the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: camera owner: TiltSeries diff --git a/schema/v1.1.0/metadata-docs/CellComponent.md b/schema/v1.1.0/metadata-docs/CellComponent.md index f1a057b81..7e75b02f1 100644 --- a/schema/v1.1.0/metadata-docs/CellComponent.md +++ b/schema/v1.1.0/metadata-docs/CellComponent.md @@ -7,7 +7,7 @@ _The cellular component from which the sample was derived._ -URI: [cdp-meta:CellComponent](https://cryoetdataportal.czscience.com/schema/metadata/CellComponent) +URI: [cdp-meta:CellComponent](metadataCellComponent) @@ -66,7 +66,7 @@ URI: [cdp-meta:CellComponent](https://cryoetdataportal.czscience.com/schema/meta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -93,11 +93,11 @@ URI: [cdp-meta:CellComponent](https://cryoetdataportal.czscience.com/schema/meta ```yaml name: CellComponent description: The cellular component from which the sample was derived. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_component_name alias: name @@ -116,7 +116,7 @@ attributes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_component_id alias: id @@ -140,11 +140,11 @@ attributes: ```yaml name: CellComponent description: The cellular component from which the sample was derived. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_component_name alias: name @@ -163,7 +163,7 @@ attributes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_component_id alias: id diff --git a/schema/v1.1.0/metadata-docs/CellStrain.md b/schema/v1.1.0/metadata-docs/CellStrain.md index 273177312..a8ea47c75 100644 --- a/schema/v1.1.0/metadata-docs/CellStrain.md +++ b/schema/v1.1.0/metadata-docs/CellStrain.md @@ -7,7 +7,7 @@ _The strain or cell line from which the sample was derived._ -URI: [cdp-meta:CellStrain](https://cryoetdataportal.czscience.com/schema/metadata/CellStrain) +URI: [cdp-meta:CellStrain](metadataCellStrain) @@ -66,7 +66,7 @@ URI: [cdp-meta:CellStrain](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -93,11 +93,11 @@ URI: [cdp-meta:CellStrain](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: CellStrain description: The strain or cell line from which the sample was derived. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_strain_name alias: name @@ -116,7 +116,7 @@ attributes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_strain_id alias: id @@ -140,11 +140,11 @@ attributes: ```yaml name: CellStrain description: The strain or cell line from which the sample was derived. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_strain_name alias: name @@ -163,7 +163,7 @@ attributes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_strain_id alias: id diff --git a/schema/v1.1.0/metadata-docs/CellType.md b/schema/v1.1.0/metadata-docs/CellType.md index 00f5caef8..a53bc5e83 100644 --- a/schema/v1.1.0/metadata-docs/CellType.md +++ b/schema/v1.1.0/metadata-docs/CellType.md @@ -7,7 +7,7 @@ _The cell type from which the sample was derived._ -URI: [cdp-meta:CellType](https://cryoetdataportal.czscience.com/schema/metadata/CellType) +URI: [cdp-meta:CellType](metadataCellType) @@ -66,7 +66,7 @@ URI: [cdp-meta:CellType](https://cryoetdataportal.czscience.com/schema/metadata/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -93,11 +93,11 @@ URI: [cdp-meta:CellType](https://cryoetdataportal.czscience.com/schema/metadata/ ```yaml name: CellType description: The cell type from which the sample was derived. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_name alias: name @@ -116,7 +116,7 @@ attributes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_type_id alias: id @@ -140,11 +140,11 @@ attributes: ```yaml name: CellType description: The cell type from which the sample was derived. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_name alias: name @@ -163,7 +163,7 @@ attributes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_type_id alias: id diff --git a/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md b/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md index bf84aeb08..f6087c443 100644 --- a/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md +++ b/schema/v1.1.0/metadata-docs/CrossReferencedEntity.md @@ -9,7 +9,7 @@ _An entity with associated cross-references to other databases and publications. * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:CrossReferencedEntity](https://cryoetdataportal.czscience.com/schema/metadata/CrossReferencedEntity) +URI: [cdp-meta:CrossReferencedEntity](metadataCrossReferencedEntity) @@ -57,7 +57,7 @@ URI: [cdp-meta:CrossReferencedEntity](https://cryoetdataportal.czscience.com/sch ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -84,13 +84,13 @@ URI: [cdp-meta:CrossReferencedEntity](https://cryoetdataportal.czscience.com/sch ```yaml name: CrossReferencedEntity description: An entity with associated cross-references to other databases and publications. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: cross_references: name: cross_references description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cross_references owner: CrossReferencedEntity @@ -110,13 +110,13 @@ attributes: ```yaml name: CrossReferencedEntity description: An entity with associated cross-references to other databases and publications. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: cross_references: name: cross_references description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cross_references owner: CrossReferencedEntity diff --git a/schema/v1.1.0/metadata-docs/CrossReferences.md b/schema/v1.1.0/metadata-docs/CrossReferences.md index e326d3c69..f46ce8a51 100644 --- a/schema/v1.1.0/metadata-docs/CrossReferences.md +++ b/schema/v1.1.0/metadata-docs/CrossReferences.md @@ -7,7 +7,7 @@ _A set of cross-references to other databases and publications._ -URI: [cdp-meta:CrossReferences](https://cryoetdataportal.czscience.com/schema/metadata/CrossReferences) +URI: [cdp-meta:CrossReferences](metadataCrossReferences) @@ -76,7 +76,7 @@ URI: [cdp-meta:CrossReferences](https://cryoetdataportal.czscience.com/schema/me ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -103,13 +103,13 @@ URI: [cdp-meta:CrossReferences](https://cryoetdataportal.czscience.com/schema/me ```yaml name: CrossReferences description: A set of cross-references to other databases and publications. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: dataset_publications: name: dataset_publications description: Comma-separated list of DOIs for publications associated with the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: dataset_publications owner: CrossReferences @@ -122,7 +122,7 @@ attributes: related_database_entries: name: related_database_entries description: Comma-separated list of related database entries for the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: related_database_entries owner: CrossReferences @@ -135,7 +135,7 @@ attributes: related_database_links: name: related_database_links description: Comma-separated list of related database links for the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: related_database_links owner: CrossReferences @@ -147,7 +147,7 @@ attributes: dataset_citations: name: dataset_citations description: Comma-separated list of DOIs for publications citing the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: dataset_citations owner: CrossReferences @@ -166,13 +166,13 @@ attributes: ```yaml name: CrossReferences description: A set of cross-references to other databases and publications. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: dataset_publications: name: dataset_publications description: Comma-separated list of DOIs for publications associated with the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: dataset_publications owner: CrossReferences @@ -185,7 +185,7 @@ attributes: related_database_entries: name: related_database_entries description: Comma-separated list of related database entries for the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: related_database_entries owner: CrossReferences @@ -198,7 +198,7 @@ attributes: related_database_links: name: related_database_links description: Comma-separated list of related database links for the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: related_database_links owner: CrossReferences @@ -210,7 +210,7 @@ attributes: dataset_citations: name: dataset_citations description: Comma-separated list of DOIs for publications citing the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: dataset_citations owner: CrossReferences diff --git a/schema/v1.1.0/metadata-docs/Dataset.md b/schema/v1.1.0/metadata-docs/Dataset.md index a0b1c4845..3ca1249ec 100644 --- a/schema/v1.1.0/metadata-docs/Dataset.md +++ b/schema/v1.1.0/metadata-docs/Dataset.md @@ -7,7 +7,7 @@ _High-level description of a cryoET dataset._ -URI: [cdp-meta:Dataset](https://cryoetdataportal.czscience.com/schema/metadata/Dataset) +URI: [cdp-meta:Dataset](metadataDataset) @@ -143,7 +143,7 @@ URI: [cdp-meta:Dataset](https://cryoetdataportal.czscience.com/schema/metadata/D ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -170,7 +170,7 @@ URI: [cdp-meta:Dataset](https://cryoetdataportal.czscience.com/schema/metadata/D ```yaml name: Dataset description: High-level description of a cryoET dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata mixins: - DatestampedEntity - AuthoredEntity @@ -183,7 +183,7 @@ attributes: name: dataset_identifier description: An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_identifier rank: 1000 @@ -197,7 +197,7 @@ attributes: dataset_title: name: dataset_title description: Title of a CryoET dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_title rank: 1000 @@ -212,7 +212,7 @@ attributes: name: dataset_description description: A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_description rank: 1000 @@ -227,7 +227,7 @@ attributes: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: Dataset domain_of: @@ -241,7 +241,7 @@ attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -260,7 +260,7 @@ attributes: name: funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: funding @@ -275,7 +275,7 @@ attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: Dataset domain_of: @@ -289,7 +289,7 @@ attributes: cross_references: name: cross_references description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cross_references owner: Dataset domain_of: @@ -301,7 +301,7 @@ attributes: sample_type: name: sample_type description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_sample_type alias: sample_type @@ -315,7 +315,7 @@ attributes: sample_preparation: name: sample_preparation description: Describes how the sample was prepared. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:sample_preparation alias: sample_preparation @@ -329,7 +329,7 @@ attributes: grid_preparation: name: grid_preparation description: Describes Cryo-ET grid preparation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:grid_preparation alias: grid_preparation @@ -344,7 +344,7 @@ attributes: name: other_setup description: Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_other_setup alias: other_setup @@ -358,7 +358,7 @@ attributes: organism: name: organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: organism owner: Dataset domain_of: @@ -370,7 +370,7 @@ attributes: tissue: name: tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: tissue owner: Dataset domain_of: @@ -382,7 +382,7 @@ attributes: cell_type: name: cell_type description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_type owner: Dataset domain_of: @@ -394,7 +394,7 @@ attributes: cell_strain: name: cell_strain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_strain owner: Dataset domain_of: @@ -406,7 +406,7 @@ attributes: cell_component: name: cell_component description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_component owner: Dataset domain_of: @@ -425,7 +425,7 @@ attributes: ```yaml name: Dataset description: High-level description of a cryoET dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata mixins: - DatestampedEntity - AuthoredEntity @@ -438,7 +438,7 @@ attributes: name: dataset_identifier description: An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_identifier rank: 1000 @@ -452,7 +452,7 @@ attributes: dataset_title: name: dataset_title description: Title of a CryoET dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_title rank: 1000 @@ -467,7 +467,7 @@ attributes: name: dataset_description description: A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_description rank: 1000 @@ -482,7 +482,7 @@ attributes: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: Dataset domain_of: @@ -496,7 +496,7 @@ attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -515,7 +515,7 @@ attributes: name: funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: funding @@ -530,7 +530,7 @@ attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: Dataset domain_of: @@ -544,7 +544,7 @@ attributes: cross_references: name: cross_references description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cross_references owner: Dataset domain_of: @@ -556,7 +556,7 @@ attributes: sample_type: name: sample_type description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_sample_type alias: sample_type @@ -570,7 +570,7 @@ attributes: sample_preparation: name: sample_preparation description: Describes how the sample was prepared. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:sample_preparation alias: sample_preparation @@ -584,7 +584,7 @@ attributes: grid_preparation: name: grid_preparation description: Describes Cryo-ET grid preparation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:grid_preparation alias: grid_preparation @@ -599,7 +599,7 @@ attributes: name: other_setup description: Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_other_setup alias: other_setup @@ -613,7 +613,7 @@ attributes: organism: name: organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: organism owner: Dataset domain_of: @@ -625,7 +625,7 @@ attributes: tissue: name: tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: tissue owner: Dataset domain_of: @@ -637,7 +637,7 @@ attributes: cell_type: name: cell_type description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_type owner: Dataset domain_of: @@ -649,7 +649,7 @@ attributes: cell_strain: name: cell_strain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_strain owner: Dataset domain_of: @@ -661,7 +661,7 @@ attributes: cell_component: name: cell_component description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_component owner: Dataset domain_of: diff --git a/schema/v1.1.0/metadata-docs/DateStamp.md b/schema/v1.1.0/metadata-docs/DateStamp.md index 18cd3fc7e..1dbed80d8 100644 --- a/schema/v1.1.0/metadata-docs/DateStamp.md +++ b/schema/v1.1.0/metadata-docs/DateStamp.md @@ -9,7 +9,7 @@ _A set of dates at which a data item was deposited, published and last modified. * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:DateStamp](https://cryoetdataportal.czscience.com/schema/metadata/DateStamp) +URI: [cdp-meta:DateStamp](metadataDateStamp) @@ -77,7 +77,7 @@ URI: [cdp-meta:DateStamp](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -105,7 +105,7 @@ URI: [cdp-meta:DateStamp](https://cryoetdataportal.czscience.com/schema/metadata name: DateStamp description: A set of dates at which a data item was deposited, published and last modified. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true slots: - deposition_date @@ -131,7 +131,7 @@ attributes: deposition_date: name: deposition_date description: The date a data item was received by the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: deposition_date owner: DateStamp @@ -144,7 +144,7 @@ attributes: release_date: name: release_date description: The date a data item was received by the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: release_date owner: DateStamp @@ -158,7 +158,7 @@ attributes: last_modified_date: name: last_modified_date description: The date a piece of data was last modified on the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: last_modified_date owner: DateStamp @@ -180,7 +180,7 @@ attributes: name: DateStamp description: A set of dates at which a data item was deposited, published and last modified. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true slot_usage: deposition_date: @@ -202,7 +202,7 @@ attributes: deposition_date: name: deposition_date description: The date a data item was received by the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: deposition_date owner: DateStamp @@ -215,7 +215,7 @@ attributes: release_date: name: release_date description: The date a data item was received by the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: release_date owner: DateStamp @@ -229,7 +229,7 @@ attributes: last_modified_date: name: last_modified_date description: The date a piece of data was last modified on the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: last_modified_date owner: DateStamp diff --git a/schema/v1.1.0/metadata-docs/DatestampedEntity.md b/schema/v1.1.0/metadata-docs/DatestampedEntity.md index 6a40b8618..062ea7ca3 100644 --- a/schema/v1.1.0/metadata-docs/DatestampedEntity.md +++ b/schema/v1.1.0/metadata-docs/DatestampedEntity.md @@ -9,7 +9,7 @@ _An entity with associated deposition, release and last modified dates._ * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:DatestampedEntity](https://cryoetdataportal.czscience.com/schema/metadata/DatestampedEntity) +URI: [cdp-meta:DatestampedEntity](metadataDatestampedEntity) @@ -58,7 +58,7 @@ URI: [cdp-meta:DatestampedEntity](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -85,14 +85,14 @@ URI: [cdp-meta:DatestampedEntity](https://cryoetdataportal.czscience.com/schema/ ```yaml name: DatestampedEntity description: An entity with associated deposition, release and last modified dates. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: dates: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: dates owner: DatestampedEntity @@ -114,14 +114,14 @@ attributes: ```yaml name: DatestampedEntity description: An entity with associated deposition, release and last modified dates. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: dates: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: dates owner: DatestampedEntity diff --git a/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md b/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md index aa3949de6..ae544edf4 100644 --- a/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md +++ b/schema/v1.1.0/metadata-docs/ExperimentalMetadata.md @@ -9,7 +9,7 @@ _Metadata describing sample and sample preparation methods used in a cryoET data * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:ExperimentalMetadata](https://cryoetdataportal.czscience.com/schema/metadata/ExperimentalMetadata) +URI: [cdp-meta:ExperimentalMetadata](metadataExperimentalMetadata) @@ -97,7 +97,7 @@ URI: [cdp-meta:ExperimentalMetadata](https://cryoetdataportal.czscience.com/sche ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -125,13 +125,13 @@ URI: [cdp-meta:ExperimentalMetadata](https://cryoetdataportal.czscience.com/sche name: ExperimentalMetadata description: Metadata describing sample and sample preparation methods used in a cryoET dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: sample_type: name: sample_type description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_sample_type rank: 1000 @@ -146,7 +146,7 @@ attributes: sample_preparation: name: sample_preparation description: Describes how the sample was prepared. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:sample_preparation rank: 1000 @@ -161,7 +161,7 @@ attributes: grid_preparation: name: grid_preparation description: Describes Cryo-ET grid preparation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:grid_preparation rank: 1000 @@ -177,7 +177,7 @@ attributes: name: other_setup description: Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_other_setup rank: 1000 @@ -192,7 +192,7 @@ attributes: organism: name: organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: organism owner: ExperimentalMetadata @@ -205,7 +205,7 @@ attributes: tissue: name: tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: tissue owner: ExperimentalMetadata @@ -218,7 +218,7 @@ attributes: cell_type: name: cell_type description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cell_type owner: ExperimentalMetadata @@ -231,7 +231,7 @@ attributes: cell_strain: name: cell_strain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cell_strain owner: ExperimentalMetadata @@ -244,7 +244,7 @@ attributes: cell_component: name: cell_component description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cell_component owner: ExperimentalMetadata @@ -265,13 +265,13 @@ attributes: name: ExperimentalMetadata description: Metadata describing sample and sample preparation methods used in a cryoET dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: sample_type: name: sample_type description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_sample_type rank: 1000 @@ -286,7 +286,7 @@ attributes: sample_preparation: name: sample_preparation description: Describes how the sample was prepared. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:sample_preparation rank: 1000 @@ -301,7 +301,7 @@ attributes: grid_preparation: name: grid_preparation description: Describes Cryo-ET grid preparation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:grid_preparation rank: 1000 @@ -317,7 +317,7 @@ attributes: name: other_setup description: Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_other_setup rank: 1000 @@ -332,7 +332,7 @@ attributes: organism: name: organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: organism owner: ExperimentalMetadata @@ -345,7 +345,7 @@ attributes: tissue: name: tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: tissue owner: ExperimentalMetadata @@ -358,7 +358,7 @@ attributes: cell_type: name: cell_type description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cell_type owner: ExperimentalMetadata @@ -371,7 +371,7 @@ attributes: cell_strain: name: cell_strain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cell_strain owner: ExperimentalMetadata @@ -384,7 +384,7 @@ attributes: cell_component: name: cell_component description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: cell_component owner: ExperimentalMetadata diff --git a/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md b/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md index 5a1afc62c..9c1e27a14 100644 --- a/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md +++ b/schema/v1.1.0/metadata-docs/FiducialAlignmentStatusEnum.md @@ -41,7 +41,7 @@ URI: [FiducialAlignmentStatusEnum](FiducialAlignmentStatusEnum.md) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -52,7 +52,7 @@ URI: [FiducialAlignmentStatusEnum](FiducialAlignmentStatusEnum.md) ```yaml name: fiducial_alignment_status_enum description: Fiducial Alignment method -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 permissible_values: FIDUCIAL: diff --git a/schema/v1.1.0/metadata-docs/FundedEntity.md b/schema/v1.1.0/metadata-docs/FundedEntity.md index 12df0f8b2..6244dbf2b 100644 --- a/schema/v1.1.0/metadata-docs/FundedEntity.md +++ b/schema/v1.1.0/metadata-docs/FundedEntity.md @@ -9,7 +9,7 @@ _An entity with associated funding sources._ * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:FundedEntity](https://cryoetdataportal.czscience.com/schema/metadata/FundedEntity) +URI: [cdp-meta:FundedEntity](metadataFundedEntity) @@ -57,7 +57,7 @@ URI: [cdp-meta:FundedEntity](https://cryoetdataportal.czscience.com/schema/metad ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -84,14 +84,14 @@ URI: [cdp-meta:FundedEntity](https://cryoetdataportal.czscience.com/schema/metad ```yaml name: FundedEntity description: An entity with associated funding sources. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: funding: name: funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true @@ -114,14 +114,14 @@ attributes: ```yaml name: FundedEntity description: An entity with associated funding sources. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: funding: name: funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true diff --git a/schema/v1.1.0/metadata-docs/Funding.md b/schema/v1.1.0/metadata-docs/Funding.md index e1e25d6a3..34ce8c067 100644 --- a/schema/v1.1.0/metadata-docs/Funding.md +++ b/schema/v1.1.0/metadata-docs/Funding.md @@ -1,6 +1,6 @@ # Slot: funding -URI: [cdp-meta:funding](https://cryoetdataportal.czscience.com/schema/metadata/funding) +URI: [cdp-meta:funding](metadatafunding) diff --git a/schema/v1.1.0/metadata-docs/Microscope.md b/schema/v1.1.0/metadata-docs/Microscope.md index 6dcc714e8..506879faa 100644 --- a/schema/v1.1.0/metadata-docs/Microscope.md +++ b/schema/v1.1.0/metadata-docs/Microscope.md @@ -5,7 +5,7 @@ _The microscope used to collect the tilt series._ -URI: [cdp-meta:microscope](https://cryoetdataportal.czscience.com/schema/metadata/microscope) +URI: [cdp-meta:microscope](metadatamicroscope) @@ -45,7 +45,7 @@ URI: [cdp-meta:microscope](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:microscope](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: microscope description: The microscope used to collect the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: microscope owner: TiltSeries diff --git a/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md b/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md index 77fcb49a9..41f08a07d 100644 --- a/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md +++ b/schema/v1.1.0/metadata-docs/MicroscopeOpticalSetup.md @@ -7,7 +7,7 @@ _The optical setup of the microscope used to collect the tilt series._ -URI: [cdp-meta:MicroscopeOpticalSetup](https://cryoetdataportal.czscience.com/schema/metadata/MicroscopeOpticalSetup) +URI: [cdp-meta:MicroscopeOpticalSetup](metadataMicroscopeOpticalSetup) @@ -70,7 +70,7 @@ URI: [cdp-meta:MicroscopeOpticalSetup](https://cryoetdataportal.czscience.com/sc ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -97,12 +97,12 @@ URI: [cdp-meta:MicroscopeOpticalSetup](https://cryoetdataportal.czscience.com/sc ```yaml name: MicroscopeOpticalSetup description: The optical setup of the microscope used to collect the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: energy_filter: name: energy_filter description: Energy filter setup used - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_energy_filter rank: 1000 @@ -116,7 +116,7 @@ attributes: phase_plate: name: phase_plate description: Phase plate configuration - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_phase_plate rank: 1000 @@ -130,7 +130,7 @@ attributes: image_corrector: name: image_corrector description: Image corrector setup - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_image_corrector rank: 1000 @@ -151,12 +151,12 @@ attributes: ```yaml name: MicroscopeOpticalSetup description: The optical setup of the microscope used to collect the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: energy_filter: name: energy_filter description: Energy filter setup used - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_energy_filter rank: 1000 @@ -170,7 +170,7 @@ attributes: phase_plate: name: phase_plate description: Phase plate configuration - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_phase_plate rank: 1000 @@ -184,7 +184,7 @@ attributes: image_corrector: name: image_corrector description: Image corrector setup - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_image_corrector rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/ORCID.md b/schema/v1.1.0/metadata-docs/ORCID.md index e9d1a7385..d4eff8897 100644 --- a/schema/v1.1.0/metadata-docs/ORCID.md +++ b/schema/v1.1.0/metadata-docs/ORCID.md @@ -1,6 +1,6 @@ # Slot: ORCID -URI: [cdp-meta:ORCID](https://cryoetdataportal.czscience.com/schema/metadata/ORCID) +URI: [cdp-meta:ORCID](metadataORCID) diff --git a/schema/v1.1.0/metadata-docs/Organism.md b/schema/v1.1.0/metadata-docs/Organism.md index 1bfc9127c..c828cc06f 100644 --- a/schema/v1.1.0/metadata-docs/Organism.md +++ b/schema/v1.1.0/metadata-docs/Organism.md @@ -1,6 +1,6 @@ # Slot: organism -URI: [cdp-meta:organism](https://cryoetdataportal.czscience.com/schema/metadata/organism) +URI: [cdp-meta:organism](metadataorganism) diff --git a/schema/v1.1.0/metadata-docs/PicturePath.md b/schema/v1.1.0/metadata-docs/PicturePath.md index 6c294a339..d980490cc 100644 --- a/schema/v1.1.0/metadata-docs/PicturePath.md +++ b/schema/v1.1.0/metadata-docs/PicturePath.md @@ -7,7 +7,7 @@ _A set of paths to representative images of a piece of data._ -URI: [cdp-meta:PicturePath](https://cryoetdataportal.czscience.com/schema/metadata/PicturePath) +URI: [cdp-meta:PicturePath](metadataPicturePath) @@ -67,7 +67,7 @@ URI: [cdp-meta:PicturePath](https://cryoetdataportal.czscience.com/schema/metada ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -94,13 +94,13 @@ URI: [cdp-meta:PicturePath](https://cryoetdataportal.czscience.com/schema/metada ```yaml name: PicturePath description: A set of paths to representative images of a piece of data. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: snapshot: name: snapshot description: Path to the dataset preview image relative to the dataset directory root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: snapshot owner: PicturePath @@ -113,7 +113,7 @@ attributes: name: thumbnail description: Path to the thumbnail of preview image relative to the dataset directory root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: thumbnail owner: PicturePath @@ -132,13 +132,13 @@ attributes: ```yaml name: PicturePath description: A set of paths to representative images of a piece of data. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: snapshot: name: snapshot description: Path to the dataset preview image relative to the dataset directory root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: snapshot owner: PicturePath @@ -151,7 +151,7 @@ attributes: name: thumbnail description: Path to the thumbnail of preview image relative to the dataset directory root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: thumbnail owner: PicturePath diff --git a/schema/v1.1.0/metadata-docs/PicturedEntity.md b/schema/v1.1.0/metadata-docs/PicturedEntity.md index 671f4bc5b..bcc3219df 100644 --- a/schema/v1.1.0/metadata-docs/PicturedEntity.md +++ b/schema/v1.1.0/metadata-docs/PicturedEntity.md @@ -9,7 +9,7 @@ _An entity with associated preview images._ * __NOTE__: this is an abstract class and should not be instantiated directly -URI: [cdp-meta:PicturedEntity](https://cryoetdataportal.czscience.com/schema/metadata/PicturedEntity) +URI: [cdp-meta:PicturedEntity](metadataPicturedEntity) @@ -58,7 +58,7 @@ URI: [cdp-meta:PicturedEntity](https://cryoetdataportal.czscience.com/schema/met ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -85,13 +85,13 @@ URI: [cdp-meta:PicturedEntity](https://cryoetdataportal.czscience.com/schema/met ```yaml name: PicturedEntity description: An entity with associated preview images. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: key_photos owner: PicturedEntity @@ -113,13 +113,13 @@ attributes: ```yaml name: PicturedEntity description: An entity with associated preview images. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata abstract: true attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: key_photos owner: PicturedEntity diff --git a/schema/v1.1.0/metadata-docs/SampleTypeEnum.md b/schema/v1.1.0/metadata-docs/SampleTypeEnum.md index 964361694..cad761278 100644 --- a/schema/v1.1.0/metadata-docs/SampleTypeEnum.md +++ b/schema/v1.1.0/metadata-docs/SampleTypeEnum.md @@ -47,7 +47,7 @@ URI: [SampleTypeEnum](SampleTypeEnum.md) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [SampleTypeEnum](SampleTypeEnum.md) ```yaml name: sample_type_enum description: Type of sample imaged in a CryoET study. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 permissible_values: cell: diff --git a/schema/v1.1.0/metadata-docs/TiltRange.md b/schema/v1.1.0/metadata-docs/TiltRange.md index a77942631..d7752fb67 100644 --- a/schema/v1.1.0/metadata-docs/TiltRange.md +++ b/schema/v1.1.0/metadata-docs/TiltRange.md @@ -7,7 +7,7 @@ _The range of tilt angles in the tilt series._ -URI: [cdp-meta:TiltRange](https://cryoetdataportal.czscience.com/schema/metadata/TiltRange) +URI: [cdp-meta:TiltRange](metadataTiltRange) @@ -65,7 +65,7 @@ URI: [cdp-meta:TiltRange](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -92,12 +92,12 @@ URI: [cdp-meta:TiltRange](https://cryoetdataportal.czscience.com/schema/metadata ```yaml name: TiltRange description: The range of tilt angles in the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: min: name: min description: Minimal tilt angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_min rank: 1000 @@ -111,7 +111,7 @@ attributes: max: name: max description: Maximal tilt angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_max rank: 1000 @@ -132,12 +132,12 @@ attributes: ```yaml name: TiltRange description: The range of tilt angles in the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: min: name: min description: Minimal tilt angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_min rank: 1000 @@ -151,7 +151,7 @@ attributes: max: name: max description: Maximal tilt angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_max rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/TiltSeries.md b/schema/v1.1.0/metadata-docs/TiltSeries.md index 5dac42624..2fabc6e6b 100644 --- a/schema/v1.1.0/metadata-docs/TiltSeries.md +++ b/schema/v1.1.0/metadata-docs/TiltSeries.md @@ -7,7 +7,7 @@ _Metadata describing a tilt series._ -URI: [cdp-meta:TiltSeries](https://cryoetdataportal.czscience.com/schema/metadata/TiltSeries) +URI: [cdp-meta:TiltSeries](metadataTiltSeries) @@ -133,7 +133,7 @@ URI: [cdp-meta:TiltSeries](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -160,12 +160,12 @@ URI: [cdp-meta:TiltSeries](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: TiltSeries description: Metadata describing a tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: acceleration_voltage: name: acceleration_voltage description: Electron Microscope Accelerator voltage in volts - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_acceleration_voltage rank: 1000 @@ -179,7 +179,7 @@ attributes: spherical_aberration_constant: name: spherical_aberration_constant description: Spherical Aberration Constant of the objective lens in millimeters - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_spherical_aberration_constant rank: 1000 @@ -194,7 +194,7 @@ attributes: name: microscope_additional_info description: Other microscope optical setup information, in addition to energy filter, phase plate and image corrector - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_additional_info rank: 1000 @@ -208,7 +208,7 @@ attributes: tilt_axis: name: tilt_axis description: Rotation angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_axis rank: 1000 @@ -222,7 +222,7 @@ attributes: tilt_step: name: tilt_step description: Tilt step in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_step rank: 1000 @@ -236,7 +236,7 @@ attributes: tilting_scheme: name: tilting_scheme description: The order of stage tilting during acquisition of the data - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilting_scheme rank: 1000 @@ -251,7 +251,7 @@ attributes: name: total_flux description: Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_total_flux rank: 1000 @@ -265,7 +265,7 @@ attributes: data_acquisition_software: name: data_acquisition_software description: Software used to collect data - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_data_acquisition_software rank: 1000 @@ -279,7 +279,7 @@ attributes: binning_from_frames: name: binning_from_frames description: Describes the binning factor from frames to tilt series file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_binning_from_frames rank: 1000 @@ -294,7 +294,7 @@ attributes: name: tilt_series_quality description: Author assessment of tilt series quality within the dataset (1-5, 5 is best) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_series_quality rank: 1000 @@ -308,7 +308,7 @@ attributes: pixel_spacing: name: pixel_spacing description: Pixel spacing for the tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_pixel_spacing rank: 1000 @@ -322,7 +322,7 @@ attributes: aligned_tiltseries_binning: name: aligned_tiltseries_binning description: Binning factor of the aligned tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_aligned_tiltseries_binning rank: 1000 @@ -336,7 +336,7 @@ attributes: frames_count: name: frames_count description: Number of frames associated with this tiltseries - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_frames_count rank: 1000 @@ -350,7 +350,7 @@ attributes: camera: name: camera description: The camera used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: camera owner: TiltSeries @@ -362,7 +362,7 @@ attributes: microscope: name: microscope description: The microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: microscope owner: TiltSeries @@ -374,7 +374,7 @@ attributes: microscope_optical_setup: name: microscope_optical_setup description: The optical setup of the microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: microscope_optical_setup owner: TiltSeries @@ -386,7 +386,7 @@ attributes: tilt_range: name: tilt_range description: The range of tilt angles in the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: tilt_range owner: TiltSeries @@ -405,12 +405,12 @@ attributes: ```yaml name: TiltSeries description: Metadata describing a tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: acceleration_voltage: name: acceleration_voltage description: Electron Microscope Accelerator voltage in volts - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_acceleration_voltage rank: 1000 @@ -424,7 +424,7 @@ attributes: spherical_aberration_constant: name: spherical_aberration_constant description: Spherical Aberration Constant of the objective lens in millimeters - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_spherical_aberration_constant rank: 1000 @@ -439,7 +439,7 @@ attributes: name: microscope_additional_info description: Other microscope optical setup information, in addition to energy filter, phase plate and image corrector - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_additional_info rank: 1000 @@ -453,7 +453,7 @@ attributes: tilt_axis: name: tilt_axis description: Rotation angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_axis rank: 1000 @@ -467,7 +467,7 @@ attributes: tilt_step: name: tilt_step description: Tilt step in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_step rank: 1000 @@ -481,7 +481,7 @@ attributes: tilting_scheme: name: tilting_scheme description: The order of stage tilting during acquisition of the data - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilting_scheme rank: 1000 @@ -496,7 +496,7 @@ attributes: name: total_flux description: Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_total_flux rank: 1000 @@ -510,7 +510,7 @@ attributes: data_acquisition_software: name: data_acquisition_software description: Software used to collect data - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_data_acquisition_software rank: 1000 @@ -524,7 +524,7 @@ attributes: binning_from_frames: name: binning_from_frames description: Describes the binning factor from frames to tilt series file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_binning_from_frames rank: 1000 @@ -539,7 +539,7 @@ attributes: name: tilt_series_quality description: Author assessment of tilt series quality within the dataset (1-5, 5 is best) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_series_quality rank: 1000 @@ -553,7 +553,7 @@ attributes: pixel_spacing: name: pixel_spacing description: Pixel spacing for the tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_pixel_spacing rank: 1000 @@ -567,7 +567,7 @@ attributes: aligned_tiltseries_binning: name: aligned_tiltseries_binning description: Binning factor of the aligned tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_aligned_tiltseries_binning rank: 1000 @@ -581,7 +581,7 @@ attributes: frames_count: name: frames_count description: Number of frames associated with this tiltseries - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_frames_count rank: 1000 @@ -595,7 +595,7 @@ attributes: camera: name: camera description: The camera used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: camera owner: TiltSeries @@ -607,7 +607,7 @@ attributes: microscope: name: microscope description: The microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: microscope owner: TiltSeries @@ -619,7 +619,7 @@ attributes: microscope_optical_setup: name: microscope_optical_setup description: The optical setup of the microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: microscope_optical_setup owner: TiltSeries @@ -631,7 +631,7 @@ attributes: tilt_range: name: tilt_range description: The range of tilt angles in the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: tilt_range owner: TiltSeries diff --git a/schema/v1.1.0/metadata-docs/Tissue.md b/schema/v1.1.0/metadata-docs/Tissue.md index bcecda29b..df32f56b0 100644 --- a/schema/v1.1.0/metadata-docs/Tissue.md +++ b/schema/v1.1.0/metadata-docs/Tissue.md @@ -1,6 +1,6 @@ # Slot: tissue -URI: [cdp-meta:tissue](https://cryoetdataportal.czscience.com/schema/metadata/tissue) +URI: [cdp-meta:tissue](metadatatissue) diff --git a/schema/v1.1.0/metadata-docs/Tomogram.md b/schema/v1.1.0/metadata-docs/Tomogram.md index 80f7562bf..c4f3b2717 100644 --- a/schema/v1.1.0/metadata-docs/Tomogram.md +++ b/schema/v1.1.0/metadata-docs/Tomogram.md @@ -7,7 +7,7 @@ _Metadata describing a tomogram._ -URI: [cdp-meta:Tomogram](https://cryoetdataportal.czscience.com/schema/metadata/Tomogram) +URI: [cdp-meta:Tomogram](metadataTomogram) @@ -119,7 +119,7 @@ URI: [cdp-meta:Tomogram](https://cryoetdataportal.czscience.com/schema/metadata/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -146,7 +146,7 @@ URI: [cdp-meta:Tomogram](https://cryoetdataportal.czscience.com/schema/metadata/ ```yaml name: Tomogram description: Metadata describing a tomogram. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata mixins: - AuthoredEntity - PicturedEntity @@ -154,7 +154,7 @@ attributes: voxel_spacing: name: voxel_spacing description: Voxel spacing equal in all three axes in angstroms - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_voxel_spacing rank: 1000 @@ -169,7 +169,7 @@ attributes: name: fiducial_alignment_status description: Whether the tomographic alignment was computed based on fiducial markers. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_fiducial_alignment_status rank: 1000 @@ -183,7 +183,7 @@ attributes: ctf_corrected: name: ctf_corrected description: Whether this tomogram is CTF corrected - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_ctf_corrected rank: 1000 @@ -197,7 +197,7 @@ attributes: reconstruction_method: name: reconstruction_method description: Describe reconstruction method (Weighted back-projection, SART, SIRT) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_method rank: 1000 @@ -211,7 +211,7 @@ attributes: reconstruction_software: name: reconstruction_software description: Name of software used for reconstruction - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_software rank: 1000 @@ -225,7 +225,7 @@ attributes: processing: name: processing description: Describe additional processing used to derive the tomogram - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_processing rank: 1000 @@ -239,7 +239,7 @@ attributes: processing_software: name: processing_software description: Processing software used to derive the tomogram - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_processing_software rank: 1000 @@ -255,7 +255,7 @@ attributes: description: Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_version rank: 1000 @@ -270,7 +270,7 @@ attributes: name: affine_transformation_matrix description: The flip or rotation transformation of this author submitted tomogram is indicated here - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_affine_transformation_matrix rank: 1000 @@ -284,7 +284,7 @@ attributes: size: name: size description: The size of a tomogram in voxels in each dimension. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: size owner: Tomogram @@ -297,7 +297,7 @@ attributes: name: offset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: offset owner: Tomogram @@ -309,7 +309,7 @@ attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -327,7 +327,7 @@ attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: Tomogram domain_of: @@ -348,7 +348,7 @@ attributes: ```yaml name: Tomogram description: Metadata describing a tomogram. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata mixins: - AuthoredEntity - PicturedEntity @@ -356,7 +356,7 @@ attributes: voxel_spacing: name: voxel_spacing description: Voxel spacing equal in all three axes in angstroms - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_voxel_spacing rank: 1000 @@ -371,7 +371,7 @@ attributes: name: fiducial_alignment_status description: Whether the tomographic alignment was computed based on fiducial markers. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_fiducial_alignment_status rank: 1000 @@ -385,7 +385,7 @@ attributes: ctf_corrected: name: ctf_corrected description: Whether this tomogram is CTF corrected - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_ctf_corrected rank: 1000 @@ -399,7 +399,7 @@ attributes: reconstruction_method: name: reconstruction_method description: Describe reconstruction method (Weighted back-projection, SART, SIRT) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_method rank: 1000 @@ -413,7 +413,7 @@ attributes: reconstruction_software: name: reconstruction_software description: Name of software used for reconstruction - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_software rank: 1000 @@ -427,7 +427,7 @@ attributes: processing: name: processing description: Describe additional processing used to derive the tomogram - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_processing rank: 1000 @@ -441,7 +441,7 @@ attributes: processing_software: name: processing_software description: Processing software used to derive the tomogram - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_processing_software rank: 1000 @@ -457,7 +457,7 @@ attributes: description: Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_version rank: 1000 @@ -472,7 +472,7 @@ attributes: name: affine_transformation_matrix description: The flip or rotation transformation of this author submitted tomogram is indicated here - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_affine_transformation_matrix rank: 1000 @@ -486,7 +486,7 @@ attributes: size: name: size description: The size of a tomogram in voxels in each dimension. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: size owner: Tomogram @@ -499,7 +499,7 @@ attributes: name: offset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata rank: 1000 alias: offset owner: Tomogram @@ -511,7 +511,7 @@ attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -529,7 +529,7 @@ attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: Tomogram domain_of: diff --git a/schema/v1.1.0/metadata-docs/TomogramOffset.md b/schema/v1.1.0/metadata-docs/TomogramOffset.md index a739c7c9e..b511787cb 100644 --- a/schema/v1.1.0/metadata-docs/TomogramOffset.md +++ b/schema/v1.1.0/metadata-docs/TomogramOffset.md @@ -7,7 +7,7 @@ _The offset of a tomogram in voxels in each dimension relative to the canonical -URI: [cdp-meta:TomogramOffset](https://cryoetdataportal.czscience.com/schema/metadata/TomogramOffset) +URI: [cdp-meta:TomogramOffset](metadataTomogramOffset) @@ -70,7 +70,7 @@ URI: [cdp-meta:TomogramOffset](https://cryoetdataportal.czscience.com/schema/met ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -98,11 +98,11 @@ URI: [cdp-meta:TomogramOffset](https://cryoetdataportal.czscience.com/schema/met name: TomogramOffset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: x: name: x - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_x alias: x @@ -115,7 +115,7 @@ attributes: inlined_as_list: true y: name: y - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_y alias: y @@ -128,7 +128,7 @@ attributes: inlined_as_list: true z: name: z - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_z alias: z @@ -150,11 +150,11 @@ attributes: name: TomogramOffset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: x: name: x - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_x alias: x @@ -167,7 +167,7 @@ attributes: inlined_as_list: true y: name: y - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_y alias: y @@ -180,7 +180,7 @@ attributes: inlined_as_list: true z: name: z - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_z alias: z diff --git a/schema/v1.1.0/metadata-docs/TomogramSize.md b/schema/v1.1.0/metadata-docs/TomogramSize.md index 8ad184076..bbc98c5f4 100644 --- a/schema/v1.1.0/metadata-docs/TomogramSize.md +++ b/schema/v1.1.0/metadata-docs/TomogramSize.md @@ -7,7 +7,7 @@ _The size of a tomogram in voxels in each dimension._ -URI: [cdp-meta:TomogramSize](https://cryoetdataportal.czscience.com/schema/metadata/TomogramSize) +URI: [cdp-meta:TomogramSize](metadataTomogramSize) @@ -70,7 +70,7 @@ URI: [cdp-meta:TomogramSize](https://cryoetdataportal.czscience.com/schema/metad ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -97,12 +97,12 @@ URI: [cdp-meta:TomogramSize](https://cryoetdataportal.czscience.com/schema/metad ```yaml name: TomogramSize description: The size of a tomogram in voxels in each dimension. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: x: name: x description: Number of pixels in the 3D data fast axis - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_x rank: 1000 @@ -117,7 +117,7 @@ attributes: y: name: y description: Number of pixels in the 3D data medium axis - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_y rank: 1000 @@ -133,7 +133,7 @@ attributes: name: z description: Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_z rank: 1000 @@ -155,12 +155,12 @@ attributes: ```yaml name: TomogramSize description: The size of a tomogram in voxels in each dimension. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata attributes: x: name: x description: Number of pixels in the 3D data fast axis - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_x rank: 1000 @@ -175,7 +175,7 @@ attributes: y: name: y description: Number of pixels in the 3D data medium axis - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_y rank: 1000 @@ -191,7 +191,7 @@ attributes: name: z description: Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_z rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md b/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md index 09aadb185..17bd338f1 100644 --- a/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md +++ b/schema/v1.1.0/metadata-docs/TomogramTypeEnum.md @@ -34,7 +34,7 @@ URI: [TomogramTypeEnum](TomogramTypeEnum.md) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -45,7 +45,7 @@ URI: [TomogramTypeEnum](TomogramTypeEnum.md) ```yaml name: tomogram_type_enum description: Tomogram type -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 permissible_values: CANONICAL: diff --git a/schema/v1.1.0/metadata-docs/acceleration_voltage.md b/schema/v1.1.0/metadata-docs/acceleration_voltage.md index ee3d8cb51..037599600 100644 --- a/schema/v1.1.0/metadata-docs/acceleration_voltage.md +++ b/schema/v1.1.0/metadata-docs/acceleration_voltage.md @@ -5,7 +5,7 @@ _Electron Microscope Accelerator voltage in volts_ -URI: [cdp-meta:acceleration_voltage](https://cryoetdataportal.czscience.com/schema/metadata/acceleration_voltage) +URI: [cdp-meta:acceleration_voltage](metadataacceleration_voltage) @@ -45,7 +45,7 @@ URI: [cdp-meta:acceleration_voltage](https://cryoetdataportal.czscience.com/sche ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:acceleration_voltage](https://cryoetdataportal.czscience.com/sche ```yaml name: acceleration_voltage description: Electron Microscope Accelerator voltage in volts -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_acceleration_voltage rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/affiliation_address.md b/schema/v1.1.0/metadata-docs/affiliation_address.md index 5952e5c8a..b68184190 100644 --- a/schema/v1.1.0/metadata-docs/affiliation_address.md +++ b/schema/v1.1.0/metadata-docs/affiliation_address.md @@ -1,6 +1,6 @@ # Slot: affiliation_address -URI: [cdp-meta:affiliation_address](https://cryoetdataportal.czscience.com/schema/metadata/affiliation_address) +URI: [cdp-meta:affiliation_address](metadataaffiliation_address) diff --git a/schema/v1.1.0/metadata-docs/affiliation_identifier.md b/schema/v1.1.0/metadata-docs/affiliation_identifier.md index e1a8187df..cf672a703 100644 --- a/schema/v1.1.0/metadata-docs/affiliation_identifier.md +++ b/schema/v1.1.0/metadata-docs/affiliation_identifier.md @@ -1,6 +1,6 @@ # Slot: affiliation_identifier -URI: [cdp-meta:affiliation_identifier](https://cryoetdataportal.czscience.com/schema/metadata/affiliation_identifier) +URI: [cdp-meta:affiliation_identifier](metadataaffiliation_identifier) diff --git a/schema/v1.1.0/metadata-docs/affiliation_name.md b/schema/v1.1.0/metadata-docs/affiliation_name.md index 9b711b430..d4aa2539b 100644 --- a/schema/v1.1.0/metadata-docs/affiliation_name.md +++ b/schema/v1.1.0/metadata-docs/affiliation_name.md @@ -1,6 +1,6 @@ # Slot: affiliation_name -URI: [cdp-meta:affiliation_name](https://cryoetdataportal.czscience.com/schema/metadata/affiliation_name) +URI: [cdp-meta:affiliation_name](metadataaffiliation_name) diff --git a/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md b/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md index 35b10c3d2..aa503dfc3 100644 --- a/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md +++ b/schema/v1.1.0/metadata-docs/affine_transformation_matrix.md @@ -5,7 +5,7 @@ _The flip or rotation transformation of this author submitted tomogram is indica -URI: [cdp-meta:affine_transformation_matrix](https://cryoetdataportal.czscience.com/schema/metadata/affine_transformation_matrix) +URI: [cdp-meta:affine_transformation_matrix](metadataaffine_transformation_matrix) @@ -45,7 +45,7 @@ URI: [cdp-meta:affine_transformation_matrix](https://cryoetdataportal.czscience. ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:affine_transformation_matrix](https://cryoetdataportal.czscience. name: affine_transformation_matrix description: The flip or rotation transformation of this author submitted tomogram is indicated here -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_affine_transformation_matrix rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md b/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md index 2fc143347..c5e92c8f7 100644 --- a/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md +++ b/schema/v1.1.0/metadata-docs/aligned_tiltseries_binning.md @@ -5,7 +5,7 @@ _Binning factor of the aligned tilt series_ -URI: [cdp-meta:aligned_tiltseries_binning](https://cryoetdataportal.czscience.com/schema/metadata/aligned_tiltseries_binning) +URI: [cdp-meta:aligned_tiltseries_binning](metadataaligned_tiltseries_binning) @@ -45,7 +45,7 @@ URI: [cdp-meta:aligned_tiltseries_binning](https://cryoetdataportal.czscience.co ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:aligned_tiltseries_binning](https://cryoetdataportal.czscience.co ```yaml name: aligned_tiltseries_binning description: Binning factor of the aligned tilt series -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_aligned_tiltseries_binning rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/annotation_method.md b/schema/v1.1.0/metadata-docs/annotation_method.md index 7b3b960ae..6b313fd31 100644 --- a/schema/v1.1.0/metadata-docs/annotation_method.md +++ b/schema/v1.1.0/metadata-docs/annotation_method.md @@ -5,7 +5,7 @@ _Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Le -URI: [cdp-meta:annotation_method](https://cryoetdataportal.czscience.com/schema/metadata/annotation_method) +URI: [cdp-meta:annotation_method](metadataannotation_method) @@ -45,7 +45,7 @@ URI: [cdp-meta:annotation_method](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:annotation_method](https://cryoetdataportal.czscience.com/schema/ name: annotation_method description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_method rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/annotation_method_type.md b/schema/v1.1.0/metadata-docs/annotation_method_type.md index a97e87735..6dad9b308 100644 --- a/schema/v1.1.0/metadata-docs/annotation_method_type.md +++ b/schema/v1.1.0/metadata-docs/annotation_method_type.md @@ -5,7 +5,7 @@ _Classification of the annotation method based on supervision._ -URI: [cdp-meta:annotation_method_type](https://cryoetdataportal.czscience.com/schema/metadata/annotation_method_type) +URI: [cdp-meta:annotation_method_type](metadataannotation_method_type) @@ -45,7 +45,7 @@ URI: [cdp-meta:annotation_method_type](https://cryoetdataportal.czscience.com/sc ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:annotation_method_type](https://cryoetdataportal.czscience.com/sc ```yaml name: annotation_method_type description: Classification of the annotation method based on supervision. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_method_type rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/annotation_object.md b/schema/v1.1.0/metadata-docs/annotation_object.md index 7894a7aef..d6dd6479e 100644 --- a/schema/v1.1.0/metadata-docs/annotation_object.md +++ b/schema/v1.1.0/metadata-docs/annotation_object.md @@ -5,7 +5,7 @@ _Metadata describing the object being annotated._ -URI: [cdp-meta:annotation_object](https://cryoetdataportal.czscience.com/schema/metadata/annotation_object) +URI: [cdp-meta:annotation_object](metadataannotation_object) @@ -45,7 +45,7 @@ URI: [cdp-meta:annotation_object](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:annotation_object](https://cryoetdataportal.czscience.com/schema/ ```yaml name: annotation_object description: Metadata describing the object being annotated. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: annotation_object owner: Annotation diff --git a/schema/v1.1.0/metadata-docs/annotation_publications.md b/schema/v1.1.0/metadata-docs/annotation_publications.md index 6ae49d083..81636aab9 100644 --- a/schema/v1.1.0/metadata-docs/annotation_publications.md +++ b/schema/v1.1.0/metadata-docs/annotation_publications.md @@ -5,7 +5,7 @@ _DOIs for publications that describe the dataset. Use a comma to separate multip -URI: [cdp-meta:annotation_publications](https://cryoetdataportal.czscience.com/schema/metadata/annotation_publications) +URI: [cdp-meta:annotation_publications](metadataannotation_publications) @@ -45,7 +45,7 @@ URI: [cdp-meta:annotation_publications](https://cryoetdataportal.czscience.com/s ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:annotation_publications](https://cryoetdataportal.czscience.com/s name: annotation_publications description: DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_publication rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/annotation_software.md b/schema/v1.1.0/metadata-docs/annotation_software.md index 85eac7fc1..dd5a28f95 100644 --- a/schema/v1.1.0/metadata-docs/annotation_software.md +++ b/schema/v1.1.0/metadata-docs/annotation_software.md @@ -5,7 +5,7 @@ _Software used for generating this annotation_ -URI: [cdp-meta:annotation_software](https://cryoetdataportal.czscience.com/schema/metadata/annotation_software) +URI: [cdp-meta:annotation_software](metadataannotation_software) @@ -45,7 +45,7 @@ URI: [cdp-meta:annotation_software](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:annotation_software](https://cryoetdataportal.czscience.com/schem ```yaml name: annotation_software description: Software used for generating this annotation -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_software rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/authors.md b/schema/v1.1.0/metadata-docs/authors.md index a9c758be0..8fafbbf7c 100644 --- a/schema/v1.1.0/metadata-docs/authors.md +++ b/schema/v1.1.0/metadata-docs/authors.md @@ -1,6 +1,6 @@ # Slot: authors -URI: [cdp-meta:authors](https://cryoetdataportal.czscience.com/schema/metadata/authors) +URI: [cdp-meta:authors](metadataauthors) diff --git a/schema/v1.1.0/metadata-docs/binning_from_frames.md b/schema/v1.1.0/metadata-docs/binning_from_frames.md index 922306895..0ae4d86ce 100644 --- a/schema/v1.1.0/metadata-docs/binning_from_frames.md +++ b/schema/v1.1.0/metadata-docs/binning_from_frames.md @@ -5,7 +5,7 @@ _Describes the binning factor from frames to tilt series file_ -URI: [cdp-meta:binning_from_frames](https://cryoetdataportal.czscience.com/schema/metadata/binning_from_frames) +URI: [cdp-meta:binning_from_frames](metadatabinning_from_frames) @@ -45,7 +45,7 @@ URI: [cdp-meta:binning_from_frames](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:binning_from_frames](https://cryoetdataportal.czscience.com/schem ```yaml name: binning_from_frames description: Describes the binning factor from frames to tilt series file -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_binning_from_frames rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/cdp-meta.md b/schema/v1.1.0/metadata-docs/cdp-meta.md index 9f8cb135e..cc99c9074 100644 --- a/schema/v1.1.0/metadata-docs/cdp-meta.md +++ b/schema/v1.1.0/metadata-docs/cdp-meta.md @@ -2,5 +2,5 @@ None -URI: https://cryoetdataportal.czscience.com/schema-docs/metadata +URI: metadata diff --git a/schema/v1.1.0/metadata-docs/cell_component.md b/schema/v1.1.0/metadata-docs/cell_component.md index 6573d7fc2..dce288b00 100644 --- a/schema/v1.1.0/metadata-docs/cell_component.md +++ b/schema/v1.1.0/metadata-docs/cell_component.md @@ -1,6 +1,6 @@ # Slot: cell_component -URI: [cdp-meta:cell_component](https://cryoetdataportal.czscience.com/schema/metadata/cell_component) +URI: [cdp-meta:cell_component](metadatacell_component) diff --git a/schema/v1.1.0/metadata-docs/cell_strain.md b/schema/v1.1.0/metadata-docs/cell_strain.md index 22a518234..f8c903afd 100644 --- a/schema/v1.1.0/metadata-docs/cell_strain.md +++ b/schema/v1.1.0/metadata-docs/cell_strain.md @@ -1,6 +1,6 @@ # Slot: cell_strain -URI: [cdp-meta:cell_strain](https://cryoetdataportal.czscience.com/schema/metadata/cell_strain) +URI: [cdp-meta:cell_strain](metadatacell_strain) diff --git a/schema/v1.1.0/metadata-docs/cell_type.md b/schema/v1.1.0/metadata-docs/cell_type.md index cbf8dda64..339857380 100644 --- a/schema/v1.1.0/metadata-docs/cell_type.md +++ b/schema/v1.1.0/metadata-docs/cell_type.md @@ -1,6 +1,6 @@ # Slot: cell_type -URI: [cdp-meta:cell_type](https://cryoetdataportal.czscience.com/schema/metadata/cell_type) +URI: [cdp-meta:cell_type](metadatacell_type) diff --git a/schema/v1.1.0/metadata-docs/confidence.md b/schema/v1.1.0/metadata-docs/confidence.md index fc2def7a2..bd0849dd9 100644 --- a/schema/v1.1.0/metadata-docs/confidence.md +++ b/schema/v1.1.0/metadata-docs/confidence.md @@ -5,7 +5,7 @@ _Metadata describing the confidence of an annotation._ -URI: [cdp-meta:confidence](https://cryoetdataportal.czscience.com/schema/metadata/confidence) +URI: [cdp-meta:confidence](metadataconfidence) @@ -45,7 +45,7 @@ URI: [cdp-meta:confidence](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:confidence](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: confidence description: Metadata describing the confidence of an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: confidence owner: Annotation diff --git a/schema/v1.1.0/metadata-docs/cross_references.md b/schema/v1.1.0/metadata-docs/cross_references.md index e082729cc..4fdfa0ca5 100644 --- a/schema/v1.1.0/metadata-docs/cross_references.md +++ b/schema/v1.1.0/metadata-docs/cross_references.md @@ -1,6 +1,6 @@ # Slot: cross_references -URI: [cdp-meta:cross_references](https://cryoetdataportal.czscience.com/schema/metadata/cross_references) +URI: [cdp-meta:cross_references](metadatacross_references) diff --git a/schema/v1.1.0/metadata-docs/ctf_corrected.md b/schema/v1.1.0/metadata-docs/ctf_corrected.md index c967baac5..69128a587 100644 --- a/schema/v1.1.0/metadata-docs/ctf_corrected.md +++ b/schema/v1.1.0/metadata-docs/ctf_corrected.md @@ -5,7 +5,7 @@ _Whether this tomogram is CTF corrected_ -URI: [cdp-meta:ctf_corrected](https://cryoetdataportal.czscience.com/schema/metadata/ctf_corrected) +URI: [cdp-meta:ctf_corrected](metadatactf_corrected) @@ -45,7 +45,7 @@ URI: [cdp-meta:ctf_corrected](https://cryoetdataportal.czscience.com/schema/meta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:ctf_corrected](https://cryoetdataportal.czscience.com/schema/meta ```yaml name: ctf_corrected description: Whether this tomogram is CTF corrected -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_ctf_corrected rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/data_acquisition_software.md b/schema/v1.1.0/metadata-docs/data_acquisition_software.md index 54ec77ae1..015273e8c 100644 --- a/schema/v1.1.0/metadata-docs/data_acquisition_software.md +++ b/schema/v1.1.0/metadata-docs/data_acquisition_software.md @@ -5,7 +5,7 @@ _Software used to collect data_ -URI: [cdp-meta:data_acquisition_software](https://cryoetdataportal.czscience.com/schema/metadata/data_acquisition_software) +URI: [cdp-meta:data_acquisition_software](metadatadata_acquisition_software) @@ -45,7 +45,7 @@ URI: [cdp-meta:data_acquisition_software](https://cryoetdataportal.czscience.com ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:data_acquisition_software](https://cryoetdataportal.czscience.com ```yaml name: data_acquisition_software description: Software used to collect data -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_data_acquisition_software rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/dataset_citations.md b/schema/v1.1.0/metadata-docs/dataset_citations.md index 4b98fc247..d6a3406c9 100644 --- a/schema/v1.1.0/metadata-docs/dataset_citations.md +++ b/schema/v1.1.0/metadata-docs/dataset_citations.md @@ -5,7 +5,7 @@ _Comma-separated list of DOIs for publications citing the dataset._ -URI: [cdp-meta:dataset_citations](https://cryoetdataportal.czscience.com/schema/metadata/dataset_citations) +URI: [cdp-meta:dataset_citations](metadatadataset_citations) @@ -45,7 +45,7 @@ URI: [cdp-meta:dataset_citations](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:dataset_citations](https://cryoetdataportal.czscience.com/schema/ ```yaml name: dataset_citations description: Comma-separated list of DOIs for publications citing the dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: dataset_citations owner: CrossReferences diff --git a/schema/v1.1.0/metadata-docs/dataset_description.md b/schema/v1.1.0/metadata-docs/dataset_description.md index 0c1263647..af43109b2 100644 --- a/schema/v1.1.0/metadata-docs/dataset_description.md +++ b/schema/v1.1.0/metadata-docs/dataset_description.md @@ -5,7 +5,7 @@ _A short description of a CryoET dataset, similar to an abstract for a journal a -URI: [cdp-meta:dataset_description](https://cryoetdataportal.czscience.com/schema/metadata/dataset_description) +URI: [cdp-meta:dataset_description](metadatadataset_description) @@ -45,7 +45,7 @@ URI: [cdp-meta:dataset_description](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:dataset_description](https://cryoetdataportal.czscience.com/schem name: dataset_description description: A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:dataset_description rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/dataset_identifier.md b/schema/v1.1.0/metadata-docs/dataset_identifier.md index 94dd88ebc..50d17cd80 100644 --- a/schema/v1.1.0/metadata-docs/dataset_identifier.md +++ b/schema/v1.1.0/metadata-docs/dataset_identifier.md @@ -5,7 +5,7 @@ _An identifier for a CryoET dataset, assigned by the Data Portal. Used to identi -URI: [cdp-meta:dataset_identifier](https://cryoetdataportal.czscience.com/schema/metadata/dataset_identifier) +URI: [cdp-meta:dataset_identifier](metadatadataset_identifier) @@ -45,7 +45,7 @@ URI: [cdp-meta:dataset_identifier](https://cryoetdataportal.czscience.com/schema ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:dataset_identifier](https://cryoetdataportal.czscience.com/schema name: dataset_identifier description: An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:dataset_identifier rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/dataset_publications.md b/schema/v1.1.0/metadata-docs/dataset_publications.md index 3729b4464..af008dd94 100644 --- a/schema/v1.1.0/metadata-docs/dataset_publications.md +++ b/schema/v1.1.0/metadata-docs/dataset_publications.md @@ -5,7 +5,7 @@ _Comma-separated list of DOIs for publications associated with the dataset._ -URI: [cdp-meta:dataset_publications](https://cryoetdataportal.czscience.com/schema/metadata/dataset_publications) +URI: [cdp-meta:dataset_publications](metadatadataset_publications) @@ -47,7 +47,7 @@ URI: [cdp-meta:dataset_publications](https://cryoetdataportal.czscience.com/sche ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [cdp-meta:dataset_publications](https://cryoetdataportal.czscience.com/sche ```yaml name: dataset_publications description: Comma-separated list of DOIs for publications associated with the dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: dataset_publications owner: CrossReferences diff --git a/schema/v1.1.0/metadata-docs/dataset_title.md b/schema/v1.1.0/metadata-docs/dataset_title.md index 8536705f4..4c45f093e 100644 --- a/schema/v1.1.0/metadata-docs/dataset_title.md +++ b/schema/v1.1.0/metadata-docs/dataset_title.md @@ -5,7 +5,7 @@ _Title of a CryoET dataset._ -URI: [cdp-meta:dataset_title](https://cryoetdataportal.czscience.com/schema/metadata/dataset_title) +URI: [cdp-meta:dataset_title](metadatadataset_title) @@ -45,7 +45,7 @@ URI: [cdp-meta:dataset_title](https://cryoetdataportal.czscience.com/schema/meta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:dataset_title](https://cryoetdataportal.czscience.com/schema/meta ```yaml name: dataset_title description: Title of a CryoET dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:dataset_title rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/dates.md b/schema/v1.1.0/metadata-docs/dates.md index ce8f19d38..00f206bec 100644 --- a/schema/v1.1.0/metadata-docs/dates.md +++ b/schema/v1.1.0/metadata-docs/dates.md @@ -1,6 +1,6 @@ # Slot: dates -URI: [cdp-meta:dates](https://cryoetdataportal.czscience.com/schema/metadata/dates) +URI: [cdp-meta:dates](metadatadates) diff --git a/schema/v1.1.0/metadata-docs/deposition_date.md b/schema/v1.1.0/metadata-docs/deposition_date.md index 78b5c466b..5bfe5c44c 100644 --- a/schema/v1.1.0/metadata-docs/deposition_date.md +++ b/schema/v1.1.0/metadata-docs/deposition_date.md @@ -5,7 +5,7 @@ _The date a data item was received by the cryoET data portal._ -URI: [cdp-meta:deposition_date](https://cryoetdataportal.czscience.com/schema/metadata/deposition_date) +URI: [cdp-meta:deposition_date](metadatadeposition_date) @@ -47,7 +47,7 @@ URI: [cdp-meta:deposition_date](https://cryoetdataportal.czscience.com/schema/me ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [cdp-meta:deposition_date](https://cryoetdataportal.czscience.com/schema/me ```yaml name: deposition_date description: The date a data item was received by the cryoET data portal. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: deposition_date owner: DateStamp diff --git a/schema/v1.1.0/metadata-docs/description.md b/schema/v1.1.0/metadata-docs/description.md index c29b0af67..0c0ce90f7 100644 --- a/schema/v1.1.0/metadata-docs/description.md +++ b/schema/v1.1.0/metadata-docs/description.md @@ -5,7 +5,7 @@ _A textual description of the annotation object, can be a longer description to -URI: [cdp-meta:description](https://cryoetdataportal.czscience.com/schema/metadata/description) +URI: [cdp-meta:description](metadatadescription) @@ -45,7 +45,7 @@ URI: [cdp-meta:description](https://cryoetdataportal.czscience.com/schema/metada ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ name: description description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_object_description rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/email.md b/schema/v1.1.0/metadata-docs/email.md index 82d876da2..16a3247ba 100644 --- a/schema/v1.1.0/metadata-docs/email.md +++ b/schema/v1.1.0/metadata-docs/email.md @@ -1,6 +1,6 @@ # Slot: email -URI: [cdp-meta:email](https://cryoetdataportal.czscience.com/schema/metadata/email) +URI: [cdp-meta:email](metadataemail) diff --git a/schema/v1.1.0/metadata-docs/energy_filter.md b/schema/v1.1.0/metadata-docs/energy_filter.md index d6bfa5229..780d912ef 100644 --- a/schema/v1.1.0/metadata-docs/energy_filter.md +++ b/schema/v1.1.0/metadata-docs/energy_filter.md @@ -5,7 +5,7 @@ _Energy filter setup used_ -URI: [cdp-meta:energy_filter](https://cryoetdataportal.czscience.com/schema/metadata/energy_filter) +URI: [cdp-meta:energy_filter](metadataenergy_filter) @@ -45,7 +45,7 @@ URI: [cdp-meta:energy_filter](https://cryoetdataportal.czscience.com/schema/meta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:energy_filter](https://cryoetdataportal.czscience.com/schema/meta ```yaml name: energy_filter description: Energy filter setup used -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_energy_filter rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md b/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md index 209612612..b6594d57e 100644 --- a/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md +++ b/schema/v1.1.0/metadata-docs/fiducial_alignment_status.md @@ -5,7 +5,7 @@ _Whether the tomographic alignment was computed based on fiducial markers._ -URI: [cdp-meta:fiducial_alignment_status](https://cryoetdataportal.czscience.com/schema/metadata/fiducial_alignment_status) +URI: [cdp-meta:fiducial_alignment_status](metadatafiducial_alignment_status) @@ -45,7 +45,7 @@ URI: [cdp-meta:fiducial_alignment_status](https://cryoetdataportal.czscience.com ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:fiducial_alignment_status](https://cryoetdataportal.czscience.com ```yaml name: fiducial_alignment_status description: Whether the tomographic alignment was computed based on fiducial markers. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_fiducial_alignment_status rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/files.md b/schema/v1.1.0/metadata-docs/files.md index 250fdbba0..f03410a5c 100644 --- a/schema/v1.1.0/metadata-docs/files.md +++ b/schema/v1.1.0/metadata-docs/files.md @@ -5,7 +5,7 @@ _Metadata describing a file containing an annotation._ -URI: [cdp-meta:files](https://cryoetdataportal.czscience.com/schema/metadata/files) +URI: [cdp-meta:files](metadatafiles) @@ -47,7 +47,7 @@ URI: [cdp-meta:files](https://cryoetdataportal.czscience.com/schema/metadata/fil ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [cdp-meta:files](https://cryoetdataportal.czscience.com/schema/metadata/fil ```yaml name: files description: Metadata describing a file containing an annotation. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 multivalued: true list_elements_ordered: true diff --git a/schema/v1.1.0/metadata-docs/format.md b/schema/v1.1.0/metadata-docs/format.md index 5c62c3b89..85210df02 100644 --- a/schema/v1.1.0/metadata-docs/format.md +++ b/schema/v1.1.0/metadata-docs/format.md @@ -5,7 +5,7 @@ _File format for this file_ -URI: [cdp-meta:format](https://cryoetdataportal.czscience.com/schema/metadata/format) +URI: [cdp-meta:format](metadataformat) @@ -45,7 +45,7 @@ URI: [cdp-meta:format](https://cryoetdataportal.czscience.com/schema/metadata/fo ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:format](https://cryoetdataportal.czscience.com/schema/metadata/fo ```yaml name: format description: File format for this file -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_file_format rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/frames_count.md b/schema/v1.1.0/metadata-docs/frames_count.md index 82535ce19..30d8859a6 100644 --- a/schema/v1.1.0/metadata-docs/frames_count.md +++ b/schema/v1.1.0/metadata-docs/frames_count.md @@ -5,7 +5,7 @@ _Number of frames associated with this tiltseries_ -URI: [cdp-meta:frames_count](https://cryoetdataportal.czscience.com/schema/metadata/frames_count) +URI: [cdp-meta:frames_count](metadataframes_count) @@ -45,7 +45,7 @@ URI: [cdp-meta:frames_count](https://cryoetdataportal.czscience.com/schema/metad ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:frames_count](https://cryoetdataportal.czscience.com/schema/metad ```yaml name: frames_count description: Number of frames associated with this tiltseries -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_frames_count rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/funding_agency_name.md b/schema/v1.1.0/metadata-docs/funding_agency_name.md index 4b44ab802..a4fbca7c1 100644 --- a/schema/v1.1.0/metadata-docs/funding_agency_name.md +++ b/schema/v1.1.0/metadata-docs/funding_agency_name.md @@ -5,7 +5,7 @@ _The name of the funding source._ -URI: [cdp-meta:funding_agency_name](https://cryoetdataportal.czscience.com/schema/metadata/funding_agency_name) +URI: [cdp-meta:funding_agency_name](metadatafunding_agency_name) @@ -45,7 +45,7 @@ URI: [cdp-meta:funding_agency_name](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:funding_agency_name](https://cryoetdataportal.czscience.com/schem ```yaml name: funding_agency_name description: The name of the funding source. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:funding_agency_name rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/grant_id.md b/schema/v1.1.0/metadata-docs/grant_id.md index 77622aea6..a68cdd632 100644 --- a/schema/v1.1.0/metadata-docs/grant_id.md +++ b/schema/v1.1.0/metadata-docs/grant_id.md @@ -5,7 +5,7 @@ _Grant identifier provided by the funding agency_ -URI: [cdp-meta:grant_id](https://cryoetdataportal.czscience.com/schema/metadata/grant_id) +URI: [cdp-meta:grant_id](metadatagrant_id) @@ -45,7 +45,7 @@ URI: [cdp-meta:grant_id](https://cryoetdataportal.czscience.com/schema/metadata/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:grant_id](https://cryoetdataportal.czscience.com/schema/metadata/ ```yaml name: grant_id description: Grant identifier provided by the funding agency -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:funding_grant_id rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/grid_preparation.md b/schema/v1.1.0/metadata-docs/grid_preparation.md index cd741089d..baa80d51f 100644 --- a/schema/v1.1.0/metadata-docs/grid_preparation.md +++ b/schema/v1.1.0/metadata-docs/grid_preparation.md @@ -1,6 +1,6 @@ # Slot: grid_preparation -URI: [cdp-meta:grid_preparation](https://cryoetdataportal.czscience.com/schema/metadata/grid_preparation) +URI: [cdp-meta:grid_preparation](metadatagrid_preparation) diff --git a/schema/v1.1.0/metadata-docs/ground_truth_status.md b/schema/v1.1.0/metadata-docs/ground_truth_status.md index d9ce70fbf..4c0df4141 100644 --- a/schema/v1.1.0/metadata-docs/ground_truth_status.md +++ b/schema/v1.1.0/metadata-docs/ground_truth_status.md @@ -5,7 +5,7 @@ _Whether an annotation is considered ground truth, as determined by the annotato -URI: [cdp-meta:ground_truth_status](https://cryoetdataportal.czscience.com/schema/metadata/ground_truth_status) +URI: [cdp-meta:ground_truth_status](metadataground_truth_status) @@ -45,7 +45,7 @@ URI: [cdp-meta:ground_truth_status](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:ground_truth_status](https://cryoetdataportal.czscience.com/schem name: ground_truth_status description: Whether an annotation is considered ground truth, as determined by the annotator. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_status rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/ground_truth_used.md b/schema/v1.1.0/metadata-docs/ground_truth_used.md index fe00c1727..18d36f3f8 100644 --- a/schema/v1.1.0/metadata-docs/ground_truth_used.md +++ b/schema/v1.1.0/metadata-docs/ground_truth_used.md @@ -5,7 +5,7 @@ _Annotation filename used as ground truth for precision and recall_ -URI: [cdp-meta:ground_truth_used](https://cryoetdataportal.czscience.com/schema/metadata/ground_truth_used) +URI: [cdp-meta:ground_truth_used](metadataground_truth_used) @@ -45,7 +45,7 @@ URI: [cdp-meta:ground_truth_used](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:ground_truth_used](https://cryoetdataportal.czscience.com/schema/ ```yaml name: ground_truth_used description: Annotation filename used as ground truth for precision and recall -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_used rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/id.md b/schema/v1.1.0/metadata-docs/id.md index 3e2e5bad5..3dbb58b07 100644 --- a/schema/v1.1.0/metadata-docs/id.md +++ b/schema/v1.1.0/metadata-docs/id.md @@ -1,6 +1,6 @@ # Slot: id -URI: [cdp-meta:id](https://cryoetdataportal.czscience.com/schema/metadata/id) +URI: [cdp-meta:id](metadataid) diff --git a/schema/v1.1.0/metadata-docs/image_corrector.md b/schema/v1.1.0/metadata-docs/image_corrector.md index 90797f8e1..6e8a1e8d0 100644 --- a/schema/v1.1.0/metadata-docs/image_corrector.md +++ b/schema/v1.1.0/metadata-docs/image_corrector.md @@ -5,7 +5,7 @@ _Image corrector setup_ -URI: [cdp-meta:image_corrector](https://cryoetdataportal.czscience.com/schema/metadata/image_corrector) +URI: [cdp-meta:image_corrector](metadataimage_corrector) @@ -45,7 +45,7 @@ URI: [cdp-meta:image_corrector](https://cryoetdataportal.czscience.com/schema/me ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:image_corrector](https://cryoetdataportal.czscience.com/schema/me ```yaml name: image_corrector description: Image corrector setup -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_image_corrector rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/index.md b/schema/v1.1.0/metadata-docs/index.md index e9c1ddc62..18409657a 100644 --- a/schema/v1.1.0/metadata-docs/index.md +++ b/schema/v1.1.0/metadata-docs/index.md @@ -2,7 +2,7 @@ -URI: https://cryoetdataportal.czscience.com/schema-docs/metadata +URI: metadata Name: cdp-meta diff --git a/schema/v1.1.0/metadata-docs/is_corresponding.md b/schema/v1.1.0/metadata-docs/is_corresponding.md index 67226abb2..c82c6767c 100644 --- a/schema/v1.1.0/metadata-docs/is_corresponding.md +++ b/schema/v1.1.0/metadata-docs/is_corresponding.md @@ -1,6 +1,6 @@ # Slot: is_corresponding -URI: [cdp-meta:is_corresponding](https://cryoetdataportal.czscience.com/schema/metadata/is_corresponding) +URI: [cdp-meta:is_corresponding](metadatais_corresponding) diff --git a/schema/v1.1.0/metadata-docs/is_curator_recommended.md b/schema/v1.1.0/metadata-docs/is_curator_recommended.md index dcea34198..42ee82f41 100644 --- a/schema/v1.1.0/metadata-docs/is_curator_recommended.md +++ b/schema/v1.1.0/metadata-docs/is_curator_recommended.md @@ -5,7 +5,7 @@ _This annotation is recommended by the curator to be preferred for this object t -URI: [cdp-meta:is_curator_recommended](https://cryoetdataportal.czscience.com/schema/metadata/is_curator_recommended) +URI: [cdp-meta:is_curator_recommended](metadatais_curator_recommended) @@ -45,7 +45,7 @@ URI: [cdp-meta:is_curator_recommended](https://cryoetdataportal.czscience.com/sc ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:is_curator_recommended](https://cryoetdataportal.czscience.com/sc name: is_curator_recommended description: This annotation is recommended by the curator to be preferred for this object type. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_is_curator_recommended rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/is_primary_annotator.md b/schema/v1.1.0/metadata-docs/is_primary_annotator.md index 6dc61da38..8026d3990 100644 --- a/schema/v1.1.0/metadata-docs/is_primary_annotator.md +++ b/schema/v1.1.0/metadata-docs/is_primary_annotator.md @@ -5,7 +5,7 @@ _Whether the author is a primary author._ -URI: [cdp-meta:is_primary_annotator](https://cryoetdataportal.czscience.com/schema/metadata/is_primary_annotator) +URI: [cdp-meta:is_primary_annotator](metadatais_primary_annotator) @@ -45,7 +45,7 @@ URI: [cdp-meta:is_primary_annotator](https://cryoetdataportal.czscience.com/sche ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:is_primary_annotator](https://cryoetdataportal.czscience.com/sche ```yaml name: is_primary_annotator description: Whether the author is a primary author. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/is_primary_author.md b/schema/v1.1.0/metadata-docs/is_primary_author.md index 8d832acb9..6d1c495a8 100644 --- a/schema/v1.1.0/metadata-docs/is_primary_author.md +++ b/schema/v1.1.0/metadata-docs/is_primary_author.md @@ -5,7 +5,7 @@ _Whether the author is a primary author._ -URI: [cdp-meta:is_primary_author](https://cryoetdataportal.czscience.com/schema/metadata/is_primary_author) +URI: [cdp-meta:is_primary_author](metadatais_primary_author) @@ -45,7 +45,7 @@ URI: [cdp-meta:is_primary_author](https://cryoetdataportal.czscience.com/schema/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:is_primary_author](https://cryoetdataportal.czscience.com/schema/ ```yaml name: is_primary_author description: Whether the author is a primary author. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/is_visualization_default.md b/schema/v1.1.0/metadata-docs/is_visualization_default.md index c3eaf1159..b88deff37 100644 --- a/schema/v1.1.0/metadata-docs/is_visualization_default.md +++ b/schema/v1.1.0/metadata-docs/is_visualization_default.md @@ -5,7 +5,7 @@ _This annotation will be rendered in neuroglancer by default._ -URI: [cdp-meta:is_visualization_default](https://cryoetdataportal.czscience.com/schema/metadata/is_visualization_default) +URI: [cdp-meta:is_visualization_default](metadatais_visualization_default) @@ -45,7 +45,7 @@ URI: [cdp-meta:is_visualization_default](https://cryoetdataportal.czscience.com/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:is_visualization_default](https://cryoetdataportal.czscience.com/ ```yaml name: is_visualization_default description: This annotation will be rendered in neuroglancer by default. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_file_is_visualization_default rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/key_photos.md b/schema/v1.1.0/metadata-docs/key_photos.md index d3d3ae8cf..230915f42 100644 --- a/schema/v1.1.0/metadata-docs/key_photos.md +++ b/schema/v1.1.0/metadata-docs/key_photos.md @@ -1,6 +1,6 @@ # Slot: key_photos -URI: [cdp-meta:key_photos](https://cryoetdataportal.czscience.com/schema/metadata/key_photos) +URI: [cdp-meta:key_photos](metadatakey_photos) diff --git a/schema/v1.1.0/metadata-docs/last_modified_date.md b/schema/v1.1.0/metadata-docs/last_modified_date.md index 6e7c8a5c2..0de70f700 100644 --- a/schema/v1.1.0/metadata-docs/last_modified_date.md +++ b/schema/v1.1.0/metadata-docs/last_modified_date.md @@ -5,7 +5,7 @@ _The date a piece of data was last modified on the cryoET data portal._ -URI: [cdp-meta:last_modified_date](https://cryoetdataportal.czscience.com/schema/metadata/last_modified_date) +URI: [cdp-meta:last_modified_date](metadatalast_modified_date) @@ -47,7 +47,7 @@ URI: [cdp-meta:last_modified_date](https://cryoetdataportal.czscience.com/schema ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [cdp-meta:last_modified_date](https://cryoetdataportal.czscience.com/schema ```yaml name: last_modified_date description: The date a piece of data was last modified on the cryoET data portal. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: last_modified_date owner: DateStamp diff --git a/schema/v1.1.0/metadata-docs/manufacturer.md b/schema/v1.1.0/metadata-docs/manufacturer.md index fd08619bf..f7e49cc29 100644 --- a/schema/v1.1.0/metadata-docs/manufacturer.md +++ b/schema/v1.1.0/metadata-docs/manufacturer.md @@ -1,6 +1,6 @@ # Slot: manufacturer -URI: [cdp-meta:manufacturer](https://cryoetdataportal.czscience.com/schema/metadata/manufacturer) +URI: [cdp-meta:manufacturer](metadatamanufacturer) diff --git a/schema/v1.1.0/metadata-docs/max.md b/schema/v1.1.0/metadata-docs/max.md index ae462b631..082159479 100644 --- a/schema/v1.1.0/metadata-docs/max.md +++ b/schema/v1.1.0/metadata-docs/max.md @@ -5,7 +5,7 @@ _Maximal tilt angle in degrees_ -URI: [cdp-meta:max](https://cryoetdataportal.czscience.com/schema/metadata/max) +URI: [cdp-meta:max](metadatamax) @@ -45,7 +45,7 @@ URI: [cdp-meta:max](https://cryoetdataportal.czscience.com/schema/metadata/max) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:max](https://cryoetdataportal.czscience.com/schema/metadata/max) ```yaml name: max description: Maximal tilt angle in degrees -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_max rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/microscope_additional_info.md b/schema/v1.1.0/metadata-docs/microscope_additional_info.md index d9440aee4..4b463e36c 100644 --- a/schema/v1.1.0/metadata-docs/microscope_additional_info.md +++ b/schema/v1.1.0/metadata-docs/microscope_additional_info.md @@ -5,7 +5,7 @@ _Other microscope optical setup information, in addition to energy filter, phase -URI: [cdp-meta:microscope_additional_info](https://cryoetdataportal.czscience.com/schema/metadata/microscope_additional_info) +URI: [cdp-meta:microscope_additional_info](metadatamicroscope_additional_info) @@ -45,7 +45,7 @@ URI: [cdp-meta:microscope_additional_info](https://cryoetdataportal.czscience.co ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:microscope_additional_info](https://cryoetdataportal.czscience.co name: microscope_additional_info description: Other microscope optical setup information, in addition to energy filter, phase plate and image corrector -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_additional_info rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/microscope_optical_setup.md b/schema/v1.1.0/metadata-docs/microscope_optical_setup.md index 6087adc4e..d1de6ce81 100644 --- a/schema/v1.1.0/metadata-docs/microscope_optical_setup.md +++ b/schema/v1.1.0/metadata-docs/microscope_optical_setup.md @@ -5,7 +5,7 @@ _The optical setup of the microscope used to collect the tilt series._ -URI: [cdp-meta:microscope_optical_setup](https://cryoetdataportal.czscience.com/schema/metadata/microscope_optical_setup) +URI: [cdp-meta:microscope_optical_setup](metadatamicroscope_optical_setup) @@ -45,7 +45,7 @@ URI: [cdp-meta:microscope_optical_setup](https://cryoetdataportal.czscience.com/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:microscope_optical_setup](https://cryoetdataportal.czscience.com/ ```yaml name: microscope_optical_setup description: The optical setup of the microscope used to collect the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: microscope_optical_setup owner: TiltSeries diff --git a/schema/v1.1.0/metadata-docs/min.md b/schema/v1.1.0/metadata-docs/min.md index a1b6a4fa1..9611ef767 100644 --- a/schema/v1.1.0/metadata-docs/min.md +++ b/schema/v1.1.0/metadata-docs/min.md @@ -5,7 +5,7 @@ _Minimal tilt angle in degrees_ -URI: [cdp-meta:min](https://cryoetdataportal.czscience.com/schema/metadata/min) +URI: [cdp-meta:min](metadatamin) @@ -45,7 +45,7 @@ URI: [cdp-meta:min](https://cryoetdataportal.czscience.com/schema/metadata/min) ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:min](https://cryoetdataportal.czscience.com/schema/metadata/min) ```yaml name: min description: Minimal tilt angle in degrees -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_min rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/model.md b/schema/v1.1.0/metadata-docs/model.md index 18d976904..162542d05 100644 --- a/schema/v1.1.0/metadata-docs/model.md +++ b/schema/v1.1.0/metadata-docs/model.md @@ -1,6 +1,6 @@ # Slot: model -URI: [cdp-meta:model](https://cryoetdataportal.czscience.com/schema/metadata/model) +URI: [cdp-meta:model](metadatamodel) diff --git a/schema/v1.1.0/metadata-docs/name.md b/schema/v1.1.0/metadata-docs/name.md index 90e8901fc..2cbccc771 100644 --- a/schema/v1.1.0/metadata-docs/name.md +++ b/schema/v1.1.0/metadata-docs/name.md @@ -1,6 +1,6 @@ # Slot: name -URI: [cdp-meta:name](https://cryoetdataportal.czscience.com/schema/metadata/name) +URI: [cdp-meta:name](metadataname) diff --git a/schema/v1.1.0/metadata-docs/object_count.md b/schema/v1.1.0/metadata-docs/object_count.md index 27db3f5a1..7ed2b2289 100644 --- a/schema/v1.1.0/metadata-docs/object_count.md +++ b/schema/v1.1.0/metadata-docs/object_count.md @@ -5,7 +5,7 @@ _Number of objects identified_ -URI: [cdp-meta:object_count](https://cryoetdataportal.czscience.com/schema/metadata/object_count) +URI: [cdp-meta:object_count](metadataobject_count) @@ -45,7 +45,7 @@ URI: [cdp-meta:object_count](https://cryoetdataportal.czscience.com/schema/metad ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:object_count](https://cryoetdataportal.czscience.com/schema/metad ```yaml name: object_count description: Number of objects identified -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_object_count rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/offset.md b/schema/v1.1.0/metadata-docs/offset.md index c03694aae..f5c82ccc6 100644 --- a/schema/v1.1.0/metadata-docs/offset.md +++ b/schema/v1.1.0/metadata-docs/offset.md @@ -5,7 +5,7 @@ _The offset of a tomogram in voxels in each dimension relative to the canonical -URI: [cdp-meta:offset](https://cryoetdataportal.czscience.com/schema/metadata/offset) +URI: [cdp-meta:offset](metadataoffset) @@ -45,7 +45,7 @@ URI: [cdp-meta:offset](https://cryoetdataportal.czscience.com/schema/metadata/of ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:offset](https://cryoetdataportal.czscience.com/schema/metadata/of name: offset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: offset owner: Tomogram diff --git a/schema/v1.1.0/metadata-docs/other_setup.md b/schema/v1.1.0/metadata-docs/other_setup.md index 14664c5b4..72b67d1ef 100644 --- a/schema/v1.1.0/metadata-docs/other_setup.md +++ b/schema/v1.1.0/metadata-docs/other_setup.md @@ -1,6 +1,6 @@ # Slot: other_setup -URI: [cdp-meta:other_setup](https://cryoetdataportal.czscience.com/schema/metadata/other_setup) +URI: [cdp-meta:other_setup](metadataother_setup) diff --git a/schema/v1.1.0/metadata-docs/path.md b/schema/v1.1.0/metadata-docs/path.md index 483c7425c..02440c9e6 100644 --- a/schema/v1.1.0/metadata-docs/path.md +++ b/schema/v1.1.0/metadata-docs/path.md @@ -5,7 +5,7 @@ _Path to the annotation file relative to the dataset root._ -URI: [cdp-meta:path](https://cryoetdataportal.czscience.com/schema/metadata/path) +URI: [cdp-meta:path](metadatapath) @@ -45,7 +45,7 @@ URI: [cdp-meta:path](https://cryoetdataportal.czscience.com/schema/metadata/path ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:path](https://cryoetdataportal.czscience.com/schema/metadata/path ```yaml name: path description: Path to the annotation file relative to the dataset root. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_file_path rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/phase_plate.md b/schema/v1.1.0/metadata-docs/phase_plate.md index d1271287f..8dfabd07d 100644 --- a/schema/v1.1.0/metadata-docs/phase_plate.md +++ b/schema/v1.1.0/metadata-docs/phase_plate.md @@ -5,7 +5,7 @@ _Phase plate configuration_ -URI: [cdp-meta:phase_plate](https://cryoetdataportal.czscience.com/schema/metadata/phase_plate) +URI: [cdp-meta:phase_plate](metadataphase_plate) @@ -45,7 +45,7 @@ URI: [cdp-meta:phase_plate](https://cryoetdataportal.czscience.com/schema/metada ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:phase_plate](https://cryoetdataportal.czscience.com/schema/metada ```yaml name: phase_plate description: Phase plate configuration -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_phase_plate rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/pixel_spacing.md b/schema/v1.1.0/metadata-docs/pixel_spacing.md index 5bb126e57..fb7e441a8 100644 --- a/schema/v1.1.0/metadata-docs/pixel_spacing.md +++ b/schema/v1.1.0/metadata-docs/pixel_spacing.md @@ -5,7 +5,7 @@ _Pixel spacing for the tilt series_ -URI: [cdp-meta:pixel_spacing](https://cryoetdataportal.czscience.com/schema/metadata/pixel_spacing) +URI: [cdp-meta:pixel_spacing](metadatapixel_spacing) @@ -45,7 +45,7 @@ URI: [cdp-meta:pixel_spacing](https://cryoetdataportal.czscience.com/schema/meta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:pixel_spacing](https://cryoetdataportal.czscience.com/schema/meta ```yaml name: pixel_spacing description: Pixel spacing for the tilt series -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_pixel_spacing rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/precision.md b/schema/v1.1.0/metadata-docs/precision.md index 1ac0b5301..b56815d5e 100644 --- a/schema/v1.1.0/metadata-docs/precision.md +++ b/schema/v1.1.0/metadata-docs/precision.md @@ -5,7 +5,7 @@ _Describe the confidence level of the annotation. Precision is defined as the % -URI: [cdp-meta:precision](https://cryoetdataportal.czscience.com/schema/metadata/precision) +URI: [cdp-meta:precision](metadataprecision) @@ -45,7 +45,7 @@ URI: [cdp-meta:precision](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:precision](https://cryoetdataportal.czscience.com/schema/metadata name: precision description: Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_precision rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/processing.md b/schema/v1.1.0/metadata-docs/processing.md index 7e7f70f76..372d17edc 100644 --- a/schema/v1.1.0/metadata-docs/processing.md +++ b/schema/v1.1.0/metadata-docs/processing.md @@ -5,7 +5,7 @@ _Describe additional processing used to derive the tomogram_ -URI: [cdp-meta:processing](https://cryoetdataportal.czscience.com/schema/metadata/processing) +URI: [cdp-meta:processing](metadataprocessing) @@ -45,7 +45,7 @@ URI: [cdp-meta:processing](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:processing](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: processing description: Describe additional processing used to derive the tomogram -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_processing rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/processing_software.md b/schema/v1.1.0/metadata-docs/processing_software.md index 315182f18..30bbce95c 100644 --- a/schema/v1.1.0/metadata-docs/processing_software.md +++ b/schema/v1.1.0/metadata-docs/processing_software.md @@ -5,7 +5,7 @@ _Processing software used to derive the tomogram_ -URI: [cdp-meta:processing_software](https://cryoetdataportal.czscience.com/schema/metadata/processing_software) +URI: [cdp-meta:processing_software](metadataprocessing_software) @@ -45,7 +45,7 @@ URI: [cdp-meta:processing_software](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:processing_software](https://cryoetdataportal.czscience.com/schem ```yaml name: processing_software description: Processing software used to derive the tomogram -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_processing_software rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/recall.md b/schema/v1.1.0/metadata-docs/recall.md index 0be0f3a3d..8d8c39d71 100644 --- a/schema/v1.1.0/metadata-docs/recall.md +++ b/schema/v1.1.0/metadata-docs/recall.md @@ -5,7 +5,7 @@ _Describe the confidence level of the annotation. Recall is defined as the % of -URI: [cdp-meta:recall](https://cryoetdataportal.czscience.com/schema/metadata/recall) +URI: [cdp-meta:recall](metadatarecall) @@ -45,7 +45,7 @@ URI: [cdp-meta:recall](https://cryoetdataportal.czscience.com/schema/metadata/re ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:recall](https://cryoetdataportal.czscience.com/schema/metadata/re name: recall description: Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_recall rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/reconstruction_method.md b/schema/v1.1.0/metadata-docs/reconstruction_method.md index 515d881d9..4271f498f 100644 --- a/schema/v1.1.0/metadata-docs/reconstruction_method.md +++ b/schema/v1.1.0/metadata-docs/reconstruction_method.md @@ -5,7 +5,7 @@ _Describe reconstruction method (Weighted back-projection, SART, SIRT)_ -URI: [cdp-meta:reconstruction_method](https://cryoetdataportal.czscience.com/schema/metadata/reconstruction_method) +URI: [cdp-meta:reconstruction_method](metadatareconstruction_method) @@ -45,7 +45,7 @@ URI: [cdp-meta:reconstruction_method](https://cryoetdataportal.czscience.com/sch ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:reconstruction_method](https://cryoetdataportal.czscience.com/sch ```yaml name: reconstruction_method description: Describe reconstruction method (Weighted back-projection, SART, SIRT) -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_method rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/reconstruction_software.md b/schema/v1.1.0/metadata-docs/reconstruction_software.md index 698a347ab..e1f88adf6 100644 --- a/schema/v1.1.0/metadata-docs/reconstruction_software.md +++ b/schema/v1.1.0/metadata-docs/reconstruction_software.md @@ -5,7 +5,7 @@ _Name of software used for reconstruction_ -URI: [cdp-meta:reconstruction_software](https://cryoetdataportal.czscience.com/schema/metadata/reconstruction_software) +URI: [cdp-meta:reconstruction_software](metadatareconstruction_software) @@ -45,7 +45,7 @@ URI: [cdp-meta:reconstruction_software](https://cryoetdataportal.czscience.com/s ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:reconstruction_software](https://cryoetdataportal.czscience.com/s ```yaml name: reconstruction_software description: Name of software used for reconstruction -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_software rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/related_database_entries.md b/schema/v1.1.0/metadata-docs/related_database_entries.md index fce85dc73..e60497b01 100644 --- a/schema/v1.1.0/metadata-docs/related_database_entries.md +++ b/schema/v1.1.0/metadata-docs/related_database_entries.md @@ -5,7 +5,7 @@ _Comma-separated list of related database entries for the dataset._ -URI: [cdp-meta:related_database_entries](https://cryoetdataportal.czscience.com/schema/metadata/related_database_entries) +URI: [cdp-meta:related_database_entries](metadatarelated_database_entries) @@ -47,7 +47,7 @@ URI: [cdp-meta:related_database_entries](https://cryoetdataportal.czscience.com/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [cdp-meta:related_database_entries](https://cryoetdataportal.czscience.com/ ```yaml name: related_database_entries description: Comma-separated list of related database entries for the dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: related_database_entries owner: CrossReferences diff --git a/schema/v1.1.0/metadata-docs/related_database_links.md b/schema/v1.1.0/metadata-docs/related_database_links.md index 6bd0922c4..1e38a7a68 100644 --- a/schema/v1.1.0/metadata-docs/related_database_links.md +++ b/schema/v1.1.0/metadata-docs/related_database_links.md @@ -5,7 +5,7 @@ _Comma-separated list of related database links for the dataset._ -URI: [cdp-meta:related_database_links](https://cryoetdataportal.czscience.com/schema/metadata/related_database_links) +URI: [cdp-meta:related_database_links](metadatarelated_database_links) @@ -45,7 +45,7 @@ URI: [cdp-meta:related_database_links](https://cryoetdataportal.czscience.com/sc ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:related_database_links](https://cryoetdataportal.czscience.com/sc ```yaml name: related_database_links description: Comma-separated list of related database links for the dataset. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: related_database_links owner: CrossReferences diff --git a/schema/v1.1.0/metadata-docs/release_date.md b/schema/v1.1.0/metadata-docs/release_date.md index 7539c4ea5..5aa8e7f42 100644 --- a/schema/v1.1.0/metadata-docs/release_date.md +++ b/schema/v1.1.0/metadata-docs/release_date.md @@ -5,7 +5,7 @@ _The date a data item was received by the cryoET data portal._ -URI: [cdp-meta:release_date](https://cryoetdataportal.czscience.com/schema/metadata/release_date) +URI: [cdp-meta:release_date](metadatarelease_date) @@ -47,7 +47,7 @@ URI: [cdp-meta:release_date](https://cryoetdataportal.czscience.com/schema/metad ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ URI: [cdp-meta:release_date](https://cryoetdataportal.czscience.com/schema/metad ```yaml name: release_date description: The date a data item was received by the cryoET data portal. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: release_date owner: DateStamp diff --git a/schema/v1.1.0/metadata-docs/sample_preparation.md b/schema/v1.1.0/metadata-docs/sample_preparation.md index 4458c6da0..c9da0de1c 100644 --- a/schema/v1.1.0/metadata-docs/sample_preparation.md +++ b/schema/v1.1.0/metadata-docs/sample_preparation.md @@ -1,6 +1,6 @@ # Slot: sample_preparation -URI: [cdp-meta:sample_preparation](https://cryoetdataportal.czscience.com/schema/metadata/sample_preparation) +URI: [cdp-meta:sample_preparation](metadatasample_preparation) diff --git a/schema/v1.1.0/metadata-docs/sample_type.md b/schema/v1.1.0/metadata-docs/sample_type.md index 357a9aadc..5fa35f9ca 100644 --- a/schema/v1.1.0/metadata-docs/sample_type.md +++ b/schema/v1.1.0/metadata-docs/sample_type.md @@ -1,6 +1,6 @@ # Slot: sample_type -URI: [cdp-meta:sample_type](https://cryoetdataportal.czscience.com/schema/metadata/sample_type) +URI: [cdp-meta:sample_type](metadatasample_type) diff --git a/schema/v1.1.0/metadata-docs/shape.md b/schema/v1.1.0/metadata-docs/shape.md index 0256d25c2..a66575760 100644 --- a/schema/v1.1.0/metadata-docs/shape.md +++ b/schema/v1.1.0/metadata-docs/shape.md @@ -5,7 +5,7 @@ _Describe whether this is a Point, OrientedPoint, or SegmentationMask file_ -URI: [cdp-meta:shape](https://cryoetdataportal.czscience.com/schema/metadata/shape) +URI: [cdp-meta:shape](metadatashape) @@ -45,7 +45,7 @@ URI: [cdp-meta:shape](https://cryoetdataportal.czscience.com/schema/metadata/sha ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:shape](https://cryoetdataportal.czscience.com/schema/metadata/sha name: shape description: Describe whether this is a Point, OrientedPoint, or SegmentationMask file -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_file_shape_type rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/size.md b/schema/v1.1.0/metadata-docs/size.md index 8fe80ba4e..af9deee6d 100644 --- a/schema/v1.1.0/metadata-docs/size.md +++ b/schema/v1.1.0/metadata-docs/size.md @@ -5,7 +5,7 @@ _The size of a tomogram in voxels in each dimension._ -URI: [cdp-meta:size](https://cryoetdataportal.czscience.com/schema/metadata/size) +URI: [cdp-meta:size](metadatasize) @@ -45,7 +45,7 @@ URI: [cdp-meta:size](https://cryoetdataportal.czscience.com/schema/metadata/size ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:size](https://cryoetdataportal.czscience.com/schema/metadata/size ```yaml name: size description: The size of a tomogram in voxels in each dimension. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: size owner: Tomogram diff --git a/schema/v1.1.0/metadata-docs/snapshot.md b/schema/v1.1.0/metadata-docs/snapshot.md index cbde5245f..8e4aa43d2 100644 --- a/schema/v1.1.0/metadata-docs/snapshot.md +++ b/schema/v1.1.0/metadata-docs/snapshot.md @@ -5,7 +5,7 @@ _Path to the dataset preview image relative to the dataset directory root._ -URI: [cdp-meta:snapshot](https://cryoetdataportal.czscience.com/schema/metadata/snapshot) +URI: [cdp-meta:snapshot](metadatasnapshot) @@ -45,7 +45,7 @@ URI: [cdp-meta:snapshot](https://cryoetdataportal.czscience.com/schema/metadata/ ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:snapshot](https://cryoetdataportal.czscience.com/schema/metadata/ ```yaml name: snapshot description: Path to the dataset preview image relative to the dataset directory root. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: snapshot owner: PicturePath diff --git a/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md b/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md index 8272e12c2..6dc77f368 100644 --- a/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md +++ b/schema/v1.1.0/metadata-docs/spherical_aberration_constant.md @@ -5,7 +5,7 @@ _Spherical Aberration Constant of the objective lens in millimeters_ -URI: [cdp-meta:spherical_aberration_constant](https://cryoetdataportal.czscience.com/schema/metadata/spherical_aberration_constant) +URI: [cdp-meta:spherical_aberration_constant](metadataspherical_aberration_constant) @@ -45,7 +45,7 @@ URI: [cdp-meta:spherical_aberration_constant](https://cryoetdataportal.czscience ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:spherical_aberration_constant](https://cryoetdataportal.czscience ```yaml name: spherical_aberration_constant description: Spherical Aberration Constant of the objective lens in millimeters -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_spherical_aberration_constant rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/state.md b/schema/v1.1.0/metadata-docs/state.md index 180cc88e7..e42d35e6a 100644 --- a/schema/v1.1.0/metadata-docs/state.md +++ b/schema/v1.1.0/metadata-docs/state.md @@ -5,7 +5,7 @@ _Molecule state annotated (e.g. open, closed)_ -URI: [cdp-meta:state](https://cryoetdataportal.czscience.com/schema/metadata/state) +URI: [cdp-meta:state](metadatastate) @@ -45,7 +45,7 @@ URI: [cdp-meta:state](https://cryoetdataportal.czscience.com/schema/metadata/sta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:state](https://cryoetdataportal.czscience.com/schema/metadata/sta ```yaml name: state description: Molecule state annotated (e.g. open, closed) -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:annotation_object_state rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/taxonomy_id.md b/schema/v1.1.0/metadata-docs/taxonomy_id.md index b4bc7262a..9fc089fc4 100644 --- a/schema/v1.1.0/metadata-docs/taxonomy_id.md +++ b/schema/v1.1.0/metadata-docs/taxonomy_id.md @@ -5,7 +5,7 @@ _NCBI taxonomy identifier for the organism, e.g. 9606_ -URI: [cdp-meta:taxonomy_id](https://cryoetdataportal.czscience.com/schema/metadata/taxonomy_id) +URI: [cdp-meta:taxonomy_id](metadatataxonomy_id) @@ -45,7 +45,7 @@ URI: [cdp-meta:taxonomy_id](https://cryoetdataportal.czscience.com/schema/metada ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:taxonomy_id](https://cryoetdataportal.czscience.com/schema/metada ```yaml name: taxonomy_id description: NCBI taxonomy identifier for the organism, e.g. 9606 -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:organism_taxid rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/thumbnail.md b/schema/v1.1.0/metadata-docs/thumbnail.md index 5763ed6fd..5651f62a7 100644 --- a/schema/v1.1.0/metadata-docs/thumbnail.md +++ b/schema/v1.1.0/metadata-docs/thumbnail.md @@ -5,7 +5,7 @@ _Path to the thumbnail of preview image relative to the dataset directory root._ -URI: [cdp-meta:thumbnail](https://cryoetdataportal.czscience.com/schema/metadata/thumbnail) +URI: [cdp-meta:thumbnail](metadatathumbnail) @@ -45,7 +45,7 @@ URI: [cdp-meta:thumbnail](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:thumbnail](https://cryoetdataportal.czscience.com/schema/metadata name: thumbnail description: Path to the thumbnail of preview image relative to the dataset directory root. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: thumbnail owner: PicturePath diff --git a/schema/v1.1.0/metadata-docs/tilt_axis.md b/schema/v1.1.0/metadata-docs/tilt_axis.md index b8c721d98..d82dbaf4b 100644 --- a/schema/v1.1.0/metadata-docs/tilt_axis.md +++ b/schema/v1.1.0/metadata-docs/tilt_axis.md @@ -5,7 +5,7 @@ _Rotation angle in degrees_ -URI: [cdp-meta:tilt_axis](https://cryoetdataportal.czscience.com/schema/metadata/tilt_axis) +URI: [cdp-meta:tilt_axis](metadatatilt_axis) @@ -45,7 +45,7 @@ URI: [cdp-meta:tilt_axis](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:tilt_axis](https://cryoetdataportal.czscience.com/schema/metadata ```yaml name: tilt_axis description: Rotation angle in degrees -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_axis rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/tilt_range.md b/schema/v1.1.0/metadata-docs/tilt_range.md index 851388156..32669b776 100644 --- a/schema/v1.1.0/metadata-docs/tilt_range.md +++ b/schema/v1.1.0/metadata-docs/tilt_range.md @@ -5,7 +5,7 @@ _The range of tilt angles in the tilt series._ -URI: [cdp-meta:tilt_range](https://cryoetdataportal.czscience.com/schema/metadata/tilt_range) +URI: [cdp-meta:tilt_range](metadatatilt_range) @@ -45,7 +45,7 @@ URI: [cdp-meta:tilt_range](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:tilt_range](https://cryoetdataportal.czscience.com/schema/metadat ```yaml name: tilt_range description: The range of tilt angles in the tilt series. -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata rank: 1000 alias: tilt_range owner: TiltSeries diff --git a/schema/v1.1.0/metadata-docs/tilt_series_quality.md b/schema/v1.1.0/metadata-docs/tilt_series_quality.md index 2284fe3fa..d290d0c6d 100644 --- a/schema/v1.1.0/metadata-docs/tilt_series_quality.md +++ b/schema/v1.1.0/metadata-docs/tilt_series_quality.md @@ -5,7 +5,7 @@ _Author assessment of tilt series quality within the dataset (1-5, 5 is best)_ -URI: [cdp-meta:tilt_series_quality](https://cryoetdataportal.czscience.com/schema/metadata/tilt_series_quality) +URI: [cdp-meta:tilt_series_quality](metadatatilt_series_quality) @@ -45,7 +45,7 @@ URI: [cdp-meta:tilt_series_quality](https://cryoetdataportal.czscience.com/schem ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:tilt_series_quality](https://cryoetdataportal.czscience.com/schem name: tilt_series_quality description: Author assessment of tilt series quality within the dataset (1-5, 5 is best) -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_series_quality rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/tilt_step.md b/schema/v1.1.0/metadata-docs/tilt_step.md index 24ba20963..7e475d9a8 100644 --- a/schema/v1.1.0/metadata-docs/tilt_step.md +++ b/schema/v1.1.0/metadata-docs/tilt_step.md @@ -5,7 +5,7 @@ _Tilt step in degrees_ -URI: [cdp-meta:tilt_step](https://cryoetdataportal.czscience.com/schema/metadata/tilt_step) +URI: [cdp-meta:tilt_step](metadatatilt_step) @@ -45,7 +45,7 @@ URI: [cdp-meta:tilt_step](https://cryoetdataportal.czscience.com/schema/metadata ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:tilt_step](https://cryoetdataportal.czscience.com/schema/metadata ```yaml name: tilt_step description: Tilt step in degrees -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_step rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/tilting_scheme.md b/schema/v1.1.0/metadata-docs/tilting_scheme.md index b09425d62..222b6e6ac 100644 --- a/schema/v1.1.0/metadata-docs/tilting_scheme.md +++ b/schema/v1.1.0/metadata-docs/tilting_scheme.md @@ -5,7 +5,7 @@ _The order of stage tilting during acquisition of the data_ -URI: [cdp-meta:tilting_scheme](https://cryoetdataportal.czscience.com/schema/metadata/tilting_scheme) +URI: [cdp-meta:tilting_scheme](metadatatilting_scheme) @@ -45,7 +45,7 @@ URI: [cdp-meta:tilting_scheme](https://cryoetdataportal.czscience.com/schema/met ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:tilting_scheme](https://cryoetdataportal.czscience.com/schema/met ```yaml name: tilting_scheme description: The order of stage tilting during acquisition of the data -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilting_scheme rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/tomogram_version.md b/schema/v1.1.0/metadata-docs/tomogram_version.md index b817bc549..797ef3d73 100644 --- a/schema/v1.1.0/metadata-docs/tomogram_version.md +++ b/schema/v1.1.0/metadata-docs/tomogram_version.md @@ -5,7 +5,7 @@ _Version of tomogram using the same software and post-processing. Version of tom -URI: [cdp-meta:tomogram_version](https://cryoetdataportal.czscience.com/schema/metadata/tomogram_version) +URI: [cdp-meta:tomogram_version](metadatatomogram_version) @@ -45,7 +45,7 @@ URI: [cdp-meta:tomogram_version](https://cryoetdataportal.czscience.com/schema/m ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -58,7 +58,7 @@ name: tomogram_version description: Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_version rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/total_flux.md b/schema/v1.1.0/metadata-docs/total_flux.md index be3067c1c..ff0adc024 100644 --- a/schema/v1.1.0/metadata-docs/total_flux.md +++ b/schema/v1.1.0/metadata-docs/total_flux.md @@ -5,7 +5,7 @@ _Number of Electrons reaching the specimen in a square Angstrom area for the ent -URI: [cdp-meta:total_flux](https://cryoetdataportal.czscience.com/schema/metadata/total_flux) +URI: [cdp-meta:total_flux](metadatatotal_flux) @@ -45,7 +45,7 @@ URI: [cdp-meta:total_flux](https://cryoetdataportal.czscience.com/schema/metadat ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -57,7 +57,7 @@ URI: [cdp-meta:total_flux](https://cryoetdataportal.czscience.com/schema/metadat name: total_flux description: Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tiltseries_total_flux rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/voxel_spacing.md b/schema/v1.1.0/metadata-docs/voxel_spacing.md index 96683715d..240fa18bc 100644 --- a/schema/v1.1.0/metadata-docs/voxel_spacing.md +++ b/schema/v1.1.0/metadata-docs/voxel_spacing.md @@ -5,7 +5,7 @@ _Voxel spacing equal in all three axes in angstroms_ -URI: [cdp-meta:voxel_spacing](https://cryoetdataportal.czscience.com/schema/metadata/voxel_spacing) +URI: [cdp-meta:voxel_spacing](metadatavoxel_spacing) @@ -45,7 +45,7 @@ URI: [cdp-meta:voxel_spacing](https://cryoetdataportal.czscience.com/schema/meta ### Schema Source -* from schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +* from schema: metadata @@ -56,7 +56,7 @@ URI: [cdp-meta:voxel_spacing](https://cryoetdataportal.czscience.com/schema/meta ```yaml name: voxel_spacing description: Voxel spacing equal in all three axes in angstroms -from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata +from_schema: metadata exact_mappings: - cdp-common:tomogram_voxel_spacing rank: 1000 diff --git a/schema/v1.1.0/metadata-docs/x.md b/schema/v1.1.0/metadata-docs/x.md index 89107b370..252c747af 100644 --- a/schema/v1.1.0/metadata-docs/x.md +++ b/schema/v1.1.0/metadata-docs/x.md @@ -1,6 +1,6 @@ # Slot: x -URI: [cdp-meta:x](https://cryoetdataportal.czscience.com/schema/metadata/x) +URI: [cdp-meta:x](metadatax) diff --git a/schema/v1.1.0/metadata-docs/y.md b/schema/v1.1.0/metadata-docs/y.md index a54ae633f..dd9a506f5 100644 --- a/schema/v1.1.0/metadata-docs/y.md +++ b/schema/v1.1.0/metadata-docs/y.md @@ -1,6 +1,6 @@ # Slot: y -URI: [cdp-meta:y](https://cryoetdataportal.czscience.com/schema/metadata/y) +URI: [cdp-meta:y](metadatay) diff --git a/schema/v1.1.0/metadata-docs/z.md b/schema/v1.1.0/metadata-docs/z.md index 656be1293..adcb436cc 100644 --- a/schema/v1.1.0/metadata-docs/z.md +++ b/schema/v1.1.0/metadata-docs/z.md @@ -1,6 +1,6 @@ # Slot: z -URI: [cdp-meta:z](https://cryoetdataportal.czscience.com/schema/metadata/z) +URI: [cdp-meta:z](metadataz) diff --git a/schema/v1.1.0/metadata.yaml b/schema/v1.1.0/metadata.yaml index 404bd08c3..c4bc136f5 100644 --- a/schema/v1.1.0/metadata.yaml +++ b/schema/v1.1.0/metadata.yaml @@ -1,9 +1,9 @@ -id: https://cryoetdataportal.czscience.com/schema-docs/metadata +id: metadata name: cdp-meta version: 1.1.0 prefixes: linkml: https://w3id.org/linkml/ - cdp-meta: https://cryoetdataportal.czscience.com/schema/metadata/ + cdp-meta: metadata ORCID: https://orcid.org/ ROR: https://ror.org/ UBERON: http://purl.obolibrary.org/obo/UBERON_ diff --git a/schema/v1.1.0/metadata_materialized.yaml b/schema/v1.1.0/metadata_materialized.yaml index 4e79821e6..3cd766209 100644 --- a/schema/v1.1.0/metadata_materialized.yaml +++ b/schema/v1.1.0/metadata_materialized.yaml @@ -1,5 +1,5 @@ name: cdp-meta -id: https://cryoetdataportal.czscience.com/schema-docs/metadata +id: metadata version: 1.1.0 imports: - linkml:types @@ -9,7 +9,7 @@ prefixes: prefix_reference: https://w3id.org/linkml/ cdp-meta: prefix_prefix: cdp-meta - prefix_reference: https://cryoetdataportal.czscience.com/schema/metadata/ + prefix_reference: metadata ORCID: prefix_prefix: ORCID prefix_reference: https://orcid.org/ @@ -31,7 +31,7 @@ enums: sample_type_enum: name: sample_type_enum description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata permissible_values: cell: text: cell @@ -61,7 +61,7 @@ enums: fiducial_alignment_status_enum: name: fiducial_alignment_status_enum description: Fiducial Alignment method - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata permissible_values: FIDUCIAL: text: FIDUCIAL @@ -72,7 +72,7 @@ enums: tomogram_type_enum: name: tomogram_type_enum description: Tomogram type - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata permissible_values: CANONICAL: text: CANONICAL @@ -80,7 +80,7 @@ enums: annotation_method_type_enum: name: annotation_method_type_enum description: Describes how the annotations were generated. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata permissible_values: manual: text: manual @@ -94,7 +94,7 @@ enums: annotation_shape_enum: name: annotation_shape_enum description: Annotation shape types available on the data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata permissible_values: Point: text: Point @@ -109,13 +109,13 @@ classes: PicturePath: name: PicturePath description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: snapshot: name: snapshot description: Path to the dataset preview image relative to the dataset directory root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: snapshot owner: PicturePath domain_of: @@ -127,7 +127,7 @@ classes: name: thumbnail description: Path to the thumbnail of preview image relative to the dataset directory root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: thumbnail owner: PicturePath domain_of: @@ -138,12 +138,12 @@ classes: Author: name: Author description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name description: The full name of the author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_name alias: name @@ -163,7 +163,7 @@ classes: email: name: email description: The email address of the author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_email alias: email @@ -177,7 +177,7 @@ classes: affiliation_name: name: affiliation_name description: The name of the author's affiliation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_name alias: affiliation_name @@ -191,7 +191,7 @@ classes: affiliation_address: name: affiliation_address description: The address of the author's affiliation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_address alias: affiliation_address @@ -205,7 +205,7 @@ classes: affiliation_identifier: name: affiliation_identifier description: A Research Organization Registry (ROR) identifier. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:affiliation_identifier alias: affiliation_identifier @@ -221,7 +221,7 @@ classes: is_corresponding: name: is_corresponding description: Whether the author is a corresponding author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_corresponding_author_status alias: is_corresponding @@ -235,7 +235,7 @@ classes: is_primary_author: name: is_primary_author description: Whether the author is a primary author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status alias: is_primary_author @@ -249,7 +249,7 @@ classes: name: ORCID description: A unique, persistent identifier for researchers, provided by ORCID. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:orcid alias: ORCID @@ -265,11 +265,11 @@ classes: Annotator: name: Annotator description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_name alias: name @@ -288,7 +288,7 @@ classes: inlined_as_list: true email: name: email - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_email alias: email @@ -301,7 +301,7 @@ classes: inlined_as_list: true affiliation_name: name: affiliation_name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_name alias: affiliation_name @@ -314,7 +314,7 @@ classes: inlined_as_list: true affiliation_address: name: affiliation_address - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_affiliation_address alias: affiliation_address @@ -327,7 +327,7 @@ classes: inlined_as_list: true affiliation_identifier: name: affiliation_identifier - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:affiliation_identifier alias: affiliation_identifier @@ -341,7 +341,7 @@ classes: inlined_as_list: true is_corresponding: name: is_corresponding - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_corresponding_author_status alias: is_corresponding @@ -355,7 +355,7 @@ classes: is_primary_annotator: name: is_primary_annotator description: Whether the author is a primary author. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:author_primary_author_status alias: is_primary_annotator @@ -367,7 +367,7 @@ classes: inlined_as_list: true ORCID: name: ORCID - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:orcid alias: ORCID @@ -383,12 +383,12 @@ classes: name: Funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: funding_agency_name: name: funding_agency_name description: The name of the funding source. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:funding_agency_name alias: funding_agency_name @@ -401,7 +401,7 @@ classes: grant_id: name: grant_id description: Grant identifier provided by the funding agency - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:funding_grant_id alias: grant_id @@ -415,7 +415,7 @@ classes: name: DateStamp description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true slots: - deposition_date @@ -441,7 +441,7 @@ classes: deposition_date: name: deposition_date description: The date a data item was received by the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: deposition_date owner: DateStamp domain_of: @@ -453,7 +453,7 @@ classes: release_date: name: release_date description: The date a data item was received by the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: release_date owner: DateStamp domain_of: @@ -467,7 +467,7 @@ classes: name: last_modified_date description: The date a piece of data was last modified on the cryoET data portal. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: last_modified_date owner: DateStamp domain_of: @@ -480,14 +480,14 @@ classes: DatestampedEntity: name: DatestampedEntity description: An entity with associated deposition, release and last modified dates. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: dates: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: DatestampedEntity domain_of: @@ -499,13 +499,13 @@ classes: AuthoredEntity: name: AuthoredEntity description: An entity with associated authors. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -520,13 +520,13 @@ classes: AnnotatoredEntity: name: AnnotatoredEntity description: An entity with associated annotation authors. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: authors: name: authors description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -541,14 +541,14 @@ classes: FundedEntity: name: FundedEntity description: An entity with associated funding sources. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: funding: name: funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: funding @@ -563,13 +563,13 @@ classes: name: CrossReferencedEntity description: An entity with associated cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: cross_references: name: cross_references description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cross_references owner: CrossReferencedEntity domain_of: @@ -580,13 +580,13 @@ classes: PicturedEntity: name: PicturedEntity description: An entity with associated preview images. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: PicturedEntity domain_of: @@ -598,11 +598,11 @@ classes: Organism: name: Organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:organism_name alias: name @@ -622,7 +622,7 @@ classes: taxonomy_id: name: taxonomy_id description: NCBI taxonomy identifier for the organism, e.g. 9606 - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:organism_taxid alias: taxonomy_id @@ -635,11 +635,11 @@ classes: Tissue: name: Tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tissue_name alias: name @@ -659,7 +659,7 @@ classes: id: name: id description: The UBERON identifier for the tissue. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tissue_id alias: id @@ -676,11 +676,11 @@ classes: CellType: name: CellType description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_name alias: name @@ -699,7 +699,7 @@ classes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_type_id alias: id @@ -716,11 +716,11 @@ classes: CellStrain: name: CellStrain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_strain_name alias: name @@ -739,7 +739,7 @@ classes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_strain_id alias: id @@ -756,11 +756,11 @@ classes: CellComponent: name: CellComponent description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_component_name alias: name @@ -779,7 +779,7 @@ classes: inlined_as_list: true id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:cell_component_id alias: id @@ -797,13 +797,13 @@ classes: name: ExperimentalMetadata description: Metadata describing sample and sample preparation methods used in a cryoET dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata abstract: true attributes: sample_type: name: sample_type description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_sample_type alias: sample_type @@ -816,7 +816,7 @@ classes: sample_preparation: name: sample_preparation description: Describes how the sample was prepared. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:sample_preparation alias: sample_preparation @@ -829,7 +829,7 @@ classes: grid_preparation: name: grid_preparation description: Describes Cryo-ET grid preparation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:grid_preparation alias: grid_preparation @@ -843,7 +843,7 @@ classes: name: other_setup description: Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_other_setup alias: other_setup @@ -856,7 +856,7 @@ classes: organism: name: organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: organism owner: ExperimentalMetadata domain_of: @@ -867,7 +867,7 @@ classes: tissue: name: tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: tissue owner: ExperimentalMetadata domain_of: @@ -878,7 +878,7 @@ classes: cell_type: name: cell_type description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_type owner: ExperimentalMetadata domain_of: @@ -889,7 +889,7 @@ classes: cell_strain: name: cell_strain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_strain owner: ExperimentalMetadata domain_of: @@ -900,7 +900,7 @@ classes: cell_component: name: cell_component description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_component owner: ExperimentalMetadata domain_of: @@ -911,7 +911,7 @@ classes: Dataset: name: Dataset description: High-level description of a cryoET dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata mixins: - DatestampedEntity - AuthoredEntity @@ -924,7 +924,7 @@ classes: name: dataset_identifier description: An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_identifier alias: dataset_identifier @@ -937,7 +937,7 @@ classes: dataset_title: name: dataset_title description: Title of a CryoET dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_title alias: dataset_title @@ -951,7 +951,7 @@ classes: name: dataset_description description: A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:dataset_description alias: dataset_description @@ -965,7 +965,7 @@ classes: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: Dataset domain_of: @@ -977,7 +977,7 @@ classes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -993,7 +993,7 @@ classes: name: funding description: A funding source for a scientific data entity (base for JSON and DB representation). - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: funding @@ -1007,7 +1007,7 @@ classes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: Dataset domain_of: @@ -1019,7 +1019,7 @@ classes: cross_references: name: cross_references description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cross_references owner: Dataset domain_of: @@ -1030,7 +1030,7 @@ classes: sample_type: name: sample_type description: Type of sample imaged in a CryoET study. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_sample_type alias: sample_type @@ -1043,7 +1043,7 @@ classes: sample_preparation: name: sample_preparation description: Describes how the sample was prepared. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:sample_preparation alias: sample_preparation @@ -1056,7 +1056,7 @@ classes: grid_preparation: name: grid_preparation description: Describes Cryo-ET grid preparation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:grid_preparation alias: grid_preparation @@ -1070,7 +1070,7 @@ classes: name: other_setup description: Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:preparation_other_setup alias: other_setup @@ -1083,7 +1083,7 @@ classes: organism: name: organism description: The species from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: organism owner: Dataset domain_of: @@ -1094,7 +1094,7 @@ classes: tissue: name: tissue description: The type of tissue from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: tissue owner: Dataset domain_of: @@ -1105,7 +1105,7 @@ classes: cell_type: name: cell_type description: The cell type from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_type owner: Dataset domain_of: @@ -1116,7 +1116,7 @@ classes: cell_strain: name: cell_strain description: The strain or cell line from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_strain owner: Dataset domain_of: @@ -1127,7 +1127,7 @@ classes: cell_component: name: cell_component description: The cellular component from which the sample was derived. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: cell_component owner: Dataset domain_of: @@ -1138,12 +1138,12 @@ classes: Camera: name: Camera description: The camera used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: manufacturer: name: manufacturer description: Name of the camera manufacturer - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_camera_manufacturer alias: manufacturer @@ -1157,7 +1157,7 @@ classes: model: name: model description: Camera model name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_camera_model alias: model @@ -1171,11 +1171,11 @@ classes: Microscope: name: Microscope description: The microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: manufacturer: name: manufacturer - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_manufacturer alias: manufacturer @@ -1188,7 +1188,7 @@ classes: inlined_as_list: true model: name: model - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_model alias: model @@ -1202,12 +1202,12 @@ classes: MicroscopeOpticalSetup: name: MicroscopeOpticalSetup description: The optical setup of the microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: energy_filter: name: energy_filter description: Energy filter setup used - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_energy_filter alias: energy_filter @@ -1220,7 +1220,7 @@ classes: phase_plate: name: phase_plate description: Phase plate configuration - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_phase_plate alias: phase_plate @@ -1233,7 +1233,7 @@ classes: image_corrector: name: image_corrector description: Image corrector setup - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_image_corrector alias: image_corrector @@ -1246,12 +1246,12 @@ classes: TiltRange: name: TiltRange description: The range of tilt angles in the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: min: name: min description: Minimal tilt angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_min alias: min @@ -1264,7 +1264,7 @@ classes: max: name: max description: Maximal tilt angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_max alias: max @@ -1277,12 +1277,12 @@ classes: TiltSeries: name: TiltSeries description: Metadata describing a tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: acceleration_voltage: name: acceleration_voltage description: Electron Microscope Accelerator voltage in volts - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_acceleration_voltage alias: acceleration_voltage @@ -1295,7 +1295,7 @@ classes: spherical_aberration_constant: name: spherical_aberration_constant description: Spherical Aberration Constant of the objective lens in millimeters - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_spherical_aberration_constant alias: spherical_aberration_constant @@ -1309,7 +1309,7 @@ classes: name: microscope_additional_info description: Other microscope optical setup information, in addition to energy filter, phase plate and image corrector - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_microscope_additional_info alias: microscope_additional_info @@ -1322,7 +1322,7 @@ classes: tilt_axis: name: tilt_axis description: Rotation angle in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_axis alias: tilt_axis @@ -1335,7 +1335,7 @@ classes: tilt_step: name: tilt_step description: Tilt step in degrees - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_step alias: tilt_step @@ -1348,7 +1348,7 @@ classes: tilting_scheme: name: tilting_scheme description: The order of stage tilting during acquisition of the data - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilting_scheme alias: tilting_scheme @@ -1362,7 +1362,7 @@ classes: name: total_flux description: Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_total_flux alias: total_flux @@ -1375,7 +1375,7 @@ classes: data_acquisition_software: name: data_acquisition_software description: Software used to collect data - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_data_acquisition_software alias: data_acquisition_software @@ -1388,7 +1388,7 @@ classes: binning_from_frames: name: binning_from_frames description: Describes the binning factor from frames to tilt series file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_binning_from_frames alias: binning_from_frames @@ -1402,7 +1402,7 @@ classes: name: tilt_series_quality description: Author assessment of tilt series quality within the dataset (1-5, 5 is best) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_tilt_series_quality alias: tilt_series_quality @@ -1415,7 +1415,7 @@ classes: pixel_spacing: name: pixel_spacing description: Pixel spacing for the tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_pixel_spacing alias: pixel_spacing @@ -1428,7 +1428,7 @@ classes: aligned_tiltseries_binning: name: aligned_tiltseries_binning description: Binning factor of the aligned tilt series - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_aligned_tiltseries_binning alias: aligned_tiltseries_binning @@ -1441,7 +1441,7 @@ classes: frames_count: name: frames_count description: Number of frames associated with this tiltseries - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tiltseries_frames_count alias: frames_count @@ -1454,7 +1454,7 @@ classes: camera: name: camera description: The camera used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: camera owner: TiltSeries domain_of: @@ -1465,7 +1465,7 @@ classes: microscope: name: microscope description: The microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: microscope owner: TiltSeries domain_of: @@ -1477,7 +1477,7 @@ classes: name: microscope_optical_setup description: The optical setup of the microscope used to collect the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: microscope_optical_setup owner: TiltSeries domain_of: @@ -1488,7 +1488,7 @@ classes: tilt_range: name: tilt_range description: The range of tilt angles in the tilt series. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: tilt_range owner: TiltSeries domain_of: @@ -1499,12 +1499,12 @@ classes: TomogramSize: name: TomogramSize description: The size of a tomogram in voxels in each dimension. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: x: name: x description: Number of pixels in the 3D data fast axis - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_x alias: x @@ -1518,7 +1518,7 @@ classes: y: name: y description: Number of pixels in the 3D data medium axis - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_y alias: y @@ -1533,7 +1533,7 @@ classes: name: z description: Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_size_z alias: z @@ -1548,11 +1548,11 @@ classes: name: TomogramOffset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: x: name: x - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_x alias: x @@ -1565,7 +1565,7 @@ classes: inlined_as_list: true y: name: y - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_y alias: y @@ -1578,7 +1578,7 @@ classes: inlined_as_list: true z: name: z - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_offset_z alias: z @@ -1592,7 +1592,7 @@ classes: Tomogram: name: Tomogram description: Metadata describing a tomogram. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata mixins: - AuthoredEntity - PicturedEntity @@ -1600,7 +1600,7 @@ classes: voxel_spacing: name: voxel_spacing description: Voxel spacing equal in all three axes in angstroms - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_voxel_spacing alias: voxel_spacing @@ -1614,7 +1614,7 @@ classes: name: fiducial_alignment_status description: Whether the tomographic alignment was computed based on fiducial markers. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_fiducial_alignment_status alias: fiducial_alignment_status @@ -1627,7 +1627,7 @@ classes: ctf_corrected: name: ctf_corrected description: Whether this tomogram is CTF corrected - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_ctf_corrected alias: ctf_corrected @@ -1641,7 +1641,7 @@ classes: name: reconstruction_method description: Describe reconstruction method (Weighted back-projection, SART, SIRT) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_method alias: reconstruction_method @@ -1654,7 +1654,7 @@ classes: reconstruction_software: name: reconstruction_software description: Name of software used for reconstruction - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_reconstruction_software alias: reconstruction_software @@ -1667,7 +1667,7 @@ classes: processing: name: processing description: Describe additional processing used to derive the tomogram - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_processing alias: processing @@ -1680,7 +1680,7 @@ classes: processing_software: name: processing_software description: Processing software used to derive the tomogram - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_processing_software alias: processing_software @@ -1695,7 +1695,7 @@ classes: description: Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_version alias: tomogram_version @@ -1709,7 +1709,7 @@ classes: name: affine_transformation_matrix description: The flip or rotation transformation of this author submitted tomogram is indicated here - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:tomogram_affine_transformation_matrix alias: affine_transformation_matrix @@ -1722,7 +1722,7 @@ classes: size: name: size description: The size of a tomogram in voxels in each dimension. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: size owner: Tomogram domain_of: @@ -1734,7 +1734,7 @@ classes: name: offset description: The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: offset owner: Tomogram domain_of: @@ -1745,7 +1745,7 @@ classes: authors: name: authors description: Author of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -1760,7 +1760,7 @@ classes: key_photos: name: key_photos description: A set of paths to representative images of a piece of data. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: key_photos owner: Tomogram domain_of: @@ -1772,12 +1772,12 @@ classes: AnnotationFile: name: AnnotationFile description: Metadata describing a file containing an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: format: name: format description: File format for this file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_format alias: format @@ -1791,7 +1791,7 @@ classes: name: shape description: Describe whether this is a Point, OrientedPoint, or SegmentationMask file - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_shape_type alias: shape @@ -1804,7 +1804,7 @@ classes: path: name: path description: Path to the annotation file relative to the dataset root. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_path alias: path @@ -1817,7 +1817,7 @@ classes: is_visualization_default: name: is_visualization_default description: This annotation will be rendered in neuroglancer by default. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_file_is_visualization_default alias: is_visualization_default @@ -1830,13 +1830,13 @@ classes: AnnotationConfidence: name: AnnotationConfidence description: Metadata describing the confidence of an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: precision: name: precision description: Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_precision alias: precision @@ -1850,7 +1850,7 @@ classes: name: recall description: Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_confidence_recall alias: recall @@ -1863,7 +1863,7 @@ classes: ground_truth_used: name: ground_truth_used description: Annotation filename used as ground truth for precision and recall - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_used alias: ground_truth_used @@ -1876,11 +1876,11 @@ classes: AnnotationObject: name: AnnotationObject description: Metadata describing the object being annotated. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: id: name: id - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_id alias: id @@ -1896,7 +1896,7 @@ classes: inlined_as_list: true name: name: name - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_name alias: name @@ -1918,7 +1918,7 @@ classes: description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_description alias: description @@ -1931,7 +1931,7 @@ classes: state: name: state description: Molecule state annotated (e.g. open, closed) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_state alias: state @@ -1944,7 +1944,7 @@ classes: Annotation: name: Annotation description: Metadata describing an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata mixins: - DatestampedEntity - AnnotatoredEntity @@ -1953,7 +1953,7 @@ classes: name: annotation_method description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_method alias: annotation_method @@ -1966,7 +1966,7 @@ classes: annotation_method_type: name: annotation_method_type description: Classification of the annotation method based on supervision. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_method_type alias: annotation_method_type @@ -1980,7 +1980,7 @@ classes: name: annotation_publications description: DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_publication alias: annotation_publications @@ -1993,7 +1993,7 @@ classes: annotation_software: name: annotation_software description: Software used for generating this annotation - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_software alias: annotation_software @@ -2007,7 +2007,7 @@ classes: name: ground_truth_status description: Whether an annotation is considered ground truth, as determined by the annotator. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_ground_truth_status alias: ground_truth_status @@ -2020,7 +2020,7 @@ classes: object_count: name: object_count description: Number of objects identified - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_object_count alias: object_count @@ -2034,7 +2034,7 @@ classes: name: is_curator_recommended description: This annotation is recommended by the curator to be preferred for this object type. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata exact_mappings: - cdp-common:annotation_is_curator_recommended alias: is_curator_recommended @@ -2047,7 +2047,7 @@ classes: files: name: files description: Metadata describing a file containing an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: files @@ -2060,7 +2060,7 @@ classes: confidence: name: confidence description: Metadata describing the confidence of an annotation. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: confidence owner: Annotation domain_of: @@ -2071,7 +2071,7 @@ classes: annotation_object: name: annotation_object description: Metadata describing the object being annotated. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: annotation_object owner: Annotation domain_of: @@ -2083,7 +2083,7 @@ classes: name: dates description: A set of dates at which a data item was deposited, published and last modified. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dates owner: Annotation domain_of: @@ -2095,7 +2095,7 @@ classes: authors: name: authors description: Annotator of a scientific data entity. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata multivalued: true list_elements_ordered: true alias: authors @@ -2110,13 +2110,13 @@ classes: CrossReferences: name: CrossReferences description: A set of cross-references to other databases and publications. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata attributes: dataset_publications: name: dataset_publications description: Comma-separated list of DOIs for publications associated with the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dataset_publications owner: CrossReferences domain_of: @@ -2128,7 +2128,7 @@ classes: related_database_entries: name: related_database_entries description: Comma-separated list of related database entries for the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: related_database_entries owner: CrossReferences domain_of: @@ -2140,7 +2140,7 @@ classes: related_database_links: name: related_database_links description: Comma-separated list of related database links for the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: related_database_links owner: CrossReferences domain_of: @@ -2151,7 +2151,7 @@ classes: dataset_citations: name: dataset_citations description: Comma-separated list of DOIs for publications citing the dataset. - from_schema: https://cryoetdataportal.czscience.com/schema-docs/metadata + from_schema: metadata alias: dataset_citations owner: CrossReferences domain_of: From e8eb7116732204f08b788f0d57975ab619faee5f Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 5 Mar 2024 17:53:32 -0800 Subject: [PATCH 6/7] add requirements --- schema/v1.1.0/requirements.txt | 3 +++ schema/v1.1.0/schema.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 schema/v1.1.0/requirements.txt diff --git a/schema/v1.1.0/requirements.txt b/schema/v1.1.0/requirements.txt new file mode 100644 index 000000000..9a091f72f --- /dev/null +++ b/schema/v1.1.0/requirements.txt @@ -0,0 +1,3 @@ +linkml +linkml-runtime +click \ No newline at end of file diff --git a/schema/v1.1.0/schema.py b/schema/v1.1.0/schema.py index 5e5176ea8..303f2bb5f 100644 --- a/schema/v1.1.0/schema.py +++ b/schema/v1.1.0/schema.py @@ -1,5 +1,5 @@ from linkml_runtime.utils.schemaview import SchemaView -from linkml_runtime.dumpers import json_dumper, yaml_dumper +from linkml_runtime.dumpers import yaml_dumper from linkml.utils.helpers import write_to_file import click From f891adf9a36340aa37afa25977964b31403921ae Mon Sep 17 00:00:00 2001 From: uermel Date: Tue, 5 Mar 2024 18:22:45 -0800 Subject: [PATCH 7/7] black linting during build --- schema/v1.1.0/Makefile | 1 + schema/v1.1.0/metadata_models.py | 678 ++++++++++++++++++++++--------- 2 files changed, 481 insertions(+), 198 deletions(-) diff --git a/schema/v1.1.0/Makefile b/schema/v1.1.0/Makefile index a42602a5a..92765d83c 100644 --- a/schema/v1.1.0/Makefile +++ b/schema/v1.1.0/Makefile @@ -11,3 +11,4 @@ build: python schema.py materialize metadata.yaml common.yaml metadata_materialized.yaml gen-doc -d metadata-docs --no-mergeimports --hierarchical-class-view --stacktrace metadata_materialized.yaml gen-pydantic --pydantic-version 2 metadata_materialized.yaml > metadata_models.py + black -l 88 metadata_models.py diff --git a/schema/v1.1.0/metadata_models.py b/schema/v1.1.0/metadata_models.py index 925b9db02..6ed656e75 100644 --- a/schema/v1.1.0/metadata_models.py +++ b/schema/v1.1.0/metadata_models.py @@ -4,9 +4,10 @@ from decimal import Decimal from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator +from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator import re import sys + if sys.version_info >= (3, 8): from typing import Literal else: @@ -16,22 +17,24 @@ metamodel_version = "None" version = "1.1.0" + class ConfiguredBaseModel(BaseModel): model_config = ConfigDict( validate_assignment=True, validate_default=True, - extra = 'forbid', + extra="forbid", arbitrary_types_allowed=True, - use_enum_values = True) + use_enum_values=True, + ) pass - class SampleTypeEnum(str, Enum): """ Type of sample imaged in a CryoET study. """ + # Tomographic data of whole cells or cell sections. cell = "cell" # Tomographic data of tissue sections. @@ -48,432 +51,712 @@ class SampleTypeEnum(str, Enum): in_silico = "in_silico" # Other type of sample. other = "other" - - + class FiducialAlignmentStatusEnum(str, Enum): """ Fiducial Alignment method """ + # Alignment computed based on fiducial markers FIDUCIAL = "FIDUCIAL" # Alignment computed without fiducial markers NON_FIDUCIAL = "NON_FIDUCIAL" - - + class TomogramTypeEnum(str, Enum): """ Tomogram type """ + # Canonical tomogram (basis geometry for all annotations) CANONICAL = "CANONICAL" - - + class AnnotationMethodTypeEnum(str, Enum): """ Describes how the annotations were generated. """ + # Annotations were generated manually. manual = "manual" # Annotations were generated semi-automatically. automated = "automated" # Annotations were generated automatically. hybrid = "hybrid" - - + class AnnotationShapeEnum(str, Enum): """ Annotation shape types available on the data portal. """ + # Annotations were generated manually. Point = "Point" # Annotations were generated semi-automatically. OrientedPoint = "OrientedPoint" # Annotations were generated automatically. SegmentationMask = "SegmentationMask" - - + class PicturePath(ConfiguredBaseModel): """ A set of paths to representative images of a piece of data. """ - snapshot: Optional[str] = Field(None, description="""Path to the dataset preview image relative to the dataset directory root.""") - thumbnail: Optional[str] = Field(None, description="""Path to the thumbnail of preview image relative to the dataset directory root.""") - - + + snapshot: Optional[str] = Field( + None, + description="""Path to the dataset preview image relative to the dataset directory root.""", + ) + thumbnail: Optional[str] = Field( + None, + description="""Path to the thumbnail of preview image relative to the dataset directory root.""", + ) + class Author(ConfiguredBaseModel): """ Author of a scientific data entity. """ + name: Optional[str] = Field(None, description="""The full name of the author.""") - email: Optional[str] = Field(None, description="""The email address of the author.""") - affiliation_name: Optional[str] = Field(None, description="""The name of the author's affiliation.""") - affiliation_address: Optional[str] = Field(None, description="""The address of the author's affiliation.""") - affiliation_identifier: Optional[str] = Field(None, description="""A Research Organization Registry (ROR) identifier.""") - is_corresponding: Optional[bool] = Field(None, description="""Whether the author is a corresponding author.""") - is_primary_author: Optional[bool] = Field(None, description="""Whether the author is a primary author.""") - ORCID: Optional[str] = Field(None, description="""A unique, persistent identifier for researchers, provided by ORCID.""") - - - @field_validator('affiliation_identifier') + email: Optional[str] = Field( + None, description="""The email address of the author.""" + ) + affiliation_name: Optional[str] = Field( + None, description="""The name of the author's affiliation.""" + ) + affiliation_address: Optional[str] = Field( + None, description="""The address of the author's affiliation.""" + ) + affiliation_identifier: Optional[str] = Field( + None, description="""A Research Organization Registry (ROR) identifier.""" + ) + is_corresponding: Optional[bool] = Field( + None, description="""Whether the author is a corresponding author.""" + ) + is_primary_author: Optional[bool] = Field( + None, description="""Whether the author is a primary author.""" + ) + ORCID: Optional[str] = Field( + None, + description="""A unique, persistent identifier for researchers, provided by ORCID.""", + ) + + @field_validator("affiliation_identifier") def pattern_affiliation_identifier(cls, v): - pattern=re.compile(r"^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$") - if isinstance(v,list): + pattern = re.compile(r"^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$") + if isinstance(v, list): for element in v: if not pattern.match(element): - raise ValueError(f"Invalid affiliation_identifier format: {element}") - elif isinstance(v,str): + raise ValueError( + f"Invalid affiliation_identifier format: {element}" + ) + elif isinstance(v, str): if not pattern.match(v): raise ValueError(f"Invalid affiliation_identifier format: {v}") return v - - @field_validator('ORCID') + + @field_validator("ORCID") def pattern_ORCID(cls, v): - pattern=re.compile(r"[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$") - if isinstance(v,list): + pattern = re.compile(r"[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$") + if isinstance(v, list): for element in v: if not pattern.match(element): raise ValueError(f"Invalid ORCID format: {element}") - elif isinstance(v,str): + elif isinstance(v, str): if not pattern.match(v): raise ValueError(f"Invalid ORCID format: {v}") return v - + class Annotator(ConfiguredBaseModel): """ Annotator of a scientific data entity. """ + name: Optional[str] = Field(None) email: Optional[str] = Field(None) affiliation_name: Optional[str] = Field(None) affiliation_address: Optional[str] = Field(None) affiliation_identifier: Optional[str] = Field(None) is_corresponding: Optional[str] = Field(None) - is_primary_annotator: Optional[bool] = Field(None, description="""Whether the author is a primary author.""") + is_primary_annotator: Optional[bool] = Field( + None, description="""Whether the author is a primary author.""" + ) ORCID: Optional[str] = Field(None) - - + class Funding(ConfiguredBaseModel): """ A funding source for a scientific data entity (base for JSON and DB representation). """ - funding_agency_name: Optional[str] = Field(None, description="""The name of the funding source.""") - grant_id: Optional[str] = Field(None, description="""Grant identifier provided by the funding agency""") - - + + funding_agency_name: Optional[str] = Field( + None, description="""The name of the funding source.""" + ) + grant_id: Optional[str] = Field( + None, description="""Grant identifier provided by the funding agency""" + ) + class DateStamp(ConfiguredBaseModel): """ A set of dates at which a data item was deposited, published and last modified. """ - deposition_date: date = Field(..., description="""The date a data item was received by the cryoET data portal.""") - release_date: date = Field(..., description="""The date a data item was received by the cryoET data portal.""") - last_modified_date: date = Field(..., description="""The date a piece of data was last modified on the cryoET data portal.""") - - + + deposition_date: date = Field( + ..., + description="""The date a data item was received by the cryoET data portal.""", + ) + release_date: date = Field( + ..., + description="""The date a data item was received by the cryoET data portal.""", + ) + last_modified_date: date = Field( + ..., + description="""The date a piece of data was last modified on the cryoET data portal.""", + ) + class DatestampedEntity(ConfiguredBaseModel): """ An entity with associated deposition, release and last modified dates. """ - dates: DateStamp = Field(..., description="""A set of dates at which a data item was deposited, published and last modified.""") - - + + dates: DateStamp = Field( + ..., + description="""A set of dates at which a data item was deposited, published and last modified.""", + ) + class AuthoredEntity(ConfiguredBaseModel): """ An entity with associated authors. """ - authors: List[Author] = Field(default_factory=list, description="""Author of a scientific data entity.""") - - + + authors: List[Author] = Field( + default_factory=list, description="""Author of a scientific data entity.""" + ) + class AnnotatoredEntity(ConfiguredBaseModel): """ An entity with associated annotation authors. """ - authors: List[Annotator] = Field(default_factory=list, description="""Annotator of a scientific data entity.""") - - + + authors: List[Annotator] = Field( + default_factory=list, description="""Annotator of a scientific data entity.""" + ) + class FundedEntity(ConfiguredBaseModel): """ An entity with associated funding sources. """ - funding: Optional[List[Funding]] = Field(default_factory=list, description="""A funding source for a scientific data entity (base for JSON and DB representation).""") - - + + funding: Optional[List[Funding]] = Field( + default_factory=list, + description="""A funding source for a scientific data entity (base for JSON and DB representation).""", + ) + class CrossReferencedEntity(ConfiguredBaseModel): """ An entity with associated cross-references to other databases and publications. """ - cross_references: Optional[CrossReferences] = Field(None, description="""A set of cross-references to other databases and publications.""") - - + + cross_references: Optional[CrossReferences] = Field( + None, + description="""A set of cross-references to other databases and publications.""", + ) + class PicturedEntity(ConfiguredBaseModel): """ An entity with associated preview images. """ - key_photos: PicturePath = Field(..., description="""A set of paths to representative images of a piece of data.""") - - + + key_photos: PicturePath = Field( + ..., + description="""A set of paths to representative images of a piece of data.""", + ) + class Organism(ConfiguredBaseModel): """ The species from which the sample was derived. """ + name: Optional[str] = Field(None) - taxonomy_id: Optional[str] = Field(None, description="""NCBI taxonomy identifier for the organism, e.g. 9606""") - - + taxonomy_id: Optional[str] = Field( + None, description="""NCBI taxonomy identifier for the organism, e.g. 9606""" + ) + class Tissue(ConfiguredBaseModel): """ The type of tissue from which the sample was derived. """ + name: Optional[str] = Field(None) - id: Optional[str] = Field(None, description="""The UBERON identifier for the tissue.""") - - + id: Optional[str] = Field( + None, description="""The UBERON identifier for the tissue.""" + ) + class CellType(ConfiguredBaseModel): """ The cell type from which the sample was derived. """ + name: Optional[str] = Field(None) id: Optional[str] = Field(None) - - + class CellStrain(ConfiguredBaseModel): """ The strain or cell line from which the sample was derived. """ + name: Optional[str] = Field(None) id: Optional[str] = Field(None) - - + class CellComponent(ConfiguredBaseModel): """ The cellular component from which the sample was derived. """ + name: Optional[str] = Field(None) id: Optional[str] = Field(None) - - + class ExperimentalMetadata(ConfiguredBaseModel): """ Metadata describing sample and sample preparation methods used in a cryoET dataset. """ - sample_type: Optional[SampleTypeEnum] = Field(None, description="""Type of sample imaged in a CryoET study.""") - sample_preparation: Optional[str] = Field(None, description="""Describes how the sample was prepared.""") - grid_preparation: Optional[str] = Field(None, description="""Describes Cryo-ET grid preparation.""") - other_setup: Optional[str] = Field(None, description="""Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication.""") - organism: Optional[Organism] = Field(None, description="""The species from which the sample was derived.""") - tissue: Optional[Tissue] = Field(None, description="""The type of tissue from which the sample was derived.""") - cell_type: Optional[CellType] = Field(None, description="""The cell type from which the sample was derived.""") - cell_strain: Optional[CellStrain] = Field(None, description="""The strain or cell line from which the sample was derived.""") - cell_component: Optional[CellComponent] = Field(None, description="""The cellular component from which the sample was derived.""") - - -class Dataset(ExperimentalMetadata, PicturedEntity, CrossReferencedEntity, FundedEntity, AuthoredEntity, DatestampedEntity): + sample_type: Optional[SampleTypeEnum] = Field( + None, description="""Type of sample imaged in a CryoET study.""" + ) + sample_preparation: Optional[str] = Field( + None, description="""Describes how the sample was prepared.""" + ) + grid_preparation: Optional[str] = Field( + None, description="""Describes Cryo-ET grid preparation.""" + ) + other_setup: Optional[str] = Field( + None, + description="""Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication.""", + ) + organism: Optional[Organism] = Field( + None, description="""The species from which the sample was derived.""" + ) + tissue: Optional[Tissue] = Field( + None, description="""The type of tissue from which the sample was derived.""" + ) + cell_type: Optional[CellType] = Field( + None, description="""The cell type from which the sample was derived.""" + ) + cell_strain: Optional[CellStrain] = Field( + None, + description="""The strain or cell line from which the sample was derived.""", + ) + cell_component: Optional[CellComponent] = Field( + None, + description="""The cellular component from which the sample was derived.""", + ) + + +class Dataset( + ExperimentalMetadata, + PicturedEntity, + CrossReferencedEntity, + FundedEntity, + AuthoredEntity, + DatestampedEntity, +): """ High-level description of a cryoET dataset. """ - dataset_identifier: Optional[int] = Field(None, description="""An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree.""") - dataset_title: Optional[str] = Field(None, description="""Title of a CryoET dataset.""") - dataset_description: Optional[str] = Field(None, description="""A short description of a CryoET dataset, similar to an abstract for a journal article or dataset.""") - dates: DateStamp = Field(..., description="""A set of dates at which a data item was deposited, published and last modified.""") - authors: List[Author] = Field(default_factory=list, description="""Author of a scientific data entity.""") - funding: Optional[List[Funding]] = Field(default_factory=list, description="""A funding source for a scientific data entity (base for JSON and DB representation).""") - key_photos: PicturePath = Field(..., description="""A set of paths to representative images of a piece of data.""") - cross_references: Optional[CrossReferences] = Field(None, description="""A set of cross-references to other databases and publications.""") - sample_type: Optional[str] = Field(None, description="""Type of sample imaged in a CryoET study.""") - sample_preparation: Optional[str] = Field(None, description="""Describes how the sample was prepared.""") - grid_preparation: Optional[str] = Field(None, description="""Describes Cryo-ET grid preparation.""") - other_setup: Optional[str] = Field(None, description="""Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication.""") - organism: Optional[Organism] = Field(None, description="""The species from which the sample was derived.""") - tissue: Optional[Tissue] = Field(None, description="""The type of tissue from which the sample was derived.""") - cell_type: Optional[CellType] = Field(None, description="""The cell type from which the sample was derived.""") - cell_strain: Optional[CellStrain] = Field(None, description="""The strain or cell line from which the sample was derived.""") - cell_component: Optional[CellComponent] = Field(None, description="""The cellular component from which the sample was derived.""") - - + + dataset_identifier: Optional[int] = Field( + None, + description="""An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree.""", + ) + dataset_title: Optional[str] = Field( + None, description="""Title of a CryoET dataset.""" + ) + dataset_description: Optional[str] = Field( + None, + description="""A short description of a CryoET dataset, similar to an abstract for a journal article or dataset.""", + ) + dates: DateStamp = Field( + ..., + description="""A set of dates at which a data item was deposited, published and last modified.""", + ) + authors: List[Author] = Field( + default_factory=list, description="""Author of a scientific data entity.""" + ) + funding: Optional[List[Funding]] = Field( + default_factory=list, + description="""A funding source for a scientific data entity (base for JSON and DB representation).""", + ) + key_photos: PicturePath = Field( + ..., + description="""A set of paths to representative images of a piece of data.""", + ) + cross_references: Optional[CrossReferences] = Field( + None, + description="""A set of cross-references to other databases and publications.""", + ) + sample_type: Optional[str] = Field( + None, description="""Type of sample imaged in a CryoET study.""" + ) + sample_preparation: Optional[str] = Field( + None, description="""Describes how the sample was prepared.""" + ) + grid_preparation: Optional[str] = Field( + None, description="""Describes Cryo-ET grid preparation.""" + ) + other_setup: Optional[str] = Field( + None, + description="""Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication.""", + ) + organism: Optional[Organism] = Field( + None, description="""The species from which the sample was derived.""" + ) + tissue: Optional[Tissue] = Field( + None, description="""The type of tissue from which the sample was derived.""" + ) + cell_type: Optional[CellType] = Field( + None, description="""The cell type from which the sample was derived.""" + ) + cell_strain: Optional[CellStrain] = Field( + None, + description="""The strain or cell line from which the sample was derived.""", + ) + cell_component: Optional[CellComponent] = Field( + None, + description="""The cellular component from which the sample was derived.""", + ) + class Camera(ConfiguredBaseModel): """ The camera used to collect the tilt series. """ - manufacturer: Optional[str] = Field(None, description="""Name of the camera manufacturer""") + + manufacturer: Optional[str] = Field( + None, description="""Name of the camera manufacturer""" + ) model: Optional[str] = Field(None, description="""Camera model name""") - - + class Microscope(ConfiguredBaseModel): """ The microscope used to collect the tilt series. """ + manufacturer: Optional[str] = Field(None) model: Optional[str] = Field(None) - - + class MicroscopeOpticalSetup(ConfiguredBaseModel): """ The optical setup of the microscope used to collect the tilt series. """ - energy_filter: Optional[str] = Field(None, description="""Energy filter setup used""") - phase_plate: Optional[str] = Field(None, description="""Phase plate configuration""") - image_corrector: Optional[str] = Field(None, description="""Image corrector setup""") - - + + energy_filter: Optional[str] = Field( + None, description="""Energy filter setup used""" + ) + phase_plate: Optional[str] = Field( + None, description="""Phase plate configuration""" + ) + image_corrector: Optional[str] = Field( + None, description="""Image corrector setup""" + ) + class TiltRange(ConfiguredBaseModel): """ The range of tilt angles in the tilt series. """ + min: Optional[float] = Field(None, description="""Minimal tilt angle in degrees""") max: Optional[float] = Field(None, description="""Maximal tilt angle in degrees""") - - + class TiltSeries(ConfiguredBaseModel): """ Metadata describing a tilt series. """ - acceleration_voltage: Optional[int] = Field(None, description="""Electron Microscope Accelerator voltage in volts""") - spherical_aberration_constant: Optional[float] = Field(None, description="""Spherical Aberration Constant of the objective lens in millimeters""") - microscope_additional_info: Optional[str] = Field(None, description="""Other microscope optical setup information, in addition to energy filter, phase plate and image corrector""") - tilt_axis: Optional[float] = Field(None, description="""Rotation angle in degrees""") + + acceleration_voltage: Optional[int] = Field( + None, description="""Electron Microscope Accelerator voltage in volts""" + ) + spherical_aberration_constant: Optional[float] = Field( + None, + description="""Spherical Aberration Constant of the objective lens in millimeters""", + ) + microscope_additional_info: Optional[str] = Field( + None, + description="""Other microscope optical setup information, in addition to energy filter, phase plate and image corrector""", + ) + tilt_axis: Optional[float] = Field( + None, description="""Rotation angle in degrees""" + ) tilt_step: Optional[float] = Field(None, description="""Tilt step in degrees""") - tilting_scheme: Optional[str] = Field(None, description="""The order of stage tilting during acquisition of the data""") - total_flux: Optional[float] = Field(None, description="""Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series""") - data_acquisition_software: Optional[str] = Field(None, description="""Software used to collect data""") - binning_from_frames: Optional[float] = Field(None, description="""Describes the binning factor from frames to tilt series file""") - tilt_series_quality: Optional[int] = Field(None, description="""Author assessment of tilt series quality within the dataset (1-5, 5 is best)""") - pixel_spacing: Optional[float] = Field(None, description="""Pixel spacing for the tilt series""") - aligned_tiltseries_binning: Optional[int] = Field(None, description="""Binning factor of the aligned tilt series""") - frames_count: Optional[int] = Field(None, description="""Number of frames associated with this tiltseries""") - camera: Optional[Camera] = Field(None, description="""The camera used to collect the tilt series.""") - microscope: Optional[Microscope] = Field(None, description="""The microscope used to collect the tilt series.""") - microscope_optical_setup: Optional[MicroscopeOpticalSetup] = Field(None, description="""The optical setup of the microscope used to collect the tilt series.""") - tilt_range: Optional[TiltRange] = Field(None, description="""The range of tilt angles in the tilt series.""") - - + tilting_scheme: Optional[str] = Field( + None, + description="""The order of stage tilting during acquisition of the data""", + ) + total_flux: Optional[float] = Field( + None, + description="""Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series""", + ) + data_acquisition_software: Optional[str] = Field( + None, description="""Software used to collect data""" + ) + binning_from_frames: Optional[float] = Field( + None, + description="""Describes the binning factor from frames to tilt series file""", + ) + tilt_series_quality: Optional[int] = Field( + None, + description="""Author assessment of tilt series quality within the dataset (1-5, 5 is best)""", + ) + pixel_spacing: Optional[float] = Field( + None, description="""Pixel spacing for the tilt series""" + ) + aligned_tiltseries_binning: Optional[int] = Field( + None, description="""Binning factor of the aligned tilt series""" + ) + frames_count: Optional[int] = Field( + None, description="""Number of frames associated with this tiltseries""" + ) + camera: Optional[Camera] = Field( + None, description="""The camera used to collect the tilt series.""" + ) + microscope: Optional[Microscope] = Field( + None, description="""The microscope used to collect the tilt series.""" + ) + microscope_optical_setup: Optional[MicroscopeOpticalSetup] = Field( + None, + description="""The optical setup of the microscope used to collect the tilt series.""", + ) + tilt_range: Optional[TiltRange] = Field( + None, description="""The range of tilt angles in the tilt series.""" + ) + class TomogramSize(ConfiguredBaseModel): """ The size of a tomogram in voxels in each dimension. """ - x: Optional[int] = Field(None, description="""Number of pixels in the 3D data fast axis""") - y: Optional[int] = Field(None, description="""Number of pixels in the 3D data medium axis""") - z: Optional[int] = Field(None, description="""Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt""") - - + + x: Optional[int] = Field( + None, description="""Number of pixels in the 3D data fast axis""" + ) + y: Optional[int] = Field( + None, description="""Number of pixels in the 3D data medium axis""" + ) + z: Optional[int] = Field( + None, + description="""Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt""", + ) + class TomogramOffset(ConfiguredBaseModel): """ The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. """ + x: Optional[str] = Field(None) y: Optional[str] = Field(None) z: Optional[str] = Field(None) - - + class Tomogram(PicturedEntity, AuthoredEntity): """ Metadata describing a tomogram. """ - voxel_spacing: Optional[float] = Field(None, description="""Voxel spacing equal in all three axes in angstroms""") - fiducial_alignment_status: Optional[FiducialAlignmentStatusEnum] = Field(None, description="""Whether the tomographic alignment was computed based on fiducial markers.""") - ctf_corrected: Optional[bool] = Field(None, description="""Whether this tomogram is CTF corrected""") - reconstruction_method: Optional[str] = Field(None, description="""Describe reconstruction method (Weighted back-projection, SART, SIRT)""") - reconstruction_software: Optional[str] = Field(None, description="""Name of software used for reconstruction""") - processing: Optional[str] = Field(None, description="""Describe additional processing used to derive the tomogram""") - processing_software: Optional[str] = Field(None, description="""Processing software used to derive the tomogram""") - tomogram_version: Optional[str] = Field(None, description="""Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version""") - affine_transformation_matrix: Optional[str] = Field(None, description="""The flip or rotation transformation of this author submitted tomogram is indicated here""") - size: Optional[TomogramSize] = Field(None, description="""The size of a tomogram in voxels in each dimension.""") - offset: Optional[TomogramOffset] = Field(None, description="""The offset of a tomogram in voxels in each dimension relative to the canonical tomogram.""") - authors: List[Author] = Field(default_factory=list, description="""Author of a scientific data entity.""") - key_photos: PicturePath = Field(..., description="""A set of paths to representative images of a piece of data.""") - - + + voxel_spacing: Optional[float] = Field( + None, description="""Voxel spacing equal in all three axes in angstroms""" + ) + fiducial_alignment_status: Optional[FiducialAlignmentStatusEnum] = Field( + None, + description="""Whether the tomographic alignment was computed based on fiducial markers.""", + ) + ctf_corrected: Optional[bool] = Field( + None, description="""Whether this tomogram is CTF corrected""" + ) + reconstruction_method: Optional[str] = Field( + None, + description="""Describe reconstruction method (Weighted back-projection, SART, SIRT)""", + ) + reconstruction_software: Optional[str] = Field( + None, description="""Name of software used for reconstruction""" + ) + processing: Optional[str] = Field( + None, + description="""Describe additional processing used to derive the tomogram""", + ) + processing_software: Optional[str] = Field( + None, description="""Processing software used to derive the tomogram""" + ) + tomogram_version: Optional[str] = Field( + None, + description="""Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version""", + ) + affine_transformation_matrix: Optional[str] = Field( + None, + description="""The flip or rotation transformation of this author submitted tomogram is indicated here""", + ) + size: Optional[TomogramSize] = Field( + None, description="""The size of a tomogram in voxels in each dimension.""" + ) + offset: Optional[TomogramOffset] = Field( + None, + description="""The offset of a tomogram in voxels in each dimension relative to the canonical tomogram.""", + ) + authors: List[Author] = Field( + default_factory=list, description="""Author of a scientific data entity.""" + ) + key_photos: PicturePath = Field( + ..., + description="""A set of paths to representative images of a piece of data.""", + ) + class AnnotationFile(ConfiguredBaseModel): """ Metadata describing a file containing an annotation. """ + format: Optional[str] = Field(None, description="""File format for this file""") - shape: Optional[str] = Field(None, description="""Describe whether this is a Point, OrientedPoint, or SegmentationMask file""") - path: Optional[str] = Field(None, description="""Path to the annotation file relative to the dataset root.""") - is_visualization_default: Optional[bool] = Field(None, description="""This annotation will be rendered in neuroglancer by default.""") - - + shape: Optional[str] = Field( + None, + description="""Describe whether this is a Point, OrientedPoint, or SegmentationMask file""", + ) + path: Optional[str] = Field( + None, + description="""Path to the annotation file relative to the dataset root.""", + ) + is_visualization_default: Optional[bool] = Field( + None, + description="""This annotation will be rendered in neuroglancer by default.""", + ) + class AnnotationConfidence(ConfiguredBaseModel): """ Metadata describing the confidence of an annotation. """ - precision: Optional[float] = Field(None, description="""Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive""") - recall: Optional[float] = Field(None, description="""Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly""") - ground_truth_used: Optional[str] = Field(None, description="""Annotation filename used as ground truth for precision and recall""") - - + + precision: Optional[float] = Field( + None, + description="""Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive""", + ) + recall: Optional[float] = Field( + None, + description="""Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly""", + ) + ground_truth_used: Optional[str] = Field( + None, + description="""Annotation filename used as ground truth for precision and recall""", + ) + class AnnotationObject(ConfiguredBaseModel): """ Metadata describing the object being annotated. """ + id: Optional[str] = Field(None) name: Optional[str] = Field(None) - description: Optional[str] = Field(None, description="""A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.""") - state: Optional[str] = Field(None, description="""Molecule state annotated (e.g. open, closed)""") - - + description: Optional[str] = Field( + None, + description="""A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.""", + ) + state: Optional[str] = Field( + None, description="""Molecule state annotated (e.g. open, closed)""" + ) + class Annotation(AnnotatoredEntity, DatestampedEntity): """ Metadata describing an annotation. """ - annotation_method: Optional[str] = Field(None, description="""Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching)""") - annotation_method_type: Optional[AnnotationMethodTypeEnum] = Field(None, description="""Classification of the annotation method based on supervision.""") - annotation_publications: Optional[str] = Field(None, description="""DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs.""") - annotation_software: Optional[str] = Field(None, description="""Software used for generating this annotation""") - ground_truth_status: Optional[bool] = Field(None, description="""Whether an annotation is considered ground truth, as determined by the annotator.""") - object_count: Optional[int] = Field(None, description="""Number of objects identified""") - is_curator_recommended: Optional[bool] = Field(None, description="""This annotation is recommended by the curator to be preferred for this object type.""") - files: Optional[List[AnnotationFile]] = Field(default_factory=list, description="""Metadata describing a file containing an annotation.""") - confidence: Optional[AnnotationConfidence] = Field(None, description="""Metadata describing the confidence of an annotation.""") - annotation_object: Optional[AnnotationObject] = Field(None, description="""Metadata describing the object being annotated.""") - dates: DateStamp = Field(..., description="""A set of dates at which a data item was deposited, published and last modified.""") - authors: List[Annotator] = Field(default_factory=list, description="""Annotator of a scientific data entity.""") - - + + annotation_method: Optional[str] = Field( + None, + description="""Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching)""", + ) + annotation_method_type: Optional[AnnotationMethodTypeEnum] = Field( + None, + description="""Classification of the annotation method based on supervision.""", + ) + annotation_publications: Optional[str] = Field( + None, + description="""DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs.""", + ) + annotation_software: Optional[str] = Field( + None, description="""Software used for generating this annotation""" + ) + ground_truth_status: Optional[bool] = Field( + None, + description="""Whether an annotation is considered ground truth, as determined by the annotator.""", + ) + object_count: Optional[int] = Field( + None, description="""Number of objects identified""" + ) + is_curator_recommended: Optional[bool] = Field( + None, + description="""This annotation is recommended by the curator to be preferred for this object type.""", + ) + files: Optional[List[AnnotationFile]] = Field( + default_factory=list, + description="""Metadata describing a file containing an annotation.""", + ) + confidence: Optional[AnnotationConfidence] = Field( + None, description="""Metadata describing the confidence of an annotation.""" + ) + annotation_object: Optional[AnnotationObject] = Field( + None, description="""Metadata describing the object being annotated.""" + ) + dates: DateStamp = Field( + ..., + description="""A set of dates at which a data item was deposited, published and last modified.""", + ) + authors: List[Annotator] = Field( + default_factory=list, description="""Annotator of a scientific data entity.""" + ) + class CrossReferences(ConfiguredBaseModel): """ A set of cross-references to other databases and publications. """ - dataset_publications: Optional[str] = Field(None, description="""Comma-separated list of DOIs for publications associated with the dataset.""") - related_database_entries: Optional[str] = Field(None, description="""Comma-separated list of related database entries for the dataset.""") - related_database_links: Optional[str] = Field(None, description="""Comma-separated list of related database links for the dataset.""") - dataset_citations: Optional[str] = Field(None, description="""Comma-separated list of DOIs for publications citing the dataset.""") - - + + dataset_publications: Optional[str] = Field( + None, + description="""Comma-separated list of DOIs for publications associated with the dataset.""", + ) + related_database_entries: Optional[str] = Field( + None, + description="""Comma-separated list of related database entries for the dataset.""", + ) + related_database_links: Optional[str] = Field( + None, + description="""Comma-separated list of related database links for the dataset.""", + ) + dataset_citations: Optional[str] = Field( + None, + description="""Comma-separated list of DOIs for publications citing the dataset.""", + ) # Model rebuild @@ -509,4 +792,3 @@ class CrossReferences(ConfiguredBaseModel): AnnotationObject.model_rebuild() Annotation.model_rebuild() CrossReferences.model_rebuild() -