diff --git a/ingestion_tools/dataset_configs/10000.yaml b/ingestion_tools/dataset_configs/10000.yaml index 18878c165..e8d70a0f4 100644 --- a/ingestion_tools/dataset_configs/10000.yaml +++ b/ingestion_tools/dataset_configs/10000.yaml @@ -16,8 +16,8 @@ dataset: ORCID: 0000-0003-4388-1349 - name: Mauricio Toro-Nahuelpan ORCID: 0000-0001-5333-3640 - - name: Cheng DWC - - name: Tollervey F + - name: Dorothy W. C. Cheng + - name: Fergus Tollervey - name: Constantin Pape ORCID: 0000-0001-6562-7187 - name: Martin Beck @@ -64,6 +64,7 @@ annotations: name: 'fatty acid synthase complex' dates: *repo-dates annotation_method: Cumulative template-matching trained 2D CNN predictions + visual filtering + distance constraints + manual addition + method_type: hybrid annotation_publications: &annotation_publication "EMPIAR-10988, EMD-14412, EMD-14413, EMD-14415, EMD-14417, EMD-14418, EMD-14419, EMD-14420, 10.1101/2022.04.12.488077" ground_truth_status: true authors: &annotation_authors @@ -98,27 +99,32 @@ annotations: corresponding_author_status: true annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: particle_lists/{run_name}_fas.csv shape: Point + is_visualization_default: false - metadata: annotation_object: id: GO:0022626 name: 'cytosolic ribosome' dates: *repo-dates annotation_method: Cumulative template-matching trained 2D CNN predictions + visual filtering + distance constraints + manual addition + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - shape: Point columns: xyz file_format: csv glob_string: particle_lists/{run_name}_cyto_ribosomes.csv + is_visualization_default: true # Label 1 - cytoplasm - metadata: annotation_object: @@ -128,6 +134,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: &organelle_segmask_annotation_method spectrum equalization filter + 2D CNN prediction + manual correction + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -137,11 +144,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: &segmask1_glob 'labels/180426_{mapped_segmask_name}.labels.mrc' mask_label: 1 + is_visualization_default: false # Label 2 - Mitochondria - metadata: annotation_object: @@ -151,6 +160,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -160,11 +170,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 2 + is_visualization_default: true # Label 3 - Vesicle - metadata: annotation_object: @@ -174,6 +186,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -183,11 +196,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 3 + is_visualization_default: false # Label 4 - Microtubule - metadata: annotation_object: @@ -197,6 +212,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -206,11 +222,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 4 + is_visualization_default: true # Label 5 - ER - metadata: annotation_object: @@ -220,6 +238,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -229,11 +248,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 5 + is_visualization_default: true # Label 6 - Nuclear envelope - metadata: annotation_object: @@ -243,6 +264,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -252,11 +274,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 6 + is_visualization_default: true # Label 7 - Nucleus - metadata: annotation_object: @@ -266,6 +290,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -275,11 +300,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 7 + is_visualization_default: false # Label 8 - Vacuole - metadata: annotation_object: @@ -289,6 +316,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -298,11 +326,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 8 + is_visualization_default: false # Label 9 - Lipid droplet - metadata: annotation_object: @@ -312,6 +342,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -321,11 +352,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 9 + is_visualization_default: false # Label 10 - Golgi apparatus - metadata: annotation_object: @@ -335,6 +368,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -344,11 +378,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 10 + is_visualization_default: true # Label 11 - Vesicular body - metadata: annotation_object: @@ -358,6 +394,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -367,11 +404,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 11 + is_visualization_default: false # Label 13 - Non-specified compartment - metadata: annotation_object: @@ -381,6 +420,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -390,11 +430,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: false sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 13 + is_visualization_default: false # Membranes - metadata: annotation_object: @@ -404,6 +446,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: 3D CNN prediction + manual correction + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -413,11 +456,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: 'labels/{run_name}_membranes.mrc' mask_label: 1 + is_visualization_default: false runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10001.yaml b/ingestion_tools/dataset_configs/10001.yaml index 4cf8991eb..f54a7a3fe 100644 --- a/ingestion_tools/dataset_configs/10001.yaml +++ b/ingestion_tools/dataset_configs/10001.yaml @@ -92,6 +92,7 @@ annotations: name: 'fatty acid synthase complex' dates: *repo-dates annotation_method: Cumulative template-matching trained 2D CNN predictions + visual filtering + distance constraints + manual addition + method_type: hybrid annotation_publications: &annotation_publication "EMPIAR-10988, EMD-14412, EMD-14413, EMD-14415, EMD-14417, EMD-14418, EMD-14419, EMD-14420, 10.1101/2022.04.12.488077" ground_truth_status: true authors: &annotation_authors @@ -126,27 +127,32 @@ annotations: corresponding_author_status: true annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: particle_lists/{run_name}_fas.csv shape: Point + is_visualization_default: false - metadata: annotation_object: id: GO:0022626 name: 'cytosolic ribosome' dates: *repo-dates annotation_method: Cumulative template-matching trained 2D CNN predictions + visual filtering + distance constraints + manual addition + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - shape: Point columns: xyz file_format: csv glob_string: particle_lists/{run_name}_cyto_ribosomes.csv + is_visualization_default: true # Label 1 - cytoplasm - metadata: annotation_object: @@ -156,6 +162,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: &organelle_segmask_annotation_method manual segmentation + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -165,11 +172,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: &segmask1_glob 'labels/{run_name}_organelles.mrc' mask_label: 1 + is_visualization_default: false # Label 2 - Mitochondria - metadata: annotation_object: @@ -179,6 +188,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -188,11 +198,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 2 + is_visualization_default: true # Label 3 - Vesicle - metadata: annotation_object: @@ -202,6 +214,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -211,11 +224,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 3 + is_visualization_default: false # Label 4 - Microtubule - metadata: annotation_object: @@ -225,6 +240,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -234,11 +250,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 4 + is_visualization_default: true # Label 5 - ER - metadata: annotation_object: @@ -248,6 +266,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -257,11 +276,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 5 + is_visualization_default: true # Label 6 - Nuclear envelope - metadata: annotation_object: @@ -271,6 +292,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -280,11 +302,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 6 + is_visualization_default: true # Label 7 - Nucleus - metadata: annotation_object: @@ -294,6 +318,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -303,11 +328,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 7 + is_visualization_default: false # Label 8 - Vacuole - metadata: annotation_object: @@ -317,6 +344,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -326,11 +354,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 8 + is_visualization_default: false # Label 9 - Lipid droplet - metadata: annotation_object: @@ -340,6 +370,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -349,11 +380,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 9 + is_visualization_default: false # Label 10 - Golgi apparatus - metadata: annotation_object: @@ -363,6 +396,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -372,11 +406,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 10 + is_visualization_default: true # Label 11 - Vesicular body - metadata: annotation_object: @@ -386,6 +422,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -395,11 +432,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 11 + is_visualization_default: false # Label 13 - Non-specified compartment - metadata: annotation_object: @@ -409,6 +448,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: *organelle_segmask_annotation_method + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -418,11 +458,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: false sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 13 + is_visualization_default: false # Membranes - metadata: annotation_object: @@ -432,6 +474,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: 3D CNN prediction + manual correction + method_type: hybrid annotation_publications: *annotation_publication ground_truth_status: true authors: *annotation_authors @@ -441,12 +484,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: 'labels/{run_name}_membranes.mrc' mask_label: 1 - + is_visualization_default: false tomograms: voxel_spacing: 13.48 fiducial_alignment_status: NON_FIDUCIAL diff --git a/ingestion_tools/dataset_configs/10002.yaml b/ingestion_tools/dataset_configs/10002.yaml index 47c289d15..ca06ad2b1 100644 --- a/ingestion_tools/dataset_configs/10002.yaml +++ b/ingestion_tools/dataset_configs/10002.yaml @@ -1,4 +1,7 @@ dataset: + dataset_identifier: 10002 + dataset_description: "Cryo-electron tomograms of RPE1 cells. Comprehensive annotation of actin filaments and microtubules" + dataset_title: RPE1 cytosol with actin stress fiber authors: &dataset_authors - name: Irene de Teresa Trueba ORCID: 0000-0002-4691-9501 @@ -30,7 +33,7 @@ dataset: ORCID: 0000-0001-8324-4040 corresponding_author_status: true cross_references: - dataset_publications: doi:10.1101/2022.04.12.488077, doi:10.1038/s41592-022-01746-2 + dataset_publications: &publications doi:10.1101/2022.04.12.488077, doi:10.1038/s41592-022-01746-2 related_database_entries: EMPIAR-10989 cell_component: name: ~ @@ -38,9 +41,6 @@ dataset: cell_type: id: CL:0002586 name: Retinal pigment epithelial-1 - dataset_identifier: 10002 - dataset_description: "Cryo-electron tomograms of RPE1 cells. Comprehensive annotation of actin filaments and microtubules" - dataset_title: RPE1 cytosol with actin stress fiber dates: &repo-dates deposition_date: 2023-05-01 last_modified_date: 2023-11-08 @@ -111,9 +111,10 @@ annotations: description: Actin ground truth state: ~ dates: *repo-dates - annotation_method: 2D CNN + 3D CNN hyperparameter tuning - annotation_publications: ~ - ground_truth_status: False + annotation_method: manual segmentation + method_type: manual + annotation_publications: *publications + ground_truth_status: True authors: &annotation_authors - name: Sara Goetz ORCID: 0000-0002-9903-3667 @@ -150,15 +151,18 @@ annotations: precision: ~ recall: ~ ground_truth_used: Ground truth from related paper + is_curator_recommended: true sources: - file_format: mrc shape: SegmentationMask glob_string: labels/{run_name}_actin_ground_truth.mrc + is_visualization_default: true - metadata: dates: *repo-dates - annotation_method: manual - annotation_publications: ~ - ground_truth_status: True + annotation_method: 2D CNN + 3D CNN hyperparameter tuning + method_type: automated + annotation_publications: *publications + ground_truth_status: False authors: *annotation_authors annotation_software: Amira version: '1.0' @@ -171,10 +175,12 @@ annotations: name: actin filament description: Actin DeePiCt training prediction state: ~ + is_curator_recommended: false sources: - file_format: mrc shape: SegmentationMask glob_string: prediction/{run_name}_*.mrc + is_visualization_default: false # - columns: zyx # file_format: xml # glob_string: actin_ground_truth_coordinates/{run_name}_*.xml diff --git a/ingestion_tools/dataset_configs/10003.yaml b/ingestion_tools/dataset_configs/10003.yaml index 4cccd6f5a..70f10b54a 100644 --- a/ingestion_tools/dataset_configs/10003.yaml +++ b/ingestion_tools/dataset_configs/10003.yaml @@ -58,6 +58,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: 'Template matching + manual filtering + 3D classification filtering' + method_type: hybrid annotation_publications: ground_truth_status: true authors: @@ -77,6 +78,7 @@ annotations: recall: 90 ground_truth_used: author estimation version: '1.0' + is_curator_recommended: true sources: - shape: OrientedPoint file_format: relion3_star @@ -84,6 +86,7 @@ annotations: order: zyx glob_string: run_ct17_it034_data.star filter_value: '{mapped_tomo_name}.tomostar' + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10004.yaml b/ingestion_tools/dataset_configs/10004.yaml index 4449392ed..29fcf258d 100644 --- a/ingestion_tools/dataset_configs/10004.yaml +++ b/ingestion_tools/dataset_configs/10004.yaml @@ -63,6 +63,7 @@ annotations: name: 'cytosolic ribosome' dates: *repo-dates annotation_method: Template matching + 2D classification filtering + method_type: automated annotation_publications: "10.1101/2023.04.28.538734, EMD-17241, EMD-17242, EMD-17243, EMD-17244, EMD-17245" ground_truth_status: false authors: @@ -108,11 +109,13 @@ annotations: recall: 60 ground_truth_used: Author estimation annotation_software: STOPGAP + RELION + is_curator_recommended: true sources: - columns: xyz file_format: csv_with_header glob_string: '{run_name}/annoRibosome_bin4.txt' shape: Point + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10005.yaml b/ingestion_tools/dataset_configs/10005.yaml index b25ebfa76..d234ef587 100644 --- a/ingestion_tools/dataset_configs/10005.yaml +++ b/ingestion_tools/dataset_configs/10005.yaml @@ -41,7 +41,7 @@ dataset: id: CL:0000019 name: Sperm cross_references: - dataset_publications: doi:10.1101/2022.09.28.510016 + dataset_publications: &publications doi:10.1101/2022.09.28.510016 cell_component: name: sperm flagellum id: GO:0036126 @@ -58,7 +58,8 @@ annotations: state: 48 nm repeat dates: *repo-dates annotation_method: Template matching + manual filtering + 3D classification filtering - annotation_publications: null + method_type: hybrid + annotation_publications: *publications ground_truth_status: true authors: &annotation_authors - name: Zhen Chen @@ -73,12 +74,14 @@ annotations: corresponding_author_status: true annotation_software: ~ version: '1.0' + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: coorinates_dmt48/s{run_name}_dmt48_coordinates_bin2.txt shape: Point delimiter: ' ' + is_visualization_default: true - metadata: annotation_object: id: GO:0097545 @@ -86,7 +89,8 @@ annotations: state: 96 nm repeat dates: *repo-dates annotation_method: Template matching + manual filtering + 3D classification filtering - annotation_publications: null + method_type: hybrid + annotation_publications: *publications ground_truth_status: true authors: *annotation_authors annotation_software: ~ @@ -95,12 +99,14 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: coordinates_dmt96/s{run_name}_dmt96_coordinates_bin2.txt shape: Point delimiter: ' ' + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10006.yaml b/ingestion_tools/dataset_configs/10006.yaml index ec68de7ef..d2f401bb4 100644 --- a/ingestion_tools/dataset_configs/10006.yaml +++ b/ingestion_tools/dataset_configs/10006.yaml @@ -77,7 +77,8 @@ annotations: description: SARS-CoV2 Spike protein dates: *repo-dates annotation_method: Template matching + 3D classification filtering -# annotation_publications: OPTIONAL + method_type: automated + annotation_publications: doi:10.1038/s41586-020-2665-2 ground_truth_status: true authors: - name: Zunlong Ke @@ -120,6 +121,7 @@ annotations: # precision: REQUIRED IF ground_truth_used is specified # recall: REQUIRED IF ground_truth_used is specified ground_truth_used: author estimation + is_curator_recommended: true sources: - file_format: relion4_star glob_string: motl_star/czii-remapped-points.star @@ -127,6 +129,7 @@ annotations: shape: OrientedPoint binning: 2 filter_value: '{run_name}' + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10007.yaml b/ingestion_tools/dataset_configs/10007.yaml index bd7e4af19..e85148ade 100644 --- a/ingestion_tools/dataset_configs/10007.yaml +++ b/ingestion_tools/dataset_configs/10007.yaml @@ -54,7 +54,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: crYOLO picking - annotation_publications: ~ + method_type: automated + annotation_publications: doi:10.1101/2023.08.18.553799 ground_truth_status: False authors: - name: Ramya Rangan @@ -80,6 +81,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: tomoman_relion_star @@ -87,6 +89,7 @@ annotations: order: zyx glob_string: '{run_name}/metadata/particles/*.star' filter_value: ~ + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10008.yaml b/ingestion_tools/dataset_configs/10008.yaml index a2a63a2a5..7eb3ec6e7 100644 --- a/ingestion_tools/dataset_configs/10008.yaml +++ b/ingestion_tools/dataset_configs/10008.yaml @@ -70,6 +70,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: Template matching + manual filtering + 3D classification filtering + method_type: hybrid annotation_publications: *publications ground_truth_status: true authors: &annotation_authors @@ -104,6 +105,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -111,6 +113,7 @@ annotations: order: zyx glob_string: 'subtomo/hdcr/hdcr_tm_bin2_motl_12.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0022626 @@ -119,6 +122,7 @@ annotations: state: ~ dates: *repo-dates annotation_method: Template matching + manual filtering + 3D classification filtering + method_type: hybrid annotation_publications: *publications ground_truth_status: true authors: *annotation_authors @@ -128,6 +132,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -135,6 +140,7 @@ annotations: order: zyx glob_string: 'subtomo/ribo/ribo_tm_bin1_motl_12.star' filter_value: "{run_name}" + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10009.yaml b/ingestion_tools/dataset_configs/10009.yaml index 3686d4927..819a50e9a 100644 --- a/ingestion_tools/dataset_configs/10009.yaml +++ b/ingestion_tools/dataset_configs/10009.yaml @@ -70,6 +70,7 @@ dataset: id: GO:0005929 organism: name: Chlamydomonas reinhardtii + taxonomy_id: 3055 key_photos: snapshot: https://www.ebi.ac.uk/pdbe/emdb-empiar/entryIcons/11078-l.gif thumbnail: https://www.ebi.ac.uk/pdbe/emdb-empiar/entryIcons/11078.gif @@ -124,7 +125,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: &annotation_method manual picking + line fit + pick on line + CC based filtering - annotation_publications: ~ + method_type: manual + annotation_publications: &annotation_publications doi:10.1126/science.abm6704 ground_truth_status: true authors: &annotation_authors - name: Hugo G. van den Hoek @@ -168,6 +170,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -175,6 +178,7 @@ annotations: order: zyx glob_string: "motivelists/allmotl_S_newbin2_3.star" filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0097537 @@ -183,7 +187,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: *annotation_method - annotation_publications: ~ + method_type: manual + annotation_publications: *annotation_publications ground_truth_status: true authors: *annotation_authors annotation_software: 3dmod, STOPGAP @@ -192,6 +197,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -199,6 +205,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_Y_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0035869 @@ -207,7 +214,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: *annotation_method - annotation_publications: ~ + method_type: manual + annotation_publications: *annotation_publications ground_truth_status: true authors: *annotation_authors annotation_software: 3dmod, STOPGAP @@ -216,6 +224,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -223,6 +232,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_H_cleanbin2.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0035869 @@ -231,7 +241,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: *annotation_method - annotation_publications: ~ + method_type: manual + annotation_publications: *annotation_publications ground_truth_status: true authors: *annotation_authors annotation_software: 3dmod, STOPGAP @@ -240,6 +251,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -247,6 +259,7 @@ annotations: order: zyx glob_string: 'motivelists/MTD_MIP_bin2_recentered_shiftedorg_9.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0030992 @@ -255,7 +268,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: *annotation_method - annotation_publications: ~ + method_type: manual + annotation_publications: *annotation_publications ground_truth_status: true authors: *annotation_authors annotation_software: 3dmod, STOPGAP @@ -264,6 +278,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -271,6 +286,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_B2_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0030991 @@ -279,7 +295,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: *annotation_method - annotation_publications: ~ + method_type: manual + annotation_publications: *annotation_publications ground_truth_status: true authors: *annotation_authors annotation_software: 3dmod, STOPGAP @@ -288,6 +305,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -295,6 +313,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_A2_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0005858 @@ -303,7 +322,8 @@ annotations: state: ~ dates: *repo-dates annotation_method: *annotation_method - annotation_publications: ~ + method_type: manual + annotation_publications: *annotation_publications ground_truth_status: true authors: *annotation_authors annotation_software: 3dmod, STOPGAP @@ -312,6 +332,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -319,6 +340,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_D_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true overrides_by_run: # The tiltseries / tomograms dicts will be hit with a originaldict.update(dict from this section) - run_regex: "TS_11$" tiltseries: diff --git a/ingestion_tools/dataset_configs/10010.yaml b/ingestion_tools/dataset_configs/10010.yaml index 1b1cb01b7..fa6a59fbc 100644 --- a/ingestion_tools/dataset_configs/10010.yaml +++ b/ingestion_tools/dataset_configs/10010.yaml @@ -97,8 +97,9 @@ annotations: description: ~ state: ~ dates: *repo-dates - annotation_method: REQUIRED - annotation_publications: ~ + annotation_method: &annotation_methods TomoSegMemTV segmentation + manual correction in TFS Amira + method_type: hybrid + annotation_publications: &annotation_pubs 10.1083/jcb.202204093, 10.1101/2022.01.23.477440 ground_truth_status: true authors: &annotation_authors - name: Michaela Medina @@ -113,11 +114,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - file_format: mrc shape: SemanticSegmentationMask glob_string: &segmentation_glob 'Voxel_Segmentations/{run_name}_labels.rec.mrc' mask_label: 1 + is_visualization_default: true - metadata: annotation_object: id: GO:0005743 @@ -125,18 +128,21 @@ annotations: description: ~ state: ~ dates: *repo-dates - annotation_method: REQUIRED - annotation_publications: ~ + annotation_method: *annotation_methods + method_type: hybrid + annotation_publications: *annotation_pubs ground_truth_status: true authors: *annotation_authors annotation_software: TomoSegMemTV+AMIRA version: "1.0" confidence: *annotation_confidence + is_curator_recommended: true sources: - file_format: mrc shape: SemanticSegmentationMask glob_string: *segmentation_glob mask_label: 2 + is_visualization_default: true - metadata: annotation_object: id: GO:0005789 @@ -144,18 +150,21 @@ annotations: description: ~ state: ~ dates: *repo-dates - annotation_method: REQUIRED - annotation_publications: ~ + annotation_method: *annotation_methods + method_type: hybrid + annotation_publications: *annotation_pubs ground_truth_status: true authors: *annotation_authors annotation_software: TomoSegMemTV+AMIRA version: "1.0" confidence: *annotation_confidence + is_curator_recommended: true sources: - file_format: mrc shape: SemanticSegmentationMask glob_string: *segmentation_glob mask_label: 3 + is_visualization_default: true standardization_config: destination_prefix: '10010' source_prefix: Grotjahn