Below you can see a table with description of ODM dictionaries:
| Dictionary | Description | Is used by Default template |
|---|---|---|
| NCBI Taxonomy | A standard hierarchical nomenclature and classification dictionary for organisms. The original file is available at http://www.berkeleybop.org/ontologies/ncbitaxon.owl https://s3.amazonaws.com/bio-test-data/Ontologies/ncbitaxon.owl |
Yes |
| ChEBI Ontology | The ChEBI ontology focuses on chemical nomenclature and structures, and provides a wide range of other chemical information such as formulae and links to other databases. The original file can be accessed via the web at ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl | Yes |
| Cellosaurus Controlled Vocabulary | A controlled vocabulary which describes all cell lines used in biomedical research. The original file is available at https://github.com/raw/calipho-sib/cellosaurus/4895a46f1475ed7ad62f772924d0c1ecb4b5ce6f/cellosaurus.obo | Yes |
| Uberon Anatomical Entities | An integrated cross-species ontology covering anatomical structures in animals. The original file is available at http://purl.obolibrary.org/obo/uberon/releases/2023-10-27/uberon-simple.owl | Yes |
| Cell Type | The Cell Ontology is a structured controlled vocabulary for cell types in animals. The original data is available via the link http://purl.obolibrary.org/obo/cl.owl | Yes |
| Disease Ontology Extended | An ontology for describing the classification of human diseases organized by etiology. The original file is available at http://purl.obolibrary.org/obo/doid.owl | Yes |
| Disease Ontology | An ontology for describing the classification of human diseases organized by etiology. The original file is available at http://purl.obolibrary.org/obo/doid.owl | |
| Therapeutic Area | A non-hierarchical controlled vocabulary for Therapeutic Area field | Yes |
| Sequencing Platforms | A non-hierarchical controlled vocabulary contains list of sequencing platforms | Yes |
| Sex | A non-hierarchical controlled vocabulary for Sex metainfo field | Yes |
| Experiment Instrument | This dictionary covers different experiment instruments | Yes |
| Data Species | This dictionary covers different data species | Yes |
| Library Type | This dictionary covers different library types | Yes |
| Experiment Type | This dictionary covers different experiment types | Yes |
| Scope | This dictionary covers different preparation scopes | Yes |
| miRBase microRNA database entities | Micro RNA controlled vocabulary (release 22.1). The original data (mirBase.dat and mirna_species.txt) are available at miRBase |
|
| Uniprot Homo Sapiens | Uniprot proteins dictionary for Homo Sapiens. The original data are available using query UniProt |
|
| Gene Ontology | A controlled vocabulary describing the gene functions according to three aspects: biological process, molecular function and cellular component. The original file is available at http://purl.obolibrary.org/obo/go.owl | |
| Cell Ontology | A structured controlled vocabulary for cell types. The original file is available at http://purl.obolibrary.org/obo/cl/releases/2020-03-02/cl-basic.owl | |
| Units - Dimensionless | ||
| Microarray Platforms | A non-hierarchical controlled vocabulary contains list of microarray platforms | |
| Methods | A non-hierarchical controlled vocabulary which covers methods and approaches used in bioinformatics | |
| Ethnic Groups | A non-hierarchical controlled vocabulary including list of ethnic groups |
Units - these are generated inside ODM. The most recent dictionary versions, used in ODM, are located under s3 bucket and available via http link. Example: https://odm-init.s3.amazonaws.com/dictionaries/cellosaurus.obo