This repository shows how databases can be formalized as an OBO Ontology in the OBO flat file format,
OWL format, and OBO Graph JSON format. A list of the databases whose controlled vocabularies and related
content can be readily converted to OBO can be in found in the PyOBO
source code's sources/ folder here.
Further discussion:
- Limits of ontologies: How should databases be represented in OBO? presented by Chris Mungall
- OBOFoundry/OBOFoundry.github.io#1981
Each resource gets a subdirectory in the export/ directory containing the following exports:
A manifest of all resources is available at manifest.yml.
To generate all OBO, OWL, and OFN files, run the following shell commands:
$ uv run --script build.pyIf you just want to generate one, use -x like
$ uv run --script build.py -x spdxIf you want to pin the versions of specific ontologies, use --version-override like
$ uv run --script build.py -x mesh --version-override mesh 2018See PURL configuration at https://github.com/perma-id/w3id.org/tree/master/biopragmatics. This W3ID entry makes ontology artifacts in the "export" folder (https://github.com/biopragmatics/obo-db-ingest/tree/main/export) resolvable. Here are a few examples:
| Resource | Version Type | Example PURL |
|---|---|---|
| Reactome | Sequential | https://w3id.org/biopragmatics/resources/reactome/83/reactome.obo |
| Interpro | Major/Minor | https://w3id.org/biopragmatics/resources/interpro/92.0/interpro.obo |
| DrugBank Salt | Semantic | https://w3id.org/biopragmatics/resources/drugbank.salt/5.1.9/drugbank.salt.obo |
| MeSH | Year | https://w3id.org/biopragmatics/resources/mesh/2023/mesh.obo.gz |
| UniProt | Year/Month | https://w3id.org/biopragmatics/resources/uniprot/2022_05/uniprot.obo.gz |
| HGNC | Date | https://w3id.org/biopragmatics/resources/hgnc/2023-02-01/hgnc.obo |
| CGNC | unversioned | https://w3id.org/biopragmatics/resources/cgnc/cgnc.obo |