OBO Database Ingestion

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

Contents

Each resource gets a subdirectory in the export/ directory containing the following exports:

• OWL (functional syntax)
• OBO
• OBO Graph JSON
• Simple Standard for Sharing Ontological Mappings (SSSOM)

A manifest of all resources is available at manifest.yml.

Build

To generate all OBO, OWL, and OFN files, run the following shell commands:

$ uv run --script build.py

If you just want to generate one, use -x like

$ uv run --script build.py -x spdx

If you want to pin the versions of specific ontologies, use --version-override like

$ uv run --script build.py -x mesh --version-override mesh 2018

PURLs

See 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