https://github.com/biopragmatics/obo-db-ingest
🗄️ Conversion of biomedical nomenclatures like HGNC to OBO
Science Score: 49.0%
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary
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Repository
🗄️ Conversion of biomedical nomenclatures like HGNC to OBO
Basic Info
- Host: GitHub
- Owner: biopragmatics
- Language: Python
- Default Branch: main
- Homepage: https://biopragmatics.github.io/obo-db-ingest/
- Size: 10.8 GB
Statistics
- Stars: 7
- Watchers: 1
- Forks: 1
- Open Issues: 9
- Releases: 9
Topics
Metadata Files
README.md
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
- https://github.com/OBOFoundry/OBOFoundry.github.io/discussions/1981
Contents
Each resource gets a subdirectory in the export/ directory containing the following exports:
A manifest of all resources is available at manifest.yml.
Build
To generate all OBO, OWL, and OFN files, run the following shell commands:
console
$ uv run --script build.py
If you just want to generate one, use -x like
console
$ uv run --script build.py -x spdx
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 |
Owner
- Name: Biopragmatics Stack
- Login: biopragmatics
- Kind: organization
- Website: https://biopragmatics.github.io
- Twitter: biopragmatics
- Repositories: 9
- Profile: https://github.com/biopragmatics
Software supporting biomedical semantics and pragmatics
GitHub Events
Total
- Create event: 8
- Issues event: 5
- Release event: 8
- Watch event: 1
- Delete event: 1
- Issue comment event: 11
- Push event: 54
- Pull request event: 3
Last Year
- Create event: 8
- Issues event: 5
- Release event: 8
- Watch event: 1
- Delete event: 1
- Issue comment event: 11
- Push event: 54
- Pull request event: 3
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charles Tapley Hoyt | c****t@g****m | 82 |
| github-actions | 4****] | 12 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 15
- Total pull requests: 4
- Average time to close issues: 4 months
- Average time to close pull requests: less than a minute
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 1.6
- Average comments per pull request: 0.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.25
- Average comments per pull request: 0.33
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cmungall (14)
- samseaver (1)
Pull Request Authors
- cthoyt (5)