INCATools / INCATools/ubergraph
Add some obo-db-ingests into ubergraph (EC, RHEA, SwissLipid)
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Description
A lot of useful databases-as-ontologies here:
https://github.com/biopragmatics/obo-db-ingest
We may want to be conservative in loading some of these, ensuring there is agreement on URI expansions of the prefix before creating confusion by proliferating yet new expansions.
We are also loading some of these in semsql: https://github.com/INCATools/semantic-sql/issues/45
cc @cthoyt @matentzn
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the obo-db-ingest repository and the related semsql issue #45, then identify how ubergraph currently selects and loads ontology sources. Confirm which of EC, RHEA, and SwissLipid are intended and what URI-prefix agreements are required; done should mean the selected sources are integrated without introducing conflicting expansions.
Written by the indexing model from the issue text.
Assessment
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 28/100