INCATools / INCATools/semantic-sql
Include PyOBO products
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 69
- Forks
- 7
- Avg merge
- 8m
- Merged PRs (30d)
- 1
Description
See https://github.com/biopragmatics/obo-db-ingest
It would be quite easy to add these as builds, and distribute the sqlite on s3.
Advantages:
- easy to query in OAK (though some methods and commands e.g `tree` wouldn't make sense as these wouldn't follow expected structural shapes for ontologies)
- fast to query via SQL
Note there is ongoing discussion about URIs for these, but semantic-sql doesn't care, we store things natively as CURIEs, and the prefix table can be swapped to anything.
Ideally the products would be built and distributed (obo/owl/json) upstream, to avoid running the build step, as this introduces an additional source of potential pipeline failure, we also have to determine memory/disk requirements
cc @cthoyt
Contributor guide
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 with the linked obo-db-ingest repository and semantic-sql's existing build and distribution entry points. Clarify which PyOBO products should be supported, whether upstream OBO/OWL/JSON products can be consumed, and the memory, disk, URI, and S3 distribution requirements. Done means the selected products build reliably and their SQLite databases are distributed for OAK queries.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, sqlite
- Domain
- build-system, database
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100