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Include PyOBO products

Open cmungall opened this issue 1 year ago • 6 comments

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

cmungall avatar Jul 14 '22 15:07 cmungall