Update ontology builds in S3 bucket

[rsgoncalves]

Pre-generated SQLite database are created weekly for all OBO ontologies and a selection of others (see ontologies.yaml)

It doesn't look like up-to-date builds are accessible from the S3 bucket URLs— at least not for EFO. Am I missing something or are the SQL builds not updated so regularly?

[turbomam]

I would like to have a semantic sql representation of the current EnvO release in S3

[caufieldjh]

For most ontologies on that bucket, the most recent version will be the db.gz. Looks like envo.db.gz last got updated on Feb 12 2024 - so if that's not in alignment with the most recent release then there's a bigger issue here. Same for efo.db.gz - last updated Feb 12.

[cmungall]

That's right. Note the filestamp tells you the time of build. To get the actual versionIRI you can query it:

✗ sqlite3 ~/.data/oaklib/envo.db
SQLite version 3.37.0 2021-12-09 01:34:53
Enter ".help" for usage hints.
sqlite> select * from statements where predicate='owl:versionIRI';
obo:envo.owl|obo:envo.owl|owl:versionIRI|obo:envo/releases/2024-02-05/envo.owl||||

NOTE if you are accessing ENVO via OAK be aware that pystow does not have any explicit cache management, you need to remove ~/.data/oaklib/envo.db and ~/.data/oaklib/envo.db.gz to trigger a re-download