This package constitutes a “second generation” approach to management and use of ontologies in Bioconductor.
The INCAtools Semantic SQL project (tutorial notebook) identifies an AWS S3 bucket where a large number of ontologies are available.
%vjc> aws s3 ls s3://bbop-sqlite/ |grep db.gz
2023-09-02 17:38:48 4268563 ado.db.gz
2023-09-02 17:38:48 11841154 agro.db.gz
2023-09-02 17:38:48 301889 aio.db.gz
2023-09-02 17:38:48 42842146 aism.db.gz
2023-09-02 17:38:48 294887 amphx.db.gz
2023-09-02 17:38:48 303328 apo.db.gz
2023-09-02 17:38:48 3457483 apollo_sv.db.gz
2023-09-02 17:38:48 7245916 aro.db.gz
2023-09-02 17:38:48 5939737 bao.db.gz
2023-09-02 17:38:48 767913 bcio.db.gz
2023-09-02 17:38:50 552497 bco.db.gz
2023-09-02 17:38:51 1600927276 bero.db.gz
2023-09-02 17:38:51 108284 bfo.db.gz
2023-09-02 17:38:54 575935 biolink.db.gz
2023-09-02 17:38:55 646 biopax.db.gz
2023-09-02 17:38:55 463088 biovoices.db.gz
...In this package we will provide tools to retrieve, cache, and make use of these ontologies.