improve disjoints file

[balhoff]

Currently there is a product that covers only the taxslim, containing these disjointness axioms:

• X DisjointWith Y for all sibling taxa X and Y
• (in_taxon some X) DisjointWith (in_taxon some Y) for all sibling taxa X and Y

I would like to request two enhancements:

1. Add another type of axiom to the included disjoints (needed for more complete taxon restriction reasoning):
   (in_taxon some X) DisjointWith (in_taxon some (not X)) for every taxon X
2. Publish a disjoints file for the complete taxonomy.

[matentzn]

Publish a disjoints file for the complete taxonomy.

Why is this necessary? These files will be enormous, we are talking 2-3 GB, which will severely limit the sort of servers we can use to run a release due to upload restrictions. What ontology you know of is not using the slim file?

[balhoff]

Ubergraph uses the full ontology. I think it would be good to have it for completeness. We could provide only a zipped version. I don't think it would require much memory to generate.

[balhoff]

For creating the disjoints axioms over the whole ontology, I think we should use Jena instead of owltools & robot. It should be more memory efficient. Let's do this as a separate task after releasing the update to the taxslim disjoints.

[cmungall]

It's not just ontologies that use this - this is used for validating GAFs which can theoretically come from any sequenced species

…

On Thu, Jan 12, 2023 at 4:40 AM Nico Matentzoglu ***@***.***> wrote: Publish a disjoints file for the complete taxonomy. Why is this necessary? These files will be *enormous*, we are talking 2-3 GB, which will severely limit the sort of servers we can use to run a release due to upload restrictions. What ontology you know of is not using the slim file? — Reply to this email directly, view it on GitHub <#72 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOMMPWDJJCDZSHVHGALWR73VJANCNFSM6AAAAAATYKPCRQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[balhoff]

I'm going to reopen this just to remember that we want to expand to the whole taxonomy.

[anitacaron]

New release https://github.com/obophenotype/ncbitaxon/releases/tag/v2023-06-16