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improve disjoints file

Open balhoff opened this issue 2 years ago • 6 comments

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.

balhoff avatar Jan 11 '23 18:01 balhoff

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?

matentzn avatar Jan 12 '23 12:01 matentzn

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 avatar Jan 12 '23 19:01 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.

balhoff avatar Jun 16 '23 17:06 balhoff

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 https://github.com/obophenotype/ncbitaxon/issues/72#issuecomment-1380276660, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOMMPWDJJCDZSHVHGALWR73VJANCNFSM6AAAAAATYKPCRQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

cmungall avatar Jun 16 '23 17:06 cmungall

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

balhoff avatar Jun 16 '23 17:06 balhoff

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

anitacaron avatar Jun 16 '23 20:06 anitacaron