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obophenotype / ncbitaxon

Build for NCBITaxon
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improve disjoints file #72

Open balhoff opened 1 year ago

balhoff commented 1 year ago

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

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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: @.***>

balhoff commented 1 year ago

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

anitacaron commented 1 year ago

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