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obi-ontology / obi

The Ontology for Biomedical Investigations
http://obi-ontology.org
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term update: genome coverage #1634

Open cmrn-rhi opened 1 year ago

cmrn-rhi commented 1 year ago

This is a request to update the "genome coverage" [OBI:0001939]

New parent term: sequence data [OBI:0000973] New definition: A sequence data which is the amount of a reference sequence covered by a specific genome of interest, calculated as the total number of generated bases in the sequenced genome divided by the reference/expected genome size. Definition source: https://orcid.org/0000-0002-1107-9135

Rationale: Would appreciate a more general definition that isn't eukaryotic centric, with additional information being added as comments / editor notes instead of within the definition.

Originally a new term request as part of issue #1579 ROBOT spreadsheet, but has since been removed from that request.

ddooley commented 1 year ago

We might not be able to move this under "sequence data" since that data is ostensibly a measurement, not a calculated datum? Definition source of current term is: "A beginner's guide to eukaryotic genome annotation", doi:10.1038/nrg3174 . "Gene coverage is the percentage of the genes in the genome that are contained in the assembly." "Emma Griffiths" definition source!

ddooley commented 1 year ago

I just tried editing the obi-edit.owl file with protege 5.6.1 and the text diff is gigantic. I'm wondering if all OBI editors are now using 5.6.1? The textual change in the file is often one involving dropping the "string" data type which I guess is a default.:

   - <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters</obo:IAO_0000117>
   + <obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>

   - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_is_described_by</rdfs:label>
   + <rdfs:label>obsolete_is_described_by</rdfs:label>

So I can go ahead and do this commit as long as everyone upgrades to protege 5.6.1 .

jamesaoverton commented 1 year ago

It's better if I update the ROBOT version and all the OWL files in one PR.

ddooley commented 1 year ago

Ok I'll leave that in your hands, and then redo the pull request https://github.com/obi-ontology/obi/pull/1675

jamesaoverton commented 1 year ago

1676 reformatted all the files with the new OWLAPI, so everyone should use the latest Protege and ROBOT going forward.