Add gene and related entities from SO

[cmungall]

This PR creates new classes related to a subset of root terms from SO, with the following equivalents:

subject_id	subject_label	predicate	object_id	object_label	comments
COB:0000501	gene	owl:equivalentClass	SO:0000704	gene	.
COB:0000501	gene	owl:equivalentClass	MSO:0000704	gene	.
COB:0000503	nucleotide region	owl:equivalentClass	MSO:3100210	nucleotide region	In MSO can be part of dsDNA molecule
COB:0000503	nucleotide region	owl:subClassOf	SO:0000001	region	.
COB:0000504	region of nucleic acid polymer or protein	owl:equivalentClass	SO:0000001	region	.
COB:0000504	region of nucleic acid polymer or protein	owl:equivalentClass	MSO:0000001	sequence molecular entity region	MSO defines as two or more sequence units
COB:0000506	polypeptide region	owl:equivalentClass	SO:0000839	polypeptide region	.
COB:0000506	polypeptide region	owl:equivalentClass	MSO:0000839	peptide region	MSO defines as two or more sequence units
COB:0000507	virus	owl:equivalentClass	NCBITaxon:10239	Viruses	.

For further context, see SO and COB, this was presented at the 2021 COB workshop (https://drive.google.com/drive/folders/13Ema8Ev-7fiP-pAvJIFtS9rZIV2rs5es)

[cthoyt]

Any chance this has syntax to connect your ORCID?

[matentzn]

The ID ranges files have historically been documentative with no other purpose than to say „don’t use any IDs outside your range..“. If you think we should use this for more, like retroannoating terms in a namespace belonging to someone with their orcid, this should be a ticket at the ODK repo instead, not here.

…

On Mon, 13 Sep 2021 at 11:44, Charles Tapley Hoyt ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/ontology/cob-idranges.owl <#179 (comment)>: > Datatype: idrange:2 - - Annotations: - allocatedto: "ADDITIONAL EDITOR" - - EquivalentTo: - xsd:integer[>= 1000000 , <= 1999999] - - -Datatype: xsd:integer -Datatype: rdf:PlainLiteral +Annotations: allocatedto: "Chris Mungall" Any chance this has syntax to connect your ORCID? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#179 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABV6HJYHGVKVQ3KGLB3VYDLUBW2WXANCNFSM5D437Z6A> .

[cmungall]

This PR was done quickly at a meeting with the intent to add more context later... but that was never done. I'll try to take a look later

[wdduncan]

Just noticing this ...
Should cob-edit.owl be in functional syntax?

[matentzn]

@cmungall resolved conflicts.