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Source ontology files for the Gene Ontology
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Taxon constraint for X, Y chromosome in birds #12108

Closed michaelerice closed 7 years ago

michaelerice commented 9 years ago

Request review of taxon constraint for GO terms containing X chromosome and Y chromosome. never_in Taxon:8782 Aves PMID: 20622855 Thanks GOC:mr

cmungall commented 9 years ago

And obviously restrictions on Z too

On 19 Oct 2015, at 13:37, michaelerice wrote:

Request review of taxon constraint for GO terms containing X chromosome and Y chromosome. never_in Taxon:8782 Aves PMID: 20622855 Thanks GOC:mr

Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/12108

michaelerice commented 9 years ago

Sorry,

I just realized this is an issue that was at least partially addressed by Paola.

https://sourceforge.net/p/geneontology/ontology-requests/10840/?limit=10&page=1#9882

and you are correct Chris

cmungall commented 9 years ago

Yes #11025 has some discussion, but I think this is a nice valid self-contained request so we should go ahead and do this

michaelerice commented 9 years ago

?Thank you

Michael E. Rice AgBase biocurator School of Animal and Comparative Biomedical Sciences Thomas W. Keating Bioresearch Building 1657 E. Helen St. Tucson, AZ 85721 The College of Agriculture and Life Sciences The University of Arizona 520 955-2745 mrice@email.arizona.eduhttp://mrice@email.arizona.edu

From: Chris Mungall notifications@github.com Sent: Monday, October 19, 2015 2:51 PM To: geneontology/go-ontology Cc: Rice, Michael E - (mrice) Subject: Re: [go-ontology] Taxon constraint for X, Y chromosome in birds (#12108)

Yes #11025https://github.com/geneontology/go-ontology/issues/11025 has some discussion, but I think this is a nice valid self-contained request so we should go ahead and do this

Reply to this email directly or view it on GitHubhttps://github.com/geneontology/go-ontology/issues/12108#issuecomment-149358596.

michaelerice commented 9 years ago

??so Z chromosome and W chromosome would be restricted to only_in birds and some reptiles; I am not sure of which taxons, when I am able I will look look these up and send them in. Thanks

Mike

Michael E. Rice AgBase biocurator School of Animal and Comparative Biomedical Sciences Thomas W. Keating Bioresearch Building 1657 E. Helen St. Tucson, AZ 85721 The College of Agriculture and Life Sciences The University of Arizona 520 955-2745 mrice@email.arizona.eduhttp://mrice@email.arizona.edu

From: Chris Mungall notifications@github.com Sent: Monday, October 19, 2015 2:01 PM To: geneontology/go-ontology Cc: Rice, Michael E - (mrice) Subject: Re: [go-ontology] Taxon constraint for X, Y chromosome in birds (#12108)

And obviously restrictions on Z too

On 19 Oct 2015, at 13:37, michaelerice wrote:

Request review of taxon constraint for GO terms containing X chromosome and Y chromosome. never_in Taxon:8782 Aves PMID: 20622855 Thanks GOC:mr

Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/12108

Reply to this email directly or view it on GitHubhttps://github.com/geneontology/go-ontology/issues/12108#issuecomment-149346201.

cmungall commented 9 years ago

I think only_in could be dangerous. Heterogametic sex determination has evolved multiple times, not just in vertebrates. never_ins will be safer

On 20 Oct 2015, at 12:47, michaelerice wrote:

??so Z chromosome and W chromosome would be restricted to only_in birds and some reptiles; I am not sure of which taxons, when I am able I will look look these up and send them in. Thanks

Mike

Michael E. Rice AgBase biocurator School of Animal and Comparative Biomedical Sciences Thomas W. Keating Bioresearch Building 1657 E. Helen St. Tucson, AZ 85721 The College of Agriculture and Life Sciences The University of Arizona 520 955-2745 mrice@email.arizona.eduhttp://mrice@email.arizona.edu

From: Chris Mungall notifications@github.com Sent: Monday, October 19, 2015 2:01 PM To: geneontology/go-ontology Cc: Rice, Michael E - (mrice) Subject: Re: [go-ontology] Taxon constraint for X, Y chromosome in birds (#12108)

And obviously restrictions on Z too

On 19 Oct 2015, at 13:37, michaelerice wrote:

Request review of taxon constraint for GO terms containing X chromosome and Y chromosome. never_in Taxon:8782 Aves PMID: 20622855 Thanks GOC:mr

Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/12108

Reply to this email directly or view it on GitHubhttps://github.com/geneontology/go-ontology/issues/12108#issuecomment-149346201.

Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/12108#issuecomment-149681057

michaelerice commented 9 years ago

Fiona McCarthy fionamcc@email.arizona.edu Wed 10/21/2015 8:57 AM

Also needs to be checked for ALL species, as we do computational annotation on reptiles, invertebrates, etc.

See: https://en.wikipedia.org/wiki/XY_sex-determination_system

paolaroncaglia commented 7 years ago

Note for self: terms to look at:

BPs: dosage compensation (if not applicable, look at its children: dosage compensation by hyperactivation of X chromosome dosage compensation by hypoactivation of X chromosome dosage compensation by inactivation of X chromosome) regulation of dosage compensation by inactivation of X chromosome sex determination, establishment of X:A ratio

CCs: X chromosome located dosage compensation complex, transcription activating W chromosome X chromosome XY body Y chromosome Z chromosome

paolaroncaglia commented 7 years ago

Hi @michaelerice,

The only constraints (and dbxrefs) I could safely add, based on my knowledge and on some quick reading, are the following:

A) X chromosome located dosage compensation complex, transcription activating

X chromosome

XY body

Y chromosome

dosage compensation by hyperactivation of X chromosome

dosage compensation by hypoactivation of X chromosome

dosage compensation by inactivation of X chromosome

regulation of dosage compensation by inactivation of X chromosome

sex determination, establishment of X:A ratio

=> relationship: never_in_taxon NCBITaxon:8782 ! Aves => GOC:mr, https://en.wikipedia.org/wiki/XY_sex-determination_system, PMID:20622855

B) Z chromosome

W chromosome

=> relationship: never_in_taxon NCBITaxon:40674 ! Mammalia => GOC:mr, https://en.wikipedia.org/wiki/ZW_sex-determination_system, PMID:20622855

These are done now. Addition of further never_ins might be complex and would require more in-depth knowledge. If you can pinpoint other such constraints, please indicate GO terms and suggested taxon rules for them in a new ticket. Thanks!