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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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MP proteasome regulator #6801

Closed gocentral closed 9 years ago

gocentral commented 14 years ago

any reason why this isn't under enzyme regulator activity?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/6821

gocentral commented 14 years ago

Original comment by: mah11

gocentral commented 14 years ago

It appears that the proteosome was originally associated with 2 function, ATPASE activity and endopeptidase activity. Both of the proteosome-specific terms are now obsolete. We could change the 'proteosome regulator activity' term and its children to be 'proteosome endopetidase regulator activity' which is what the definitions imply. Then we could make this a regulates 'endopeptidase cativity' and an 'enzyme regulator activity'. What do you think Val?

D&T

Original comment by: ukemi

gocentral commented 14 years ago

Yep, (just thinking ahead about function slimming)

Val

Original comment by: ValWood

gocentral commented 14 years ago

Note that we'll still have the problem of 'proteasome endopeptidase regulator activity' not having a valid target MF term because 'proteasome endopeptidase activity' is obsolete. We propose to get around it by making the regulates relationship to 'endopeptidase activity'.

I'm kind of leaning towards just getting rid of these terms. I mean, are there specific regulators of the proteasome that one would not just annotate to endopeptidase regulator/activator/inhibitor activity and also to 'regulation of proteasomal protein catabolic process' and its positive/negative children (GO:doesn't exist yet but can be created)? There might be. We have 44 genes annotated to 'proteasome activator activity' and 6 genes annotated to 'proteasome activator activity'. This proposed move would require reannotation.

What do you think?

Original comment by: tberardini

gocentral commented 14 years ago

I agree that regulation of endopeptidase would be more appropriate as a function(proteasome regulator sounds gene producty/processy, but this could be captured by the appropriate regulation of proteasome term). This would seem most sensible to me.....

Val

Original comment by: ValWood

gocentral commented 14 years ago

We will propose obsoletion of the appropriate terms.

D&T

Original comment by: ukemi

gocentral commented 14 years ago

Added the following terms today to provide suitable replacements for the proposed obsoletions:

GO:0061133; endopeptidase activator activity GO:0061135; endopeptidase regulator activity GO:0061136; regulation of proteasomal protein catabolic process

D/T

Original comment by: tberardini

gocentral commented 14 years ago

Obsoletion email sent out on May 17, 2010. Will obsolete terms unless objections are raised on June 1, 2010.

Original comment by: tberardini

gocentral commented 14 years ago

Terms are now obsolete with 'consider' terms suggested.

Original comment by: tberardini

gocentral commented 14 years ago

Original comment by: tberardini

gocentral commented 13 years ago

Original comment by: mah11