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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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update def TFIIIB complex? #9729

Closed gocentral closed 7 years ago

gocentral commented 12 years ago

TFIIIB complex is defined as

A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIB contains the TATA-binding protein (TBP) and two Pol III-specific proteins, B'' and BRF.

but, I think this involved directly in transcription? not in regulation? (i.e in PolIII assembly at the promoter)

(if so, some SPKW mappings will need moving)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9522

gocentral commented 12 years ago

I have been discussing this with Karen and when we described the molecular functions of these complexes, we decided that they both regulate and are necessary for (ie part_of) the transcription. If you look at GO:0001033 you can see this. The rational was that this complex is both part of the preinitiation complex assembly but is part of the regulatory mechanism as well. We can tweak the definitions to make this clear. What do you think?

Original comment by: ukemi

gocentral commented 12 years ago

David, this sounds good. I think it would be really helpful if it stated explicitly that it was involved directly in the assembly and the regulation/ and or that there was an ontology link to the function term (which I had not noticed yet)

GO:0001033 RNA polymerase III type 3 promoter TFIIIB recruiting transcription factor activity may also benefit from a comment that, if you use this term, you also need concurrent annotations to DNA binding?

Its also a shame, that somehow this cannot be called TFIIIC activity instead of GO:0001033 RNA polymerase III type 3 promoter TFIIIB recruiting transcription factor activity (which could be an exact synonym) with the comment "This represents TFIIIC" (using the names that users would type would make it much easier to find)

So far this term has zero annotations so even SGD did not find it during the transcription overhaul to the new terms.

Currently we are using GO:0000995 : core RNA polymerase III binding transcription factor activity for TFIIIC (with is not a parent of the recomended term)

I also found it a little confusing that this is defined as "The function of binding to a specific DNA sequence motif ..." because this made me expect it to be one of the DNA binding type terms. I think this maybe because I have got used to the less functionally oriented wording on the PolII branch, which say "Interacting selectively with a sequence of DNA to"? Does that make sense? I still have a little trouble with these types of terms. I think this is largely because the DNA binding part comes first. Maybe the "activity" should come first i.e. "The activity of increase in the frequency, rate or extent of transcription from the RNAP II promoter (this activity occurs simultaneously with the interaction selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), and concurrent annotations should be made to the appropriate DNA binding term.

Original comment by: ValWood

gocentral commented 12 years ago

I looked at the siblings of the parent therm. Some of these are the terms SGD use for TFIIC. Should these be under GO:0001033 instead? Sorry for raising more issues.

Val

Original comment by: ValWood

ValWood commented 7 years ago

duplicate of later https://github.com/geneontology/go-ontology/issues/12985