Ontology meeting 2011-08-03

Report

Chris's Ontology_Release_Files_Proposal

Discussion notes- I

strange inferred annotation (part_of link?)

Tanya:I'm just looking at an annotation that I think must have come from the inferred links (MF-BP) except the new annotation is to a molecular function term.

Original annotation (from our curation interface):

AT5G16850 has telomeric template RNA reverse transcriptase activity (GO:0003721) by ISS : manually reviewed TIGR computational analysis Evidence from TIGR_REF:GO_ref (Evidence with: NCBI_gi:20386373 )

Inferred annotation (also from our interface):

AT5G16850 involved in telomerase activity (GO:0003720) by ISS : none Evidence from TIGR_REF:GO_ref (Evidence with: NCBI_gi:20386373 )

Line from

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/gaf-inference/gene_association.tair.inf.gaf?rev=1.50;content-type=text%2Fplain

  TAIR	locus:2148975	TERT		GO:0003720	TAIR:Communication:501714663	ISS 
  NCBI_gi:20386373	P	AT5G16850	AT5G16850|ATTERT|TERT|telomerase reverse
  transcriptase|F5E19.190|F5E19_190	protein	taxon:3702	20031013	GOC		 
  TAIR:locus:2148975

I don't know why the column for aspect says 'P' when GO:0030720 is a function term.

Graph of relevant 'originating' term:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003721#term=ancchart

Can you refresh my memory what the inferred annotations are working on, is it ANY part_of link, regardless of whether it is MF-BP or MF-MF?

Chris: Quite possibly to do with the fact we now have intra-MF part_ofs. This passed me by... is GO:0003720 *really* a MF?

       is_a GO:0003720 ! telomerase activity *** 
         po GO:0000332 ! template for synthesis of G-rich strand of telomere DNA activity
         po GO:0003721 ! telomeric template RNA reverse transcriptase activity

Tanya: That is strange, isn't it? Also, aren't those other relationships has part? 332 and 3721 to 3720?

David: This seems strange to me too. I think the problem is in the telomerase activity term. Is it describing the totality of what a telomerase (like a DNA polymerase) can do or is the telomerase activity term describing the process of telomere synthesis?

Discussion notes - II

• How to precompose 'x activity involved in y process involved in z process' terms.
• This comes from a SF request from Val: https://sourceforge.net/tracker/?func=detail&aid=3303039&group_id=36855&atid=440764

Discussion notes - III

• Regulation of Y process by regulation of transcription from RNA polymerase II promoter
  • From e-mail discussions, it's clear that a general 'by' syntax can't be added to TG, but can we narrow it down to 'by regulation of transcription from RNA polymerase II promoter? See def for GO:0072361.
  • Where do we stop with joining upstream and downstream processes?
    • E.g. PMID 9427760: Ubr1p degrades the transcriptional repressor Cup9p that represses transcription of the PTR2 gene, which encodes a transporter, which transports dipeptides across a membrane.

Email notes from cjm on addition of "by" template to TG:

First we need logical definitions for existing terms.

 GO:0010881 ! regulation of cardiac muscle contraction by regulation
of the release of sequestered calcium ion [subclass: "regulation of
release of sequestered calcium ion into cytosol by sarcoplasmic
reticulum"] [subclass: "regulation of cardiac muscle contraction by
calcium ion signaling"]

This needs to be turned into a logical definition.

If you want a reasoner to infer

[1] ""regulation of X by regulation of Y" is_a "regulation of X"
[1] ""regulation of X by regulation of Y" is_a "regulation of Y"

Then we can use a template like:

"regulation of X by regulation of Y"
EquivalentTo
"regulation of Y" and regulates some X

However, it's not clear to me that we should be inferring [1] and [2].
It seems there is exactly an indirect regulation event at work here