Ontology meeting 2011-08-03
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 )
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:
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  ""regulation of X by regulation of Y" is_a "regulation of X"  ""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  and . It seems there is exactly an indirect regulation event at work here