Ontology meeting 2011-08-17
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Jane will report on the virus terms.
Discussion notes - I
(continued from Aug 3rd Ontology Meeting)
- 'regulation of Y process by regulation of transcription from RNA polymerase II promoter'
- Used to annotate TFs.
- Can we infer  and  as Chris describes below since there is an INDIRECT regulatory event?
First we need logical definitions for existing terms. 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
- See GO:0072361 and GO:0035947 for examples of how the intersections are included at the moment... (may require updating):
[Term] id: GO:0072361 name: regulation of glycolysis by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of glycolysis by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] is_a: GO:0006110 ! regulation of glycolysis is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006096 ! glycolysis intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T02:57:18Z
- is 'regulation of transcription involved in regulation of y process' a suitable option? (is_a: regulation of transcription, part_of: regulation of y process)
Discussion notes - II
- Is there any reason we can't expand the xps relationship set a little to allow us to write xps for terms as we add them? I'd like has_participant and its inverse (participes_in??) e.g. just added terms for macropinocytosis and macropinosome. located_in won't work here. [Jane]