Ontology meeting 2011-08-17

Report

Jane will report on the virus terms.

Discussion notes

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 [1] and [2] 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

[1] ""regulation of X by regulation of Y" is_a "regulation of X"
[2] ""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

• 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]

Task List