Ontology meeting 2015-07-02: Difference between revisions

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David H has been pushing for direct regulation to be reg of an MF or of some MF that is part of a process.  This sounds like it could be broader, although maybe that hinges on what 'immediately upstream of' means.
David H has been pushing for direct regulation to be reg of an MF or of some MF that is part of a process.  This sounds like it could be broader, although maybe that hinges on what 'immediately upstream of' means.
=== Follow-up: Intersections vs. relationships in children of 'protein complex' ===
Where are we? From last discussion:
To avoid mis-classification of protein complexes that may have the same function or be involved in the same process, we need to retrospectively check all children of 'protein complex' that have intersections (not relationships!) with capable_of function links and capable_of_part_of process links. David OS prepared a list:
[http://wiki.geneontology.org/images/3/31/ProComp_func_int.txt list of protein complexes with EC def + axiom linking to MF/BP]
  Sent list to Harold.  He will review.




[[Category:Ontology]]
[[Category:Ontology]]
[[Category:Meetings]]
[[Category:Meetings]]

Revision as of 15:37, 24 June 2015

Implement MF patterns using directly regulation relations ?

Chris has added relations such as 'direcly activates' and 'directly inhibits' to RO.

Background and details of relations: An OWL Model of Biological Regulation

Are these ready to use for design patterns for MF, e.g.

ubiquitin ligase activator activity EquivalentTo: 'enzyme activator activity' that 'directly activates' some 'ubiquitin protein ligase activity'

(Note - Does sound a little odd. From its name, 'activates' feels like it should have a continuant as its range...)

Is the def tight enough?: 'directly activates': "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q."

David H has been pushing for direct regulation to be reg of an MF or of some MF that is part of a process. This sounds like it could be broader, although maybe that hinges on what 'immediately upstream of' means.

Follow-up: Intersections vs. relationships in children of 'protein complex'

Where are we? From last discussion:

To avoid mis-classification of protein complexes that may have the same function or be involved in the same process, we need to retrospectively check all children of 'protein complex' that have intersections (not relationships!) with capable_of function links and capable_of_part_of process links. David OS prepared a list:

list of protein complexes with EC def + axiom linking to MF/BP

 Sent list to Harold.  He will review.