Ontology meeting 2012-10-18: Difference between revisions

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I think this is the problem - how to distinguish between cellular processes that occur within a multicellular organism, and multicellular organism processes. Perhaps use tissue? e.g.  
I think this is the problem - how to distinguish between cellular processes that occur within a multicellular organism, and multicellular organism processes. Perhaps use tissue? e.g.  


  cellular process = [biological process has_participant exactly 1 cell] OR [has_participant >1 cell AND occurs_in 1 tissue type within a multicellular organism] OR [has_participant >1 cell AND external to a multicellular organism]
  cellular process = [biological process has_participant exactly 1 cell] OR [has_participant >1 cell AND occurs_in 1 tissue type within a multicellular organism] OR  
[has_participant >1 cell AND external to a multicellular organism]


Can you express that in OWL?!
Can you express that in OWL?!

Revision as of 09:26, 17 October 2012

MINUTES: Paola

ATTENDEES:


FOLLOW-UP: ChEBI paper

Did the PIs give us any comments?

Discussion item: cell-cell junctions

Related to [1]. Basically, do cell-cell junctions have parts that belong to each of the cells they bridge, or are they part of just one of the cells?

If we say 'cell junction' has_part 'plasma membrane', is that logically the same as saying 'cell junction' has_part SOME 'plasma membrane', or 'cell junction' has_part WHOLE 'plasma membrane'? Would it better to say 'cell junction' has_part 'plasma membrane part', or is that logically equivalent to saying 'cell junction' has_part 'plasma membrane'?

FOLLOW-UP: asserting/adding tag for inferred links

Did Heiko and Chris make any progress getting Stanford to change whatever they had to change so we can move forward with this?

FOLLOW-UP: logically defining single-/multi-organism processes

We discussed last meeting defining:

cellular process = biological process has_participant exactly 1 or 2 cells
multicellular organism process = biological process has_participant 2 or more cells

This won't work for cases like flocculation, which is a cellular process which involves >2 cells.

Could we say:

multicellular organism process = biological process occurs_in multicellular organism and has_participant >2 cell

but then for cp:

cellular process = biological process has_participant exactly 1 cell OR has_participant >1 cell AND occurs_in ???

I think this is the problem - how to distinguish between cellular processes that occur within a multicellular organism, and multicellular organism processes. Perhaps use tissue? e.g.

cellular process = [biological process has_participant exactly 1 cell] OR [has_participant >1 cell AND occurs_in 1 tissue type within a multicellular organism] OR 
[has_participant >1 cell AND external to a multicellular organism]

Can you express that in OWL?!

Sorry, that's a ramble of an agenda item.

FOLLOW-UP: TermGenie template for non-template-able terms

See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-10-11


FOLLOW-UP: EC numbers in GO - feasibility study

Carried over from a previous meeting: see Action Items and background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-08-08#FOLLOW-UP:_EC_numbers_in_GO_-_feasibility_study