Ontology meeting 2012-10-18

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?

Right now we have defined and represented them as one cell. See the definition of cell junction and the placement of terms like cell-substrate cell junction.

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'?

Discussion item: non-ChEBI parents for chemical terms

Related to [2] chemical triad + regulation terms added, but no secondary metabolite M/B/C parentage

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.

Discussion item: MOP/CP - behaviour

An item related to the above. We think 'response to...' processes are always single-organism. This is because the process starts when the stimulus has been detected. It doesn't include the stimulus, even when that stimulus is another organism.

At the moment, we have behaviour classified as a response to stimulus. However, there are some behaviours that are definitely multi-organism. For example mating - this inherently has two participants!

So I think behaviour needs to be moved out from response to stimulus so I can split it into single and multi-organism behaviours. What do you think?

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

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

Question: Taxon triggers

Based on [3] and [4]. Who is in charge of these now? Anyone?

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