Ontology meeting 2013-09-19: Difference between revisions

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===single v/s multi-organism processes===
===single v/s multi-organism processes===


We could do with xps for these. Can we say in OWL biological process has_participant exactly 1/2 or more?
We could do with xps for these. Can we say in OWL biological process has_participant exactly 1? Or has_participant >1 ?

Revision as of 09:23, 19 September 2013

Minutes: Paola

Attendees:


Glycosylation

Stems from an email thread that Chris started. Do we need new terms?

High-level disjoints

Stemming from Chris's email:

We use a lot of very specific relations, especially in the development logical defs. These are necessary - if we try and use a more generic relation then the reasoner gets everything tangled.

The specific relations are causing some angst when curators use them in class expressions - they'd prefer a smaller set. I would do, but we need some disjointness axioms first.

Let's say we want to get rid of the ugly transports_or_maintains_localization_of and use a more generic has_input. Seems to make sense - we define things such that the input of a transport process is the cargo. Simple?

consider GO:0015986 ! ATP synthesis coupled proton transport

What's it's input?

It's a subtype of transport, so if the rule is that input for transport is always the cargo, then the input is the proton

It's a subtype of metabolic process, so the input is the thing that is modified - the ATP

The fix here is to get rid of the isa-overloading in the ontology, use a different relation that isa for one of the above paths, make transport and metabolism disjoint. If they are disjoint then we can safely use a broader relation without ambiguity.

There's only a handful of things we'd have to deal with if we were to make transport and metabolism disjoint (receptor internalization too). Remember, you can now do DL queries with Elk so you can just query "transport and metabolic process".

David H I know I've pestered you about this isa overloading in development before, I think this is a higher priority now with more curators ramping up to use these relations.

'during'

What's the status of the exisiting 'during' terms in the ontology? We need an xp pattern in cell cycle for cases where the processes overlap temporally but aren't necessarily dependant on one another e.g. regulation of transcription during G1 phase. Use happens_during? What about the existing terms - I think many of these are probably really involved_in.

DOCUMENTATION FOR NEW WEBSITE

  • Who is dividing up the old pages to distribute to people to rewrite?
  • Who is rewriting what?


Follow-up: Changes to external ontologies

Background here http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-12#Changes_to_external_ontologies


Follow-up: Equivalent classes for Acid/Base transport and transport activity

Background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-05#Equivalent_classes_for_Acid.2FBase_transport_and_transport_activity_.28bumped_from_last_week.29


Follow-up: protein localization to xxx

Have we fixed this? http://wiki.geneontology.org/index.php/Ontology_meeting_2013-09-12#Template_for_.27protein_localization_to_xxx.27_.3F

Heart terms - reserved for vertebrate hearts or OK for general use?

Uberon has a general term 'circulatory system organ' as well as 'heart' - comments on these terms say to reserve the term heart for vertebrate heart, using the broader term for invertebrates. But GO only uses the term heart - with invertebrate annotations clustering underneath. Should we add a whole set of more general terms based on Uberon 'circulatory system organ?'

single v/s multi-organism processes

We could do with xps for these. Can we say in OWL biological process has_participant exactly 1? Or has_participant >1 ?