Ontology meeting 2011-11-30

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Discussion notes

Discussion notes I: REGULATION OF X BY REGULATION OF TRANSCRIPTION

  • Our old favourite: is there progression on making this template in TG, so we can shift the requests out of SF?


Discussion notes II: OBSOLETE TAXON RESTRICTIONS

  • Rather than having a separate file for obsolete taxon restrictions, could we include it in taxon_go_triggers.obo, in the format (suggested by Tony):
relationship: only_in_taxon NCBITaxon:5794 {id="GOTAX:0000001", source="PMID:11111111", source="PMID:22222222", source="GOC:al", obsolete="true" } ! Apicomplexa


Discussion notes III: RESPONSE TO & DETECTION

  • This stems from a SF item from David O-S requesting sensory perception terms for humidity.
  • The sensory perception terms are not linked to 'response terms'. E.g. sensory perception of sound ; GO:0007605 (aka hearing) is not connected to 'response to auditory stimulus ; GO:0010996'.
  • The detection terms are currently is_a children of the response terms:
response to mechanical stimulus ; GO:0009612
--[isa]detection of mechanical stimulus ; GO:0050982

response to stimulus ; GO:0050896
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The  process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.

detection of stimulus ; GO:0051606
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
  • I know David H feels strongly that detection comes before the response. What do other editors think? And what was the original reasoning behind the existing layout?
  • NB: This will have an impact on the signaling terms, since the pathways (ligand-receptor binding down to regulation of a cellular process) are currently children of the cellular response terms...


Discussion notes IV: UPDATE ON PROTEGE WORKSHOP

  • Do we want presentations/demos?
  • Chris will provide us with a list of softwares etc. that we'd need to have downloaded before the workshop begins.


Discussion notes V: UPDATE ON BP_XP_CC SOURCEFORGE ITEMS

  • Chris submitted these at

https://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=440764&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=&category=&artgroup=886159&submitter=&keyword=&artifact_id=&submit=Filter&mass_category=&mass_priority=&mass_resolution=&mass_assignee=&mass_artgroup=&mass_status=&mass_cannedresponse=&_visit_cookie=e69893a83b4d9526a4d95e23b32e856e


Discussion notes VI: OORT OUTPUT

  • Request for Chris to explain the output of the Oort reasoner, now we have it working.
    • What do the Justified asserted subclasses mean (exists entailed, exists not-entailed.....)?
    • What do we need to take action on?


Task List

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