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?

From Alex: The original reasoning to the layout is found in my comments to SF1290786 in 2005, and the structure was agreed to at the TIGR GO Content Meeting of November 2005. The basic argument is that at the molecular level, a detection event is an induced response in a receptor protein upon binding of a ligand or absorption of a photon etc. that results in a conformational change leading to initiation of a signaling event. I would be interested in alternatives to this structure, possibly based on relation types not in use in 2005.

  • 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 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



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