Ontology meeting 2011-11-16

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Discussion notes


Discussion notes I: TERMGENIE UPDATE

  • Chris, can you please update us on current plans for the new TermGenie? Thanks.

http://go.termgenie.org/

Discussion notes II: TAXON RESTRICTION FILE

  • What checks are taxon_go_triggers file subject to? Currently, for example, it's allowing conflicting taxon restrictions:

Screen shot 2011-11-04 at 10.46.10.png

  • 'cyanelle ribonuclease P complex ; GO:0030679' has restrictions to both Viridiplantae (green plants) and Glaucocystophyceae (algae)'. Cyanelles are plastids of Glaucocystophyte algae, so the plant restriction is wrong (NB: I've now fixed the cyanelle cases in the taxon file because they were causing problems for SIB curators, but there's probably other examples).
  • There's lots of redundant taxon restrictions in the file. Although this isn't wrong, it does clutter up the taxon restriction display in QuickGO, and makes maintaining taxon_go_triggers more time-consuming.
  • Can taxon_go_triggers be more integrated into the main obo file: what checks are in place to check the two are in-sync (e.g. for merged/obsoleted terms).


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: GAMETE GENERATION

Chris sent round emails to GO editors asking about the definition and placement of 'gamete generation' terms. Is this the same as 'gamete formation'? or 'gamete formation AND the subsequent maintenance processes?.

Is gamete generation restricted to multicellular organisms?


Discussion notes V: AGENDA FOR PROTEGE WORKSHOP


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