Ontology meeting 2011-11-16
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Discussion notes
Discussion notes I: TAXON RESTRICTION FILE
- What checks are taxon_go_triggers file subject to? Currently, for example, it's allowing conflicting taxon restrictions:
- '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 II: 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...
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