SourceForge meeting 2013-07-24

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Attendees:

Minutes:


Channel Activity

QUESTION: Is limiting channel activity to TRANSMEMBRANE TRANSPORT too restrictive?

Comes from a SF request from Rama for a new term to annotate Rpt2, an ATPase of the regulatory particle (RP) of the proteasome. PMID 11430818

The RP controls gating of the adjacent core proteasome (CP) channel, to allow entry of proteins into the CP for degradation. The obsolete term http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008575 describes the activity of Rpt2.

See also: PMID 11062564. A gated channel into the proteasome core particle.


[Term]
id: GO:0015267
name: channel activity
namespace: molecular_function
def: "Catalysis of energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or  channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-]
synonym: "alpha-type channel activity" RELATED []
synonym: "channel-forming toxin activity" RELATED []
synonym: "channel/pore class transporter activity" EXACT []
synonym: "nonselective channel activity" EXACT []
synonym: "pore activity" BROAD []
synonym: "pore class transporter activity" RELATED []
xref: TC:1
is_a: GO:0022803 ! passive transmembrane transporter activity

Should we create a new broader channel activity term that isn't restricted to movement across a membrane?


Missing xps to metabolism terms

Could David and Tanya please fill us in about any consensus reached at JGI last week... what 'roles' do we NOT care about? ...pigment, xenobiotic...?


Taxis, tropism and kinesis terms - and their link to 'axon guidance'

https://sourceforge.net/p/geneontology/ontology-requests/10261/

Can I go ahead with my suggested strategy?


'Response to' vs. 'cellular response to'

I have created several children of 'intrinsic apoptotic pathway' of the type 'int. apo. path. _in response to_ hypoxia/DNA damage/etc' and I have them mapping to the 'response to' terms, not the 'cellular response to'. I feel I should amend that. Comments?


Ontology documentation

Where are we with this please https://www.ebi.ac.uk/panda/jira/browse/GO-154

I have a related Jira ticket https://www.ebi.ac.uk/panda/jira/browse/GO-131, Jane and Tanya have CC and BP, anything I should do on mine?


Propagating via positive and negative regulation

David and Tanya, did you get to look at this at JGI last week?