Ontology meeting 2013-02-14: Difference between revisions
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Anita from NIF has proposed that 'action potential' should be a GO BP: | Anita from NIF has proposed that 'action potential' should be a GO BP: | ||
"Ok, so with the regulation of action potential vs action potential itself, I believe that unlike the current GO thinking, the action potential itself is indeed a biological process, not a quality. The regulation of that process is also a process. | "Ok, so with the regulation of action potential vs action potential itself, I believe that unlike the current GO thinking, the action potential itself is indeed a biological process, not a quality. | ||
So to electrophysiologists, the regulation of an action potential would include things like the phosphorylation of the V-gated Na+ channels to modify the rate or quantity of open time of the channel. This would profoundly modify the action potential shape and possibly even magnitude (since many toxins do this regularly, the literature is rich in this regard). However, the definition here is the opening of Na+ or K+ channels itself, which is a set of steps involved in the core process not the regulation of the process. | The regulation of that process is also a process. | ||
I believe that the same is true for the GO:0060078 regulation of post synaptic potential branch, which also deals with a regulation of a process that seems like should be defined, but does not appear in the ontology." | So to electrophysiologists, the regulation of an action potential would include things like the phosphorylation of the V-gated Na+ channels to modify the rate or quantity of open time of the channel. | ||
This would profoundly modify the action potential shape and possibly even magnitude (since many toxins do this regularly, the literature is rich in this regard). However, the definition here is the | |||
opening of Na+ or K+ channels itself, which is a set of steps involved in the core process not the regulation of the process. | |||
I believe that the same is true for the GO:0060078 regulation of post synaptic potential branch, which also deals with a regulation of a process that seems like should be defined, but does not appear | |||
in the ontology." | |||
What do we think? | What do we think? | ||
Revision as of 11:36, 12 February 2013
MINUTES: Paola
ATTENDEES:
ChEBI paper
See AI from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#ChEBI_paper
Action potential
Anita from NIF has proposed that 'action potential' should be a GO BP:
"Ok, so with the regulation of action potential vs action potential itself, I believe that unlike the current GO thinking, the action potential itself is indeed a biological process, not a quality. The regulation of that process is also a process. So to electrophysiologists, the regulation of an action potential would include things like the phosphorylation of the V-gated Na+ channels to modify the rate or quantity of open time of the channel. This would profoundly modify the action potential shape and possibly even magnitude (since many toxins do this regularly, the literature is rich in this regard). However, the definition here is the opening of Na+ or K+ channels itself, which is a set of steps involved in the core process not the regulation of the process. I believe that the same is true for the GO:0060078 regulation of post synaptic potential branch, which also deals with a regulation of a process that seems like should be defined, but does not appear in the ontology."
What do we think?
Monthly update: Project Management in JIRA
Action Potential is a biological_process?
Stemming from an email thread (forwarded by Chris)
Protein complexes
See AI from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Protein_complexes
Interactions with CHEBI
See notes from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Interactions_with_CHEBI
protein domain specific binding
Jane to report (see AI from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#protein_domain_specific_binding
Protein/glycoprotein/lipoprotein terms in ChEBI
Harold and Judi to report (see notes from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Protein.2Fglycoprotein.2Flipoprotein_terms_in_ChEBI)