Ontology meeting 2013-02-14
MINUTES: Paola
ATTENDEES: Jane, Paola, Chris, David, Harold, Heiko, Judy, Tanya
ChEBI paper
See AI from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#ChEBI_paper
Chris added more to the methods, described how we tag axioms, etc. He started on the diagram, but now wonders if we really need it? Agree to leave it out. Will be replaced by another figure. Judy wants us to submit before the SAB meeting. David to be corresponding author (target journal: Genome Biology). Let's go ahead and submit! It's fine to write 'Submitted' on the wiki. References are reformatted properly. No pre-submission, just go for it. David will try to do it before the cell cycle meeting. We can all help write the letter if necessary.
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?
Action potential: Ok, let's make it a process, since the neurobiology community sees it that way (and so does some of the cardiac conduction people). Let's just change 'regulation of action potential' to 'action potential'. Or shall we obsolete the old term? We need to look at annotations. Maybe consult with RGD since they own most annotations. Let's make sure it stays out of neuro-only process.
AI: Paola will make a SF ticket, look at annotations, consult with others. We need to work with the neurobiology community and find a compromise.
Monthly update: Project Management in JIRA
Reviewed pending tickets.
Protein complexes
See AI from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Protein_complexes
Moved to next call.
Interactions with CHEBI
See notes from last call: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Interactions_with_CHEBI
Moved to next call.
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
Jane spoke with InterPRO and they don't remember ever producing obo files! But they can help. Jane will follow up with them. As for the mappings that Emily and Marijn produced last summer, InterPRO are using those already. There's a Jira ticket about it, to produce xps - we can follow up. The main issue is that InterPRO doesn't have much granularity under domain binding, but we'll have to live with that for the time being.
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)
Moved to next call.