Ontology meeting 2013-01-24: Difference between revisions

Revision as of 08:46, 23 January 2013

MINUTES: Jane

ATTENDEES:

ChEBI paper

Anything missing/left to do before (pre)submission?

'Releasing' TermGenie free form

Jane has prepared a list of candidate users. Next step: circulate/advertise. DONE. TermGenie gatekeepers, please remember to delete the termgenie_unvetted subset line if a new term looks straightforward. Suggested strategy for non-straightforward terms: contact submitter; if necessary, discuss among editors; any more comments/suggestions?

Sync issue between editors version and release versions?

We still haven't got to the bottom of this. The example is GO:0019064. In go.owl, go.obo etc it has three parents. In go-trunk/ontology/editors/gene_ontology_write.obo it has two (missing GO:0048610 cellular process involved in reproduction which I removed).

Protein/glycoprotein/lipoprotein terms in ChEBI

SF request on ChEBI tracker: https://sourceforge.net/tracker/?func=detail&atid=703818&aid=3592472&group_id=125463

There was an email thread ('protein in CHEBI and PRO') between Chris and Darren, but no conclusion was reached as far as I [Paola] can see. Chris, was there any further follow-up to your message below:

'CHEBI is open ended here:

CHEBI:33709 ! amino acid [DEF: "A carboxylic acid containing one or more amino groups."]

It doesn't *exclude* the amino acid including attached bits.

It seems the isa/has_part confusion permeates CHEBI even after all our work aligning with GO. Or maybe it's just me that's confused - is there some documentation I'm missing?

Anyway, it seems the direction we're going is a more liberal definition that is inclusive of attached bits. Does this fit with our intended inferences in GO?'

Daily digest emails for new/edited/obsoleted terms (obo-diff.html)

Heiko/Chris, is it feasible to 'convert' the Jenkins diff into emails (what curators really wish for)?

Update on cell cycle meeting

Dates confirmed: Feb. 28th and March 1st.

Confirmed attendees: Val, Jacqueline Hayles, David, Tanya, Jane, Paola, Bijay Jassal (Reactome/EBI), Mary Dolan (MGI - attending remotely).

TBC: Lisa Matthews? Jan Skotheim?

Agenda: to be prepared. Arrange conference call after the Berkeley workshop?

@@ Line 13: / Line 13: @@
 Jane has prepared a list of candidate users. Next step: circulate/advertise. DONE. TermGenie gatekeepers, please remember to delete the termgenie_unvetted subset line if a new term looks straightforward. Suggested strategy for non-straightforward terms: contact submitter; if necessary, discuss among editors; any more comments/suggestions?
+===Sync issue between editors version and release versions?===
+We still haven't got to the bottom of this. The example is GO:0019064. In go.owl, go.obo etc it has three parents. In go-trunk/ontology/editors/gene_ontology_write.obo it has two (missing  GO:0048610 cellular process involved in reproduction which I removed).
 ===Protein/glycoprotein/lipoprotein terms in ChEBI===