Ontology meeting 2016-10-13

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Attendees:

Minutes: Moni??

Regrets: Chris

GoToMeeting invite: https://global.gotomeeting.com/join/859015101


SOP when merging terms

David H confirmed that the problem doesn’t stem from merging in OBO-Edit (“did a test merge in obo-edit and the resulting obo stanza looks fine. I suspect that the build problems arise in the pipeline downstream. No ghost terms after the merge and save.”), and suggests the following:

“I think that whenever we merge, we need to check the inferences file [go_inferences.obo] for references to the merged terms. If they exist, they should be deleted. Then when the terms are merged, the cross-products need to be checked and edited as appropriate. Presumably then when the write file [gene_ontology_write.obo] is committed, the ghost inferences will not exist in the inference file and the ghost terms won't be created.”

Let’s confirm. Comments here please: https://github.com/geneontology/go-ontology/issues/12729

equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ?

https://github.com/geneontology/go-ontology/issues/12721

gene_ontology_write.obo imports cheb_import.owl. This lacks the equivalence axioms (GCIs). But we have a file called bio_chebi.owl which has them. bio_chebi.owl was last updated 19 months ago: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/bio-chebi.owl?view=log

Update: contacts for UniProt annotations

As already mentioned, we should email the GOA helpdesk at goa@ebi.ac.uk for annotations assigned specifically by EBI UniProt (GOA) curators. Where annotations by SIB UniProt curators are or may be involved, please email help@uniprot.org. They distribute updates to all UniProt curators (GOA + SIB). I added this info to the Google spreadsheet (https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0), but we opted not to include email contacts on the corresponding GitHub page (https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv).

Also, [one for David OS?] Chris reminds us to coordinate with Seth on any metadata related to people, see https://github.com/geneontology/go-site/issues/231.

Update: membership go-ontology mailing-list

Do we want to restrict membership of the list or should it be a public one? (The current list of subscribers can be accessed upon logging in https://mailman.stanford.edu/mailman/listinfo/go-ontology)

Pending TG requests

Just a note so we don't forget to deal with these:

regulation of memory terms (requested by Helen Attrill, FlyBase)

heteroreceptor complex assembly/disassembly (requested by Paul Denny, UCL)

Follow-up: GitHub projects

See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects

Paola added one card each to the 3 columns in https://github.com/geneontology/go-ontology/projects/1. Feel free to add as an experiment, and/or we could go over those. Then we can see how this works for us.

Melanie: https://github.com/geneontology/go-ontology/issues/12723 "hypusine pathway", discussed with David Hill and thought worthwhile to bring to editors call.

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