Ontology meeting 2012-12-06

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ATTENDEES: Jane, David, Harold, Heiko, Paola, Tanya, Judy

ChEBI paper?

All done? Action items from last week:

AI: Chris to follow up on Jane's email about flow diagrams. ? - Jane to have a go at this.

AI: David to prepare cover letter. ?

AI: Jane and Paola: check with CHEBI that it's ok to proceed to submit even without approval from Paula Matos and Steve Turner. DONE, it's ok to go.

Monthly update: Project Management in JIRA

See http://wiki.geneontology.org/index.php/Ontology_meeting_2012-09-12#Project_Management_in_JIRA

TermGenie free form terms

Report on testing.

Can the gatekeeper remove the 'unvetted' tag if the term looks perfectly fine and ready to go? Yes! Also can remove 'unvetted' tag if another GO editor entered the term.

Also: suggested restrictions:

David and Paola suggest to prevent submitters from creating regulation terms if the target term is a descendant of 'regulation of biological quality'.

E.g. 'regulation of maintenance of presynaptic active zone structure' is wrong because 'maintenance of presynaptic active zone structure' is a grandchild of 'regulation of biological quality'.

AI: one more week of testing.

AI: demote similar terms check to a warning.

Follow-up on children of 'translation' causing TPVs and questions stemming from there

For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-29#Children_of_.27translation.27_causing_TPVs and email threads.

Action items copied over;

AI: David/Tanya: work on the xps to fix Val's problem, and comment on the SF item.

  DONE: David removed offending xps and moved children that didn't belong.

AI: Paola and Jane to discuss the terms highlighted by Val with CHEBI next week.

  Will do this next week.

AI: David: Remove the is_a link between response to organophosphorus and response to insecticide


Follow-up on daily digest emails for new/edited/obsoleted terms

AI: Chris and Heiko to look into this.

Documenting decisions

We need to develop a SOP for doing this, otherwise we won't do it. Let's take the example of the metal cations from last week and figure out how we should do it. We should get into the habit of when we have come to a decision like this, making a ticket for someone to make the doc.

Wrt metal ion terms - How to handle metal ions from the CHEBI changes last week? Change term names to be 'cation' or keep as ion and implement as a GCI? Jane has already changed the xps to the CHEBI cation entities.

AI: Use 'ion' in the term name, with cation synonyms and xps. Up to the editors to catch these as they come in to TG.

Other examples?

Alerting users of long-term changes to the ontologies

Peter D'Eustachio emailed recently asking about some comments Amelia added to some catalysis terms alerting that they would be made obsolete. It lead to a discussion of whether we could provide a mechanism for our users to be alerted about upcoming changes to the ontologies, longer scale than the obsoletion notices.

I know it's something we've discussed at GOC meetings in the past, but we've never really settled on anything. The UniProt group do something ad-hoc in QuickGO where they mark some terms as being under discussion e.g. [1], but it's pretty hacky and uses reg exp.

AI: Janr to remove Amelia's obsoletion notices, for the alerts we need to think about it more.

Adding has_parts for antiporters

Arose from this SF ticket: [2]

Essentially Ruth wants to infer both calcium export and sodium import from calcium:sodium antiporter activity. I've suggested we could use has_part, but this is probably something we'd want to do globally. Do we want to do this? What would be the implications? Could we extend to other transporter types? We have transporter part_of transport elsewhere...this is kind of the inverse of what's being suggested.

AI: These relationships are already in the ontology as is_a

involved_in TG template

Can we extend this to include MFs involved_in BPs?

AI: Heiko to look into this.

Follow-up on TermGenie paper

We should start work on this, and maybe present an abstract at the Biocuration 2013 conference.

AI: Deadline end of Jan - Chris and Heiko will submit something.

Follow-up on annotating to 'part' terms (nuclear_part, etc)

Last week, Jane added the part terms to the 'do not annotate' anti-slim. Chris added a check to Jenkins. How did the check go, and do we need to do anything else?

Submission(s) to the first annual JBMS Ontology Issue


How often updated? What relations are in this file vs go_simple.owl? SVN link

It's done nightly by Jenkins.

go.owl is closer to the editors file than go_simple.owl is.