Ontology meeting 2012-12-13

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

Mapping proton/hydrogen ion terms to the correct ChEBI term

(Tanya and Paola) Stemming from a TG request for 'proton binding' (mapping to CHEBI proton). Based on the reference, the mapping should go to CHEBI oxonium (H3O+) instead.

Same for xxx:proton/hydrogen symporters/antiporters Is it always the case that whenever we are talking about a proton we are talking about a proton? Harold thinks that you can pass a proton itself. Harold will investigate. Are we going to have to lump the proton and oxonium together like we did for the acids and bases?

Discuss default relationships for the qualifier column in the new GPAD format

part_of------ Do complexes create a problem with this? Much discussion. If a complex is defined by its members is it always a part_of or is it sometimes attached to?

is_active_participant_in---- does this create problems when we have mutant phenotypes? This is reminiscent of the regulates conundrum where we annotate to the parent. Do we need a weaker relationship for process? It would be the union of is_active_participant_in and regulates_active participant_in. Should we use involved_in? We need to decide how annotators will choose these relationships.

ChEBI paper

Action items from last week - where are we?

Chris to follow up on Jane's email about flow diagrams. - Jane to have a go at this. Chris will take this over again.

David to prepare cover letter. David will draft a letter on the bus tomorrow.

TermGenie free form terms

Report on testing: is it ready to be advertised? Paola's testing seems to have worked. Perhaps we can roll it out to a few people just to see how it works.

Report on action items from last week: 1) explore feasibility of preventing submitters from creating regulation terms if the target term is a descendant of 'regulation of biological quality'; Chris and Heiko will check the existing constraint to see why this doesn't violate 'regulation of regulation'. If we create a cross product for R of BQ then we should fit the constraint.

2) demote similar terms check to a warning. (DONE)

Protein/glycoprotein/lipoprotein terms in ChEBI

Report after meeting with ChEBI:

They might take a bit more time so they can better look at the SF ChEBI ticket opened by Chris.

Their suggestion, however, would be to delete the link between 'conjugated protein' and 'protein' in ChEBI (they'd make 'conjugated protein' a 'macromolecule' or 'biomacromolecule' or similar).

We think that there is still an issue with the definition of protein being an 'amino acid chain' or 'protein-containing compound'.

Daily digest emails for new/edited/obsoleted terms

Chris and Heiko to report. Was back and is now gone again. Chris and Heiko will try to get this done by the end of the year.

Alerting users of long-term changes to the ontologies

See background from last week: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-12-06#Alerting_users_of_long-term_changes_to_the_ontologies

So can we label terms for specific projects, like the apoptosis project etc? Should we just make subsets?

MF involved_in BP - TG template

Heiko to report on this. Is now available. Someone needs to test this. David will make a JIRA item.

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

All done? A list of errors will become part of the Jenkins report. The ontology part is done. Now we need individual clean-up.

Submission(s) to the first annual JBMS Ontology Issue