Ontology meeting 2013-05-09

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Minutes: Paola

Attendees: Paola, David, Harold, Heiko, Becky, Jane, Tanya


Follow-up: Logical definitions for CL terms in GO

The asserted links went in 3 days ago. The axioms listed in these SF ticket may need checking/debugging:

https://sourceforge.net/p/geneontology/ontology-requests/10170/

https://sourceforge.net/p/geneontology/ontology-requests/10178/

https://sourceforge.net/p/geneontology/ontology-requests/10166/ (but the issue must be solved by CL first)

Plus see email thread initiated by Jane yesterday ("Problematic inferred links").

For the oogenesis issue, we've put in a ticket in the CL tracker, everything is reported in the ontology SF tickets above. For the problematic inferred links in the email thread above, we need Chris to look into it and make sure that the redundancies are captured. As for the cycle error, Chris commented:

"There are (at least) rwo kinds of cycles

1. Cycles over SubClassOf (which is equivalent to EquivalentClasses statements for all classes in the cycle)

2. Cycles over other relationship types

I think it would be hard for 1 to get through as we check for equivalance between named classes

We can't have 2 as a global constraint because with multiple relationship types the ontology can no longer be assumed to be a DAG. However, there is a lot of software that assumed the combined set of relations form a DAG. For this reason we defined a sub-language of OBO-Format called obo-basic that disallows DAGs:

http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#6.2

- Any software that assumes a DAG *must* consume go-basic

- Any software that consumes anything beyond GO-basic should not assume a DAG (although they are free to make their own basic subset and assume a DAG over that)

If it is the case that we have published go-basic with a cycle then we need some extra check in the pipeline (I'm at a meeting right now can't provide further details on this specific case yet)"

Heiko will run the next weekly assert job in a silent mode and we'll have a look at the report. Once we've figured out where the problem comes from, we'll start committing again.


Also, stemming from some of the issues above, it might be good to look at the 'gametogenesis' node again, and include a fly expert's perspective.

ACTION ITEM: David and Becky to follow up on this.

Follow-up: CL xps with obsolete classes

Are these fixed now? Full list here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-02#CL_xps_with_obsolete_classes

These have probably taken care of by Chris, but we haven't been able to check.

Update: Yes they are fixed, latest go_xp build has no errors related to obsolete classes.

Follow-up: (Feasibility and strategy for) providing hard links from apoptosis terms to the apoptosis curation manual on the wiki

Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-02#.28Feasibility_and_strategy_for.29_providing_hard_links_from_apoptosis_terms_to_the_apoptosis_curation_manual_on_the_wiki

Jira issue: (see questions at the end; who should the ticket be assigned to?) http://www.ebi.ac.uk/panda/jira/browse/GO-160

Paola emailed Chris, Tony and Rachael asking to comment on the Jira ticket, possibly breaking it into manageable items and we'll go from there. This type of strategy would be useful for other projects as well; Becky's working on a curation manual for signaling, and we'll try to do the same for cell cycle.

Follow-up: Template for receptor activities

Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-02#Template_for_receptor_activities

Becky has looked through [1] to check for anomalies, and will remove the mistakes due to synonym mis-catching in ChEBI.

Q1: Receptors in GO are generally split into transport (cargo) receptors that bind to a substrate and internalize it via endocytosis. And signaling receptors which bind to/receive a substrate and pass the signal on within the cell. Do we want to make the differentia more specific (signaling receptor activity ; GO:0038023)?

Q2: Can we have ChEBI roles in the intersections?

[Term]
id: GO:0030594  ! neurotransmitter receptor activity
intersection_of: GO:0004872  ! receptor activity
intersection_of: has_input CHEBI:25512  ! neurotransmitter

For the proteins and peptides (insulin etc), we'd be better off pulling in from protein ontology.

Leave nuclear receptors for now, as these also have parentage in the transcription node.

Bumped to the next call, we need Chris.

Obsoletion emails

Currently these go to the go-consortium mailing list, but we have the feeling they don't actually reach everyone we'd like. Possibly advertise on wider list such as go-discuss? Or create a go-announce list. Or, maybe simpler/safer, check who currently subscribes to go-consortium.

We should keep using the go-consortium mailing list, but we need to make sure that the PRO people subscribe to it.

ACTION ITEM: Harold will look into it.

Also about obsoletion: Jane has started using the 'PENDING OBSOLETION' text-tag and obsoletion explanation in definition comments (for some cell cycle terms). They're very convenient as one can retrieve them easily by search and replace the 'PENDING OBSOLETION' text with just the reason for obsoletion. So it is suggested that we adopt this as standard procedure for obsoletions.

ACTION ITEM: Jane will add these comments to the obsoletion guidelines on the wiki.

PRO mappings to GO terms

Stems from http://www.ebi.ac.uk/panda/jira/browse/GOHELP-376

We currently have no easy way of knowing if PRO references to our terms, do we?

Harold says: every PRO complex term has an is_a to a GO term. But they're not visible to the outside or deposited anywhere public.

ACTION ITEM: Harold will look into this.

Follow-up: Templates for regulation of biological qualities

Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-02#Templates_for_regulation_of_biological_qualities

Bumped to the next call, we need Chris.


Interviews for new GO Editor

We'll interview the 6 candidates via skype next week, on Thursday 16th. We hope to get down to say 3-4 candidates that we can then invite for interviews in person at EBI, probably the week starting June 10th.

ACTION ITEM: Jane to re-send schedule of skype interviews to David (and Chris), and to follow-up on confirming the date for the in-person interviews.