Ontology meeting 2013-05-30

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Minutes:

Attendees:


Metabolism terms

We need to follow up on the issues highlighted at the last GOC meeting

(minutes here: https://docs.google.com/document/d/17UNVgjGgA14icJTjLqcoLNaYv5SkDFyag30WuLxo6zQ/edit)

Paul T wrote: "I wanted to make sure we follow through with the discussion at the Churchill meeting regarding definitions of catabolic process and biosynthetic process terms. We don't simply want to define any reaction that produces X to be classified as 'X biosynthetic process', and any reaction that breaks down Y to be classified as 'Y catabolic process'. The biological goal needs to be biosynthesis of X, or catabolism of Y, and this definition should not include such reactions if they are intermediates in a different pathway, or side products of a reaction (like the nitric oxide synthase example discussed at the meeting). Are we redefining these metabolism terms now?"

No-longer-inferrable links

These are called "EXISTS, TAGGED-INFERRED, NOT-ENTAILED" in the latest weekly report. Discuss strategy to review them.


Follow-up: viable solutions to run reasoner(s) in P4 on go-plus.owl or sub-types of it

Heiko, Chris - Would it be possible to have the explanations along with the weekly inferred links report?


Follow-up on TermGenie FreeForm

Following up on last week's discussion, so we don't forget - Heiko/Chris, is it feasible to put a notice up, at the top of the page, on the lines of "IMPORTANT: before using this form, please check if there is an existing template for your term in http://go.termgenie.org/"?

DONE

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.


Follow-up: template for assembly/disassembly of CC terms

Chris/Heiko, where are we with this?


GO is_a based on ChEBI has_role? (Tanya)

Bringing back the discussion from past meeting. Recent SF request from Peter dE brings it back up . SF item

part_of is_a (David)

New check for is_a inferences of terms that are already parts.


Cell call (David)

  • Create neurotransmitter secretion terms
  • Are we using, going to use capable_of or capable_of_o_part_of?


TG template for 'cell differentiation'

Are we ready for this?

See e.g. http://sourceforge.net/p/geneontology/ontology-requests/9698/


TG template for 'anatomical structure development'

See e.g. http://sourceforge.net/p/geneontology/ontology-requests/9697/

We're probably not ready for this yet, but we may want to schedule necessary work - or push to a later date?

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