Ontology meeting 2013-05-30

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Minutes: David

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

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?"

We should certainly try to represent the objectives. Should we just go through a biochemistry textbook and represent what is there? We need to decide a strategy for which chemicals we should prioritize. We can work with Peter this Summer to start on this. What happens when someone wants to find something that is a side product of a reaction? Are we lumping things under catabolism? Is catabolism a process in and of itself? There is some question as to how much of a priority this project should have. Can we address it with better annotation guidelines? Is what we have currently working? Once we define a reaction like the nitric oxide synthase in OWL, it can automatically be classified not to be an arginine catabolism. From an annotation standpoint, we need to educate annotators to use these terms more specifically. We think this might be a better way to handle this. This way there is not objective required.

No-longer-inferrable links

These are called "EXISTS, TAGGED-INFERRED, NOT-ENTAILED" in the latest weekly report. Discuss strategy to review them. There are 315 lines in the file. Paola made a Google spreadsheet with all of the lines.

David went through the development terms yesterday. Tanya did a few yesterday. Some are easy some are not. For the ones to keep, what do we need to do to keep them? If we think it should be kept, we need to remove the link in the ontology that says it is inferred, and assert it. If we think it should be inferred, we need to correct/add the logical definition. We don't want to keep anything in the regulation branch that can't be inferred automatically. Sometimes we need to fix the core terms that are regulated.

Action plan: Ignore regulation ones and split up the spreadsheet. Mark the spreadsheet as keep or delete and then go back and look at the keep ones to see if we can figure out what is going on. We need to have a game plan for the ones that are due to changes in external ontologies. David will sort and tell everyone which lines are their responsibility. We will all have a look at the line in red. Anything that says OWL thing, can be marked as keep. When we deal with these, we should manually remove the is_inferred tag or make it so that it can be re-inferred.

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/"?


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?

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

Make sure that we create good cross-products for these. Create some tests.

  • Are we using, going to use capable_of or capable_of_o_part_of?

Yes, they are used in the complexes.

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?