Ontology meeting 2013-05-23

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Minutes: Harold

Attendees:

JBMS paper: update on the GO Cellular Component Ontology and the NIF Subcellular Anatomy Ontology

Deadline for submission is May 31st!

https://docs.google.com/document/d/1f2AUm62pyRODswx8vX4qeovNcCVkUyNsi_a3BTFZsO4/edit

Harold to add something soon.  Paola will move from Google doc to dropbox tomorrow (Fri).
 Tanya volunteers for the references

ontology file names

In SVN we have go-simple.obo but on our new downloads page we have go-basic.obo. I know these files have the same content so this seems unnecessarily confusing. Can we clarify? FlyBase would also like an announcement that these files exist.

PURL is go-basic.obo;  David OS says “simple” is used as a convention (by who?).
 SVN has both go-simple and go-basic; OORT makes go-simple and we further 
process it (2 filtering steps) to go-basic. SVN should not be checked into
 SVN, so it will be removed, so only GO-basic remains.  Chris to fix.

build-up of stale inferred links

When a source ontology changes, we get all the new inferred links from that change, and remove all the redundant links but we are left with the links that can no longer be inferred. Sometimes these are causing problems, I've noticed this especially in the cell cycle. Could we have a periodic clear-out of these? So generate a list of inferred links that can no longer be inferred and decide which ones we want to keep?

tagged inferred links should go away on rebuild if they can’t be inferred anymore.  
Heiko will try to fix (See GO-161 in JIRA)

FF Term Genie vs. templated TG

What to do if user adds a term with FFTG that should have been added using TTG?

Example: 'cellular response to reactive nitrogen species'

CHECK if there is a TEMPLATE for your term FIRST; 
Can FF recognize something that would best fit a Templated? Hard
Put notice up? Easy

Follow-up: Template for receptor activities

deferred until next week

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

Where are we with this? Chris added missing assembly/disassembly logical defs. (based only on names and exact syns.) on May 13th.

Chris and Heiko to fix.

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

Refer to http://wiki.geneontology.org/index.php/Ontology_meeting_2013-05-09#Follow-up:_.28Feasibility_and_strategy_for.29_providing_hard_links_from_apoptosis_terms_to_the_apoptosis_curation_manual_on_the_wiki

and to this Jira ticket: https://www.ebi.ac.uk/panda/jira/browse/GO-160

Any updates on this?

Put in comments it can be seen by all browsers and will be propagated to subterms

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

attributes file is flat; pulls in trait ontology, etc.  TG for bio-attribute 1st, then to GO TG.
http://batto.termgenie.org/

Ontobee

Ontobee: Can use it to see use of GO by other ontologies for their logical definitions.