Ontology meeting 2016-03-03

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Attendees:

Minutes: David OS


Follow-up: strategy for ontology requests

Summary from last two calls: We need to have a better set of guidelines for dealing with ontology tickets. Perhaps we can generalize Jane's flow chart of when to request a termgenie term.

http://go.termgenie.org/help/index.html 

 Strategies discussed:
 *Improved flow chart - remind people about flow chart's existence. (Update: flowchart is now linked to instructions below)
 *Tickets with insufficient detail will not be dealt with.  Add 'More info needed' label to tickets that 
 fall in this category so that the user will know they have to take action and don't feel ignored. (DONE)
 *Make and add a template/instructions (contributing.md file) for new tickets to GH.  Will be seen by all 
 people going to tracker (at the top of the form) when they open a new issue. (DONE, see current version)
 *Need form type interface for Noctua for simpler gene-term interface to alleviate concerns for going to 
 full blown LEGO. This might help with Val's concern about need for using LEGO for people who aren't ready 
 for LEGO.
 *Templated generation of branches of the ontology - filling in terms for classes we know must exist rather 
 than waiting for requests.
   Good example of this is components for membranes.

Assign people to pending action items.

Email go-c to point all to guidelines in GH? Present them briefly at next annotation call? DONE - discussed at annotation call on March 8th. When minutes of that call are sent round, everyone will be aware of the guidelines. 

 Tanya's suggested text to describe TG : "Term Genie can be used to
 automatically create terms that are similar in structure to many terms
 that are already in GO." 
 AI: add this text to ?? DONE - added to guideline template in GH
AI: Make a card in Trello board on templating branch: pilot project
with membranes.  :DOS:CM:

Discussion of making it clearer to users coming to the website that
they can add terms.  We have the FAQ:
http://geneontology.org/faq/how-can-i-suggest-new-go-terms
  AI: flesh this out with a link to doc on GitHub as well as tracker.
  AI: link to this from somwhere prominent on the front page with some pithy text
  Tanya: 'Help go grow' ?
  Ticket: https://github.com/geneontology/go-site/issues/161

Setting a Milestone for moving inferred classification to imports

DOS: As previously discussed, I'd like to set a target date for moving to having inferred classifications imported and regularly flushed & replaced. Is the end of March reasonable as a deadline for review of ETINEs?

Approved. How are we distributing the work?

Ticket here: https://github.com/geneontology/go-ontology/issues/12315

tsv file and instructions for collaborative editing here: https://github.com/geneontology/go-ontology/tree/master/refactoring_inference_pipeline 

AIs: DOS to tidy up a bit more
AIs: Assign blocks to editors :DOS:
AI: Eds to look over whole doc for things they think we should have a
general policy on.

How do we edit? 
GitHub vs Google docs
 Decision: stay in Github as allows scripting -> reduction of table
 based on inference report updates.

 CM: volunteers to do regulation - with a script.

How are we going to represent forward and reverse reactions?

https://github.com/geneontology/go-ontology/issues/12314

[Term]
id: GO:0047545 name: 2-hydroxyglutarate dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor." [EC:1.1.99.2, MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN]
subset: gosubset_prok
synonym: "(S)-2-hydroxyglutarate:(acceptor) 2-oxidoreductase" EXACT [EC:1.1.99.2]
synonym: "(S)-2-hydroxyglutarate:acceptor 2-oxidoreductase" EXACT [EC:1.1.99.2]
synonym: "alpha-hydroxyglutarate dehydrogenase (NAD+ specific)" NARROW [EC:1.1.99.2]
synonym: "alpha-hydroxyglutarate dehydrogenase activity" EXACT [EC:1.1.99.2]
synonym: "alpha-hydroxyglutarate oxidoreductase activity" EXACT [EC:1.1.99.2]
synonym: "alpha-ketoglutarate reductase activity" EXACT [EC:1.1.99.2]
synonym: "hydroxyglutaric dehydrogenase activity" EXACT [EC:1.1.99.2]
synonym: "L-alpha-hydroxyglutarate dehydrogenase activity" EXACT [EC:1.1.99.2]
synonym: "L-alpha-hydroxyglutarate:NAD+ 2-oxidoreductase" NARROW [EC:1.1.99.2]
xref: EC:1.1.99.2
xref: MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN
xref: RHEA:21255
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors

[Term]
id: GO:NEW1
name: 2-hydroxyglutarate dehydrogenase activity, forward reaction
namespace: molecular_function
def: "Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor -> 2-oxoglutarate + reduced acceptor." [EC:1.1.99.2, MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN]
subset: gosubset_prok
synonym: "alpha-ketoglutarate reductase activity, reverse reaction" EXACT [EC:1.1.99.2]
synonym: "hydroxyglutaric dehydrogenase activity" EXACT [EC:1.1.99.2]
xref: Reactome:REACT_24926 "(S)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2, Homo sapiens"
xref: RHEA:21253
is_a: GO:0047545 ! 2-hydroxyglutarate dehydrogenase activity

[Term]
id: GO:NEW2
name: alpha-ketoglutarate reductase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxoglutarate + reduced acceptor -> (S)-2-hydroxyglutarate + acceptor." [EC:1.1.99.2]
subset: gosubset_prok
synonym: "2-hydroxyglutarate dehydrogenase activity, reverse reaction" EXACT [EC:1.1.99.2]
xref: RHEA:21254
is_a: GO:0047545 ! 2-hydroxyglutarate dehydrogenase activity 

 Are we happy to make separate activity terms for forward and reverse
 reactions? Difficulty is - depending on the conditions in the cell, enzymes may
 work in one direction or another. 

 We may be able to deal with this by assigning process context?  That
 doesn't need new terms when it is done in LEGO - but can be done using 'involved in'
 pattern in ontology.

 All agree to add above terms as a one-off for Rob.  Also add a comment about why this is
 special + an xref link to the ticket.

Are incorrect relations showing up in AmiGO2?

http://amigo.geneontology.org/amigo/term/GO:1903293
phosphatase complex
It is being displayed as inferred capapble of part of phosphatase activity. 

AI: DH to add ticket.
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