Ontology meeting 2015-03-05: Difference between revisions

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Paola reminded us of GO_REF:00090. This process is currently manually triggered (also not a Jenkins job at the moment).
Paola reminded us of GO_REF:00090. This process is currently manually triggered (also not a Jenkins job at the moment).
Currently, there are five missing part_of links:
Currently, there were five missing part_of links:


   GO:0061459 'L-arginine transmembrane transporter activity' 'part_of' GO:1903400 'L-arginine transmembrane transport'
   GO:0061459 'L-arginine transmembrane transporter activity' 'part_of' GO:1903400 'L-arginine transmembrane transport'
Line 59: Line 59:
   GO:0015208 'guanine transmembrane transporter activity' 'part_of' GO:1903716 'guanine transmembrane transport'
   GO:0015208 'guanine transmembrane transporter activity' 'part_of' GO:1903716 'guanine transmembrane transport'


It that looks okay, Heiko will run the script and add the links.
David added the links.


=== Function-process links ===
=== Function-process links ===

Revision as of 17:55, 4 March 2015

Attendees:

Minutes:


Acids and bases in GO

Stemming from https://sourceforge.net/p/geneontology/ontology-requests/11524/

The solution we've adopted so far is proving unsatisfactory specifically with respect to NH4+, NH3 and NH2- conjugate-acid-base relations. We need to think of an alternative, with or without the direct involvement of ChEBI.

Rhea plans

Background and initial plan: https://www.ebi.ac.uk/panda/jira/browse/GO-190

Do we have resources for this? Chris, David H, Harold?

How to define protein families in enzyme binding terms

This follows up from a previous call where we resolved: "We have decided that we will include families. How we define families will need to be addresses. Is it only if there is more than one similar gene in the same organism? The bottom line here is that a gene protein is not binding the activity, it is binding the molecule."

We need to address how to define families.

Replacing has_regulation_target with more specific, chain based relations

In discussion with annotators (Ruth, Rachael, Becky, Aleks) - agreed that the confusing annotation extension relations - has_regulation_target - should be replaced by more specific relations defined using property chains. We already have some of these, but the names, which embed the property chain, are confusing to most people.

What relations to have and what to call them?

regulates_o_has_agent -> regulates_activity_of - with restriction that only applies to regulation of MFs (BPs having many agents) ? regulates_o_has_substrate -> ?

How deep to go?

reguates_transport_of ? regulates_transcription_of ? <- This might seem a step too far, but it would be much clearer than the current confusing mess.

This isn't really that confusing. All of the regulation terms in GO except for the regulation of biological quality refer to GO processes or molecular functions. The regulation chain relations are simple chains of the regulates relation with whatever relation would be used either asserted in the ontology or in the logical definition of the term. As a simple example 'regulation of protein kinase activity' would be the chain regulates_o_something. The something would be any value that can be used in the description of the kinase activity. It could refer to the kinase itself, regulates_o_has_agent (if this is the relationship between the molecular function and the annotated gene product) or it could be regulates_o_has_input to describe the protein that is being phosphorylated, or it could be regulates_o_has_output to describe the specific phosphorylated protein. The key here is getting the relations of the root process and function terms correct to describe things that are going into processes and coming out of processes. That all ties together getting good axioms in the ontology with the annotation extension relations. At the end of the day, to get proper folding and unfolding, all of these need to align. So there are two challenges; defining and determining the correct relations between entities and the primary processes and coming up with names that curators can easily use. The current chains are not user-friendly.

results_in strategy

See emails from Chris following last week's call (threads on go-ontology 'results_in outliers' and 'results_jn refactor'). Chris asked for feedback on his proposal. Discuss, then reply to email thread.

BTW, Antonia recently requested this on TG: 'positive regulation of pyrimidine-containing compound salvage by positive regulation of transcription from RNA polymerase II promoter'. Put on hold until we decide...

Transport activity part_of Transport process

Paola reminded us of GO_REF:00090. This process is currently manually triggered (also not a Jenkins job at the moment). Currently, there were five missing part_of links:

 GO:0061459 'L-arginine transmembrane transporter activity' 'part_of' GO:1903400 'L-arginine transmembrane transport'
 GO:0015093 'ferrous iron transmembrane transporter activity' 'part_of' GO:1903874 'ferrous iron transmembrane transport'
 GO:1903425 'fluoride transmembrane transporter activity' 'part_of' GO:1903424 'fluoride transmembrane transport'
 GO:0005304 'L-valine transmembrane transporter activity' 'part_of' GO:1903785 'L-valine transmembrane transport'
 GO:0015208 'guanine transmembrane transporter activity' 'part_of' GO:1903716 'guanine transmembrane transport'

David added the links.

Function-process links

Rama reminded us that we should reply to this user:

https://mailman.stanford.edu/pipermail/go-discuss/2015-February/007159.html