Ontology meeting 2015-01-27

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Minutes: Paola


We will resume our usual Thursday schedule next week.


Do we want David OS to continue to work on this given staffing constraints? Is AmiGO in shape to receive this traffic anyway?

Action items from previous week(s)

Everyone please check: http://wiki.geneontology.org/index.php?title=Ontology_meeting_2015-01-13

Anything we need to revise or discuss today?

Adding disjoints under 'binding' (and more broadly in the ontology)

Stemming from email thread "build-go-assert-inferences - Build # 117 - Successful!"

[Chris] We should be thinking of ways to structure things and add disjoints to catch these [errors] further upstream, such as making the main grouping classes under classes like 'binding' disjoint (it doesn't have to exhaustive, that would be too hard)

E.g. if this subset of the hierarchy was PD:

 macromolecule binding
  nucleic acid binding
  protein binding
 small molecule binding

[David H] This should work:

Macromolecule binding <disjoint with> small molecule binding

Nucleic acid binding <disjoint with> protein binding

The personally unsatisfying thing is all the other children of the binding term that are not going to fall into disjoint classes. We might want to have a look at those and see if we can tidy up the whole mess. Unlike the metabolism terms, the binding terms can follow on from disjoint relations of the chemical structures themselves.

Shall we make this part of a bigger (Trello) project to get disjoints into the ontology? Let's discuss and see what priority it should get.

Add chain reasoning for regulation?

There are situations where we can infer a some

Should GO:0060969 negative regulation of gene silencing be an is_a child of GO:0010628 positive regulation of gene expression

As we already assert that gene silencing subClassOf negative regulation of gene expression, this could be inferred by the property chain: -ve Reg o -veReg -> +veR

If this inference (and others like it) are always sound, we should add the property chains. But are they? In particular, do we need human judgment of the directness of regulation in order to safely make such inferences?

Remaining axioms in CHEBI that overclassify amino acids

(see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-01-06).

What do do about glyco and lipid modifies AAs -that, chemically, are alpha amino acids.

Membrane Issues

Logical definition issues with partial membranes. Many membranes are classified as 'membrane part', but have no further classification or like 'dendrite membrane' have no indication that they are part of a dendrite.


Organization branch

We could get a lot more automated classification if we relax genus to something very general - probably 'cellular process'. There doesn't seem to be any over-inference that results - although we may need to stick to a convention of using has_output in the cellular_component biogenesis branch. Should we do this?

TermGenie templates for receptor activity

Please look at https://www.ebi.ac.uk/panda/jira/browse/GO-240

Where are we with this?

Jira tickets

Need to review the situation as Chris wasn't on the call last week. (Paola has a list of tickets that need special attention. For my own reference, they're in an email thread "GO tickets in the EBI Jira instance".)