Ontology meeting 2015-01-20

Attendees:

Minutes:

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:

binding
 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?