Proposed updates to Molecular Function shape

vanaukenk commented 4 years ago

From 2019-08-07 call, here are the suggested updates to the Molecular Function shape. @balhoff @cmungall @thomaspd @pgaudet - please review

enabled_by: ( @\ OR @\ ) {0,1};

occurs_in: ( @\ ) {0,1};

QUESTION ABOUT ADDING AN OR STATEMENT HERE FOR PROTEIN-CONTAINING COMPLEX, GIVEN THE DEFINITION OF ANATOMICAL ENTITY IN CARO

https://www.ebi.ac.uk/ols/ontologies/caro/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCARO_0000000

has_output: ( @\ OR @\ ) *;

has_input: ( @\ OR @\ ) *;

happens_during: ( @\ OR @\ OR @\ ) *;

causally_upstream_of_or_within: ( @\ ) *;

causally_upstream_of: ( @\ OR @\ ) *;

causally_upstream_of_negative_effect: ( @\ OR @\ ) *;

causally_upstream_of_positive_effect: ( @\ OR @\ ) *;

Add to PREFIX:

PREFIX GoLifeCycleStage: \http://purl.obolibrary.org/obo/UBERON_0000105

PREFIX GoPlantStructureDevelopmentStage: \http://purl.obolibrary.org/obo/PO_0009012

CORRECT TERM FROM PO?

vanaukenk commented 4 years ago

QUESTION ABOUT ADDING AN OR STATEMENT HERE FOR PROTEIN-CONTAINING COMPLEX, GIVEN THE DEFINITION OF ANATOMICAL ENTITY IN CARO

https://www.ebi.ac.uk/ols/ontologies/caro/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCARO_0000000

Discussion with @pgaudet - we will not be annotating MF occurs_in protein-containing complex, so we will just use 'AnatomicalEntity' here.

balhoff commented 4 years ago

I realized there are a couple of issues with just using the AnatomicalEntity shape for occurs_in:

in the AnatomicalEntity shape, we don't say anything about part_of relations (but we do allow a single part_of for Cell and GrossAnatomicalEntity).
in the CellularComponent shape, we are allowing 3 different part_of relations: to a CellularComponent, a Cell, and an Organism.

We need some cleanup here. If we will allow all these part_ofs for cellular components, then we need to keep using it in an OR. Otherwise, we can stick with AnatomicalEntity and either say any instance can have a single part_of, or change AnatomicalEntity to allow those 3 part_of possibilities.

vanaukenk commented 4 years ago

@balhoff

Could we do something like this:

\AnatomicalEntity>@\<GoCamEntity AND EXTRA a { a @\; part_of: @\ {0,1}; part_of: @\ {0,1}; part_of: @\ {0,1}; part_of: @\ {0,1} }// rdfs:comment "an anatomical entity"

balhoff commented 4 years ago

@vanaukenk that would allow a very star-shaped graph for part_of. I thought we were trying to make this a linear chain. Is there any reason to not force it to just be a sequence of single part_of? I don't remember the discussion that resulted in the current schema for CellularComponent.

vanaukenk commented 4 years ago

@balhoff

Yes, you're right. I do think we wanted to try to model linear chains, if possible.

In that case, the single 'part of' would be the way to go.

I don't think we'd quite gone through CellularComponent yet as a group, so we should review CC on the next call.

balhoff commented 4 years ago

Oh and I forgot the third issue! We need to allow negated cellular components. Should this be generalized to negated anatomical entities?

cmungall commented 4 years ago

It seems we are tending towards a simple model that errs on the side of permissivity

e.g. just using AE, allowing part-of between AEs, and negation of AEs

Note we still get biological inference from OWL, we can prevent biological impossibilities there, e.g. prokaryote cells part of gross structures

On Thu, Aug 8, 2019 at 8:21 AM Jim Balhoff notifications@github.com wrote:

Oh and I forgot the third issue! We need to allow negated cellular components. Should this be generalized to negated anatomical entities?

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balhoff commented 4 years ago

@vanaukenk:

Discussion with @pgaudet - we will not be annotating MF occurs_in protein-containing complex, so we will just use 'AnatomicalEntity' here.

I think this will be still allowable by the schema, since we are making GO cellular_component a subclass of CARO anatomical_entity, and protein-containing complex is a cellular_component. But wasn't there discussion about moving that anyway?

vanaukenk commented 4 years ago

@balhoff Wrt the protein-containing complex and 'Anatomical Entity', I was wondering if the definition of 'Anatomical Entity' excluded protein complexes:

"A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. [ CAROC:Brownsville2014 ]"

ukemi commented 4 years ago

This would impinge on the PR that @balhoff created making GO-CC a type of CARO anatomical entity. https://github.com/geneontology/go-ontology/pull/17695

balhoff commented 4 years ago

Yes, so either we use AnatomicalEntity OR CellularComponent everywhere in the schema, or we merge the subclass axiom and we move complexes out of GO cellular_component. Is that possible?

ukemi commented 4 years ago

We have considered that before, but it is such a drastic change that I think we would need a lot of lead time. It would create three root nodes in GO.

balhoff commented 4 years ago

Here is an alternative proposal: https://github.com/geneontology/go-ontology/issues/17696

goodb commented 4 years ago

There are a number of uncontroversial changes in the above. Could these pushed live while discussion continues on the anatomical entity problem - perhaps on a separate issue ?

pgaudet commented 4 years ago

@goodb

Yes, these are the decision we had made on the call of 2019-08-07.

@goodb Can you add theese to Shex?

We have solved the issue with anatomical entity - the new term in now in the ontology https://github.com/geneontology/go-ontology/issues/17696

Thanks, Pascale

balhoff commented 4 years ago

@goodb the PR is here: #139

goodb commented 4 years ago

@balhoff is that PR ready for merge or do we wait for test file and ontology file changes? (I'm awaiting feedback on https://github.com/geneontology/minerva/pull/239 so can work on this today.)

goodb commented 4 years ago

@vanaukenk can we close this issue ?
Noting this comment on your last unmerged branch. I adjusted slightly and committed to master when it passed the tests. (Now travis is operational BTW.)

I set the occurs_in constraint for MF to be occurs_in: ( @<AnatomicalEntity> OR @<ProteinContainingComplex> ) {0,1};

vanaukenk commented 3 years ago

Closing this for now.
We can re-open or start a new ticket if there are related issues.

geneontology / go-shapes