Proposed updates to Molecular Function shape

[vanaukenk]

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

enabled_by: ( @<ProteinContainingComplex> OR @<InformationBiomacromolecule> ) {0,1};

occurs_in: ( @<AnatomicalEntity> ) {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: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;

has_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;

happens_during: ( @<BiologicalPhase> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;

causally_upstream_of_or_within: ( @<BiologicalProcess> ) *;

causally_upstream_of: ( @<BiologicalProcess> OR @<MolecularFunction> ) *;

causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> ) *;

causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> ) *;

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]

##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]

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]

@balhoff

Could we do something like this:

<AnatomicalEntity>@<GoCamEntity> AND EXTRA a {
a @<AnatomicalEntityClass>;
part_of: @<CellularComponent> {0,1};
part_of: @<Cell> {0,1};
part_of: @<GrossAnatomicalEntity> {0,1};
part_of: @<Organism> {0,1}
}// rdfs:comment "an anatomical entity"
 

[balhoff]

@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]

@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]

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

[cmungall]

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 ***@***.***> wrote: Oh and I forgot the third issue! We need to allow negated cellular components. Should this be generalized to negated anatomical entities? — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#137?email_source=notifications&email_token=AAAMMOMGGN6WQMZP4IRSQVTQDQ2WJA5CNFSM4IKEOLGKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3363WA#issuecomment-519564760>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAAMMONCLSUGM4Z4R4QQLTDQDQ2WJANCNFSM4IKEOLGA> .

[balhoff]

@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]

@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]

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

[balhoff]

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]

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]

Here is an alternative proposal: geneontology/go-ontology#17696

[goodb]

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]

@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 geneontology/go-ontology#17696

Thanks, Pascale

[balhoff]

@goodb the PR is here: #139

[goodb]

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

[goodb]

@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]

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