monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
6 stars 3 forks source link

Experiment: how would a KGCL diff statement (a single removed subclass of) look like? #487

Open matentzn opened 6 months ago

matentzn commented 6 months ago

@hrshdhgd as discussed during our last Mondo Tech call, we want to see how it would look like to have a KGCL style term history merged inside the ontology.

We currently have a pattern like this in Mondo:

[Term]
id: MONDO:0000087
name: polymicrogyria
def: "A developmental brain abnormality characterized by an excessive amount of small convolutions on the surface of the brain and cognitive dysfunction." [NCIT:C116936]
is_a: MONDO:0002320 {source="NCIT:C116936"} ! congenital nervous system disorder
relationship: excluded_subClassOf MONDO:0000508 {source="Orphanet:35981", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic intellectual disability

We want to know how it would look like if we would represent

relationship: excluded_subClassOf MONDO:0000508 {source="Orphanet:35981", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic intellectual disability

As a rdf-serialised KGCL statement that describes a removed of a subclassOf (parent) between the two classes.

Can you produce an RDF/OWL (or even obo? probably not) example of the above so we can see and understand?

@cmungall suggested to try and use KGCL for term histories. In the Tech team, no one knows how this would look like, so this is a start.

hrshdhgd commented 6 months ago

I'm not sure what a "rdf-serialised KGCL statement" means. A KGCL statement is a plain statement as you'd see in ontobot triggering issues.

e.g.:

-  change relationship between MONDO:0000508 and Orphanet:35981 from relation_1 to relation_2

I know this makes no sense but this I'm using it as an example.

cmungall commented 6 months ago

@hrshdhgd please see this issue: https://github.com/INCATools/kgcl/issues/49

Ideally mondo would use a generic mechanism here