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monarch-initiative / monarch-ontology

Top level monarch importer ontology
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ObjectProperty Label collisions #7

Open TomConlin opened 8 years ago

TomConlin commented 8 years ago

neo4j_label_iri.txt

Fetch ObjectProperty node's label and iri
(only kept first label in the case a node has multiple labels) sorted so duplicated labels are adjacent.
Shows a number of interesting cases.

A good goal would be to replace terms in some ontologies with pre existing terms from more established ontologies, and rename others seeking to minimize label redundancy across ontologies.

kshefchek commented 8 years ago

I suspect some of these have an explanation (obsolete classes/properties?, different domains having different definitions but same label?)

As a first pass we should examine the cases where a single ontology has two classes with the same label in scigraph, for example:

http://purl.obolibrary.org/obo/RO_0002202 ! develops into http://purl.obolibrary.org/obo/RO_0002203 ! develops into

and

http://purl.obolibrary.org/obo/RO_0002180 ! has component http://purl.obolibrary.org/obo/RO_0002211 ! has_component

In both of these cases we have an ontology that is importing the the property with in an incorrect label. For example: http://purl.obolibrary.org/obo/RO_0002202 should be "develops from", but ero.owl imports the property with the label "develops to". Similarly, RO_0002211 should be "regulates" but xco.owl has labelled it "has_component." Could we add a test case to catch these?

cmungall commented 8 years ago

Ideally this would be OBO Foundry activity but it's a service we can provide for the subset of ontologies we bring in.

We should report back these into the respective trackers (and link here so we have a trail)

Ideally we'd automate this but for just relations we can perhaps do this manually?

On 27 Aug 2016, at 11:49, Kent Shefchek wrote:

I suspect some of these have an explanation (obsolete classes/properties?, different domains having different definitions but same label?)

As a first pass we should examine the cases where a single ontology has two classes with the same label in scigraph, for example:

http://purl.obolibrary.org/obo/RO_0002202 ! develops into http://purl.obolibrary.org/obo/RO_0002203 ! develops into

and

http://purl.obolibrary.org/obo/RO_0002180 ! has component http://purl.obolibrary.org/obo/RO_0002211 ! has_component

In both of these cases we have an ontology that is importing the the property with in an incorrect label. For example: http://purl.obolibrary.org/obo/RO_0002202 should be "develops from", but ero.owl imports the property with the label "develops to". Similarly, RO_0002211 should be "regulates" but xco.owl has labelled it "has_component." Could we add a test case to catch these?

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