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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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isDefiningOntology API endpoint for HSapDv terms #476

Closed mshadbolt closed 2 years ago

mshadbolt commented 3 years ago

Hi

Not sure if this is the best place to post an issue but I am getting an error when searching some terms in the ols by the isDefiningOntology API endpoint eg.:

http://www.ebi.ac.uk/ols/api/terms/findByIdAndIsDefiningOntology?iri=http://purl.obolibrary.org/obo/HsapDv_0000081

http://www.ebi.ac.uk/ols/api/terms/findByIdAndIsDefiningOntology?iri=http://purl.obolibrary.org/obo/HsapDv_0000086

Is this something that can be fixed or a suggested work around to be able to choose the source ontology from an obo_id ?

Thanks!

henrietteharmse commented 3 years ago

Hey there Marion, We will try to investigate this shortly. Thanks for reporting it.

dosumis commented 3 years ago

Hi Marion - can you provide some more context about why this is needed? In particular why a call to the main OLS API? Thanks!

mshadbolt commented 3 years ago

I found a work around so you can close this if it isn't expected that these endpoints should always resolve.

henrietteharmse commented 3 years ago

The reason why this does not work on the main OLS is because the base URIs for HCAO is configured differently from what it is on the HCA OLS instance.

OLS main instance:

    base_uri:
      - http://ontology.data.humancellatlas.org/ontologies/HCA_

OLS HCA instance:

    base_uri:
      - http://ontology.data.humancellatlas.org/ontologies/HCA_
      - http://purl.obolibrary.org/obo/UBERON_
      - http://purl.obolibrary.org/obo/CL_
      - http://purl.obolibrary.org/obo/HsapDv_

Why do we have a different config on OLS main? As an example, on the main OLS we have UBERON as an ontology for which ideally users want isDefiningOntology to return UBERON rather than UBERON and HCAO.