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Registry lacks the "canonical" resource URI #923

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markwilkinson opened this issue Aug 12, 2023 · 1 comment · Fixed by #924
Closed

Registry lacks the "canonical" resource URI #923

markwilkinson opened this issue Aug 12, 2023 · 1 comment · Fixed by #924

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@markwilkinson
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markwilkinson commented Aug 12, 2023

Hi all!
I'm a bit surprised that, when brokering the registration of an ontology term, the "canonical" URI of that term is not (consistently) among the choices. For example:

https://bioregistry.io/api/reference/edam:data_1153

prefix "edam"
identifier "data_1153"
providers  
default "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/data_1153"
bioregistry "https://bioregistry.io/edam:data_1153"
miriam "https://identifiers.org/edam:data_1153"
n2t "https://n2t.net/edam:data_1153"
bio2rdf "http://bio2rdf.org/edam:data_1153"

The canonical URI of that ontology term is http://edamontology.org/data_1153, which only appears as a GET string argument to the EBI server.
I am loathe to parse URLs to obtain the identifier of an ontology term ;-)
Is there any chance this can be added as an additional parameter in the list? "canonical"?

Cheers all!

@cthoyt
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cthoyt commented Aug 12, 2023

Hi @markwilkinson, this is a good point. There are actually two issues to address here:

  1. Curated RDF URI format strings don't get properly propagated through to this API endpoint
  2. EDAM is missing a canonical RDF URI format

I've made a PR where I fix both of these things. I will properly test and deploy it on Monday.

cthoyt added a commit that referenced this issue Aug 15, 2023
Closes #923

Now, the reference page for `edam:data_1153` looks like:

<img width="962" alt="Screenshot 2023-08-12 at 18 33 15"
src="https://github.com/biopragmatics/bioregistry/assets/5069736/5081085f-b6bf-46c4-971d-fa5540b0473c">
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2 participants