Change in baseURI for NCBITaxon?

EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI

http://www.ebi.ac.uk/ols

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Change in baseURI for NCBITaxon? #427

Closed jlchang closed 3 years ago

jlchang commented 3 years ago

Up until recently (~morning of 10/14) I could use EBI OLS to look up NCBITaxon terms such as NCBITaxon_9606.

My code currently sends the following term lookup which fails with "Resource not found": https://www.ebi.ac.uk/ols/api/ontologies/ncbitaxon/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCBITAXON_9606

I can see that this query will succeed (NCBITAXON_9606 vs NCBITaxon_9606): https://www.ebi.ac.uk/ols/api/ontologies/ncbitaxon/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCBITaxon_9606

I had not made any changes to my code for the NCBITaxon term lookup but the lookup behavior changed sometime on 10/14. Your lookup service is very valuable and I would like to understand whether this change in behavior was intended and whether the change is permanent.

Thanks,

Jean

jlchang commented 3 years ago

Investigating further, it looks like a query to: https://www.ebi.ac.uk/ols/api/ontologies/NCBITaxon is returning a baseURI of http://purl.obolibrary.org/obo/NCBITAXON_

Which I am using to generate the term lookup requests. The baseURI may be the root cause of the invalid term lookups I'm experiencing.

Is http://purl.obolibrary.org/obo/NCBITAXON_ intended to be a valid baseURI (it seems to result in "Resource not found")?

If not, can a baseURI of http://purl.obolibrary.org/obo/NCBITaxon_ be supplied instead?

jlchang commented 3 years ago

Checking in to see if the invalid baseURI is intended: http://purl.obolibrary.org/obo/NCBITAXON_

Do you expect this result to change in future?

matentzn commented 3 years ago

@udp could this be solved by simply adding the baseURI to the ols ontologies.yaml config?

henrietteharmse commented 3 years ago

The base url for NCBITaxon has not changed for as long as I can see. This is the base url that is defined for NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_

matentzn commented 3 years ago

Yeah but check this: https://www.ebi.ac.uk/ols/api/ontologies/NCBITaxon

Why does it say:

henrietteharmse commented 3 years ago

Good point. I have no idea.

jamesamcl commented 3 years ago

In the process of investigating this!

jlchang commented 3 years ago

Thank you all for confirming that the change was not intended and investigating the issue!

henrietteharmse commented 3 years ago

Thanks to @udp for getting to the root cause of this issue. It seemed that an error unrelated to NCBITaxon in the .yaml config caused loading of the .yaml file to fail silently. This caused the base url config for NCBITaxon the be ignored.

This is now fixed