ols4 icon indicating copy to clipboard operation
ols4 copied to clipboard

Indexer is not working as expected for ChEBI and other ontologies

Open rombaum opened this issue 6 months ago • 0 comments
trafficstars

Describe the bug When I enter chebi as a query to the select API I didn't get ChEBI as a result. I selected ontology as type for filtering. I'm guessing that the ontology_name is not indexed at all. Since I spotted the same issue by entering cao. However I tried to use the full name (Chemical Entities of Biological Interest) instead and I faced the same issue. I used than only che as input and spotted 4 other ontologies (one of them was cao) next to ChEBI. I checked than in the following order this queries:

  1. chebi API
  2. Chemical Entities of Biological Interest https://www.ebi.ac.uk/ols4/api/select?q=Chemical Entities of Biological Interest&type=ontology (API call is not clickable via GitHub)
  3. che API
  4. che* API
  5. *che API
  6. che API

Only query 6. lists chebi as a result but it is as expected very, very slow.

To Reproduce Steps to reproduce the behavior:

  1. Go to on of the links from 1. to 5. from the list above.
  2. Click on the link called 'API'
  3. Scroll through the 'docs' section
  4. Didn't see ChEBI listed

Expected behavior For all of the request above ChEBI should be listed in the result list. I checked this in addition on an old ols3 instance hosted at ZB MED. And ChEBI is listed as an element as expected.

Screenshots Image The figure shows the first API call in a Firefox browser. The value of the request parameter is chebi. The response incorrectly doesn't have an element.

rombaum avatar May 09 '25 17:05 rombaum