Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] bioontology-support post from aaron.zhang at requires approval

Michael Dorf mdorf at
Tue Nov 21 13:23:48 PST 2017

Hi Aaron,

Thank you for your inquiry. The difference in the number of matches that you see is mostly attributed to the way our user interface presents the results. It makes a call to our /search endpoint but does some additional processing that groups the results by each ontology. A link on the bottom of each search result allows you to view the additional results (Ex: 26 more from this ontology). The REST endpoint does not perform any groupings. It presents the ALL results, ordered by their respective search ranks.

I did notice a discrepancy that between our API and documentation in the example that you presented. Namely, the parameter “roots_only” appears to be deprecated, and the search does not take it into account. CHEBI specifically, contains only three root classes:

Thus, even if the “roots_only” parameter was working you, wouldn’t get any hits on the query “valproic acid”. I will look into both updating our documentation as well as a possibility of re-introducing the “roots_only” parameter in our future releases. I’ve created this issue in our Github tracking system, so you can keep track of our progress on resolving it:

Thanks again!


Dear Sir/Madam,

I am trying to use the REST API that you provide to search for ontologies that have a class name that is the same to my query.

For example, if I search “valproic acid” through the browser (Class Search), I get matches in 26 ontologies, the names of which are what I hope to get;

however, if I run the search through API with the following paramaters, I got 100,361 results. I am confused what is the dramatic difference; how can I get a REST response that more closely reassembles the browser search?

API response: {"page":1,"pageCount":20073,"totalCount":100361,"prevPage":null,"nextPage":2, …

Response response = given()
            .param("apikey", api_key)
            .param("include", "prefLabel")
            .param("page", pageNumber)
            .param("pagesize", 5)
            .param("include_views", false)
            .param("display_context", false)
            .param("display_links", false)
            .param("ontology", "CHEBI")
            .param("roots_only", true)
        .get("search?q=" + term);

I appreciate your help.


The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

From: bioontology-support-request at<mailto:bioontology-support-request at>
Subject: confirm 379e086c8e7158b1da434a380722b7e178aa2e9e
Date: November 21, 2017 at 8:17:14 AM PST

If you reply to this message, keeping the Subject: header intact,
Mailman will discard the held message.  Do this if the message is
spam.  If you reply to this message and include an Approved: header
with the list password in it, the message will be approved for posting
to the list.  The Approved: header can also appear in the first line
of the body of the reply.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list