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

Michael Dorf mdorf at stanford.edu
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:

http://bioportal.bioontology.org/ontologies/CHEBI?p=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: https://github.com/ncbo/ontologies_api/issues/40

Thanks again!

Michael


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;

<image001.png>
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()
        .request().with()
            .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)
        .expect()
            .statusCode(200)
        .get("search?q=" + term);


I appreciate your help.
Best,
Aaron


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


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