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[bioontology-support] Questions regarding API search

John Zobolas john.zobolas at ntnu.no
Thu Jun 25 12:33:35 PDT 2020


Hi,


This is a continuation of some other Q&A I had raised some time ago.

My question back then was about the fields that a query such as `search?q=something` looks for to make a match. Michael Dorf had told me that:

"These are the fields being searched in their order of rank priority:

id
prefLabelExact (match on the full pref label)
prefLabel (match on partial pref label)
synonymExact (match on the full synonym(s))
synonym (match on the partial synonym(s))
notation (last fragment of id)
cui (for UMLS ontologies)
semantic_types"

We have been beta-testing this curation tool<https://mi2cast.github.io/causalBuilder/>, in which (long-story-short) some boxes use the BioPortal API (via a dictionary<https://github.com/UniBioDicts/vsm-dictionary-bioportal> interface I've built for it), and some curators expected something to show in one of these boxes when they were writing 'ubi' (for ubiquitination) which pretty much translated to the query:

http://data.bioontology.org/search?q=ubi&ontologies=PSIMOD&page=1&pagesize=40&display_context=false

, which returns nothing. But if you add the asterisk (dirty little trick 😎):

http://data.bioontology.org/search?q=ubi*&ontologies=PSIMOD&page=1&pagesize=40&display_context=false<http://data.bioontology.org/search?q=ubi*&ontologies=PSIMOD&page=1&pagesize=40&display_context=false&apikey=%3CTestAPIkeyToFillin%3E>

you can see that there is both prefLabel and synonym partial matches, so these items/classes should have been returned in the first query!

So my question is if this a bug (the partial match does not work properly) or something has changed in the above fields (and I should probably implement the asterisk hack cause the curators are somewhat dissatisfied with writing the whole word 😊)?

==================
Another example: Curator wants to find 'physical association', nothing is returned while they type:
http://data.bioontology.org/search?q=physi&ontologies=MI&page=1&pagesize=40&display_context=false

There is though a partial prefLabel match:
http://data.bioontology.org/search?q=physi*&ontologies=MI&page=1&pagesize=40&display_context=false
===================

BR, John.
-----------------
John Zobolas
PhD Student
Department of Biology, Faculty of Natural Sciences, NTNU
Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU

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