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[bioontology-support] How to search in synonyms using the Bioportal Search API?

Coonen Maarten (FACBURFHML) m.coonen at maastrichtuniversity.nl
Wed May 18 09:26:05 PDT 2016


Dear bioontology support,

Thanks again for the support on importing the NCBITAXON ontology in my local Bioportal VM appliance.
We are currently running in to an issue with searching this ontology.

I noticed that the NBCITAXON instance at my local VM appliance has an attribute called has_exact_synonym for each term, whereas the NCBITAXON at http://bioportal.bioontology.org has an attribute called synonym.
As a result of this, the search query on "mouse" at http://bioportal.bioontology.org successfully returns the record for "mus musculus" (=NCBITAXON_10090), whereas my local VM appliance does not resolve the query to the mus musculus prefLabel.
My explanation would be that the search engine includes prefLabel and synonym, but not has_exact_synonym.

Q1:  Is it possible for us to change the properties that will be included in search to prefLabel and has_exact_synonym?

I also noticed that I'm running the VM Appliance version 2.4. I'm not aware that my appliance downloads any updates from the Bioportal software. Your homepage http://bioportal.bioontology.org/ indicates a current release version 4.27 (May 2016)

Q2: How can I check which Bioportal release I'm running at my VM appliance and how do I install updates?


Best regards,
Maarten Coonen


Maarten Coonen
Data Architect
Research IT, Maastricht University Medical Center+
m.coonen at maastrichtuniversity.nl<mailto:m.coonen at maastrichtuniversity.nl>
maarten.coonen at mumc.nl<mailto:maarten.coonen at mumc.nl>
www.mumc.nl<http://www.mumc.nl/> <http://www.maastrichtuniversity.nl/>
Tel: +31 (0)43 388 4754

Peter Debyelaan 15, 6229 HX Maastricht
P.O. Box 616, 6200 MD Maastricht
The Netherlands


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