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[bioontology-support] Issues with searches

John Graybeal jgraybeal at stanford.edu
Thu Aug 25 17:03:48 PDT 2016


Hello Alejandra,

The first two searches that you describe -- using the BioPortal interface and the REST API to look for all terms in BioPortal matching a certain expression -- will not return all terms in BioPortal. Given the large number of ontologies and terms, the complete list would often have thousands of terms or more.

Instead, by design those searches return what BioPortal considers the "best match" in each ontology. It is expected that the user may want to explore some of those ontologies further, depending on how good a match was returned.   Unfortunately, this behavior is not clear from the user interface itself.

On the other hand, when searching a specific ontology in either the UI or the REST API, all matching terms are returned.

I have been looking for documentation of this information, but could not find it with a quick search. Will look further and/or add it as needed to make this more clear.

John




On Aug 24, 2016, at 3:44 AM, Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran at gmail.com<mailto:alejandra.gonzalez.beltran at gmail.com>> wrote:

Hello Bioportal Team,

I have noticed that searching for "design" in both the BioPortal interface and the REST API, the terms from the OBI ontology are not retrieved.

http://bioportal.bioontology.org/search?utf8=%E2%9C%93&query=design&commit=Search

http://data.bioontology.org/search?q=design

While they do show when searching OBI specifically:

http://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=root

Having experienced the same issue reported recently about NCBITaxon:homo sapiens, I noticed that searching for "sapiens" retrieves "homo sapiens' as well as "macrobiotus sapiens" in both the API and the interface. But when searching in NCBITaxon directly, it retrieves more terms (e.g. Homo sapiens/Mus musculus xenograft --> http://purl.bioontology.org/ontology/NCBITAXON/1383439).

Given that in the API the default is for the query not to be exact_match, shouldn't all the terms be retrieved?

Many thanks,

Alejandra


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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski


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