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[bioontology-support] searching by synonyms

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Aug 30 16:51:26 PDT 2018


Hi Rob,


On Aug 18, 2018, at 12:52 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi Jennifer,

Yes.  I took a look at the documentation and have tried the following calls using my key.  Neither seem to return what I’m looking for, so maybe I’m doing something wrong.

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT/search?q=Malignant

I’d like to restrict my search to just synonyms, and have classes returned that match the search value (a contains or exact match).


You can use the “include” parameter to limit what’s returned by the API. That parameter is documented in the Common Parameters section of our API documentation:

http://data.bioontology.org/documentation#nav_usage

You can also set the display_links parameter to false to eliminate the hypermedia links that are returned by default.

For example (this is the /search endpoint, not the /property_search endpoint):

http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&display_links=false

… the above call retrieves all classes from the NCIT ontology where the class name contains “Malignant”. For each class in the resulting JSON, only the preferred label and synonyms are returned:


[cid:90B15C92-ED30-4239-9D4A-D0CFB90AC09F at stanford.edu]




For an exact match search, you would add the require_exact_match parameter:

http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&require_exact_match=true&display_links=false

[cid:5924C97D-D5F4-479D-AD3C-B5CBA0CDD9A6 at stanford.edu]

Is this the type of search you’re trying to accomplish?

Kind regards,
Jennifer



Can this be done through BioPortal instead?  If I go to the Advanced Search there is an option to select all properties, but is there a way to search by a single property?

Thanks!
Rob

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Thursday, August 16, 2018 7:57 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; De Coronado, Sherri (NIH/NCI) [E] <decorons at mail.nih.gov<mailto:decorons at mail.nih.gov>>
Subject: Re: [bioontology-support] searching by synonyms

Hi Rob,

Apologies, but I’m not sure I followed your question.

We do have a search endpoint in the REST API for searching by ontology properties. It’s documented here:

http://data.bioontology.org/documentation#nav_prop_search

Is this what you meant?

Kind regards,
Jennifer




On Aug 16, 2018, at 4:35 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes?  I guess this would go for any one specific text property.  If I do this search using REST, could I specify my property?

Thanks,
Rob
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