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[bioontology-support] [BioPortal] Feedback from Maxwell Neal

Ray Fergerson rayferg at stanford.edu
Thu Oct 1 13:45:58 PDT 2015


http://data.bioontology.org/search?q=OPB:OPB_01023&ontologies=OPB&include=prefLabel,synonym,definition,notation,cui,semanticType,properties&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a&also_search_properties=true

You have two errors. The first is that the search string must include the “OPB:” prefix because it is included in the property value. See above.

The second is more subtle. The “include=” defines what information about the class is returned. It does not specify what properties are searched. To specify to search properties you need the “also_search_properties” parameter, as seen above.

Ray

From: Maxwell Neal [mailto:maxneal at gmail.com]
Sent: Friday, September 25, 2015 6:45 PM
To: Ray Fergerson
Cc: support at bioontology.org; mneal at uw.edu
Subject: Re: [bioontology-support] [BioPortal] Feedback from Maxwell Neal

Hi Ray,

Thanks for the response. If retrieving classes by their fragment is possible when you include all properties, then I'm still confused why my REST calls are turning up empty. For example, when I send this call

http://data.bioontology.org/search?q=OPB_01023&ontologies=OPB&include=prefLabel,synonym,definition,notation,cui,semanticType,properties&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a

I get the following JSON response:

{
"page": 1,
"pageCount": 0,
"prevPage": null,
"nextPage": null,
-"links": {
"nextPage": "http://data.bioontology.org/search?q=OPB_01023&ontologies=OPB&include=prefLabel%2Csynonym%2Cdefinition%2Cnotation%2Ccui%2CsemanticType%2Cproperties&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a&display=prefLabel%2Csynonym%2Cdefinition%2Cnotation%2Ccui%2CsemanticType%2Cproperties&page=2",
"prevPage": null
},
"collection": [ ]
}

Any help is appreciated.

Many thanks,

M



On Fri, Sep 25, 2015 at 6:17 PM, Ray Fergerson <rayferg at stanford.edu<mailto:rayferg at stanford.edu>> wrote:
If you search for: OPB:OPB_00528 and include all properties, this class is found. We don’t distinguish punctuation in search and thus the “word” available to the search index is the entire string.

Ray

From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>] On Behalf Of support at bioontology.org<mailto:support at bioontology.org>
Sent: Thursday, September 24, 2015 8:04 PM
To: support at bioontology.org<mailto:support at bioontology.org>; mneal at uw.edu<mailto:mneal at uw.edu>
Subject: [bioontology-support] [BioPortal] Feedback from Maxwell Neal


Name: Maxwell Neal

Email: mneal at uw.edu<mailto:mneal at uw.edu>

Location: http://bioportal.bioontology.org/

Feedback:

Hello,

I am using the BioPortal REST API to perform searches over classes in specific ontologies and I've found that searches using the fragment of class URIs don't return the class. For example, if I search for OPB_01023, I do not get any results, even though OPB:OPB_01023 is an existing class URI in the Ontology of Physics for Biology. I've tried to use all the different available values in the "include" parameter to no avail. Is it possible to retrieve classes using URI fragments with the REST search function?

Many thanks,

Max

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