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

Maxwell Neal maxneal at gmail.com
Thu Oct 1 13:55:47 PDT 2015


Fantastic. Thanks so much for the edification, Ray!

M


On Thu, Oct 1, 2015 at 4:45 PM, Ray Fergerson <rayferg at stanford.edu> wrote:

>
> 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>
> 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] *On Behalf Of *
> support at bioontology.org
> *Sent:* Thursday, September 24, 2015 8:04 PM
> *To:* support at bioontology.org; mneal at uw.edu
> *Subject:* [bioontology-support] [BioPortal] Feedback from Maxwell Neal
>
>
>
> Name: Maxwell Neal
>
> Email: 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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