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[bioontology-support] Access MP_HEALTH_TOPIC_URL value through REST API

Ray Fergerson ray.fergerson at stanford.edu
Thu Nov 7 17:16:55 PST 2013


Maxwell,



We do have a tracker item open to add this capability to all API calls
(search and annotator) but it isn’t in there yet. You should also be able
to use the batch call to retrieve the labels for a bunch of items at once.
This should be quicker than a call per class.



Ray



From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
manuelso
Sent: Thursday, November 07, 2013 2:36 PM
To: Maxwell Neal
Cc: BioPortal User Support
Subject: Re: [bioontology-support] Access MP_HEALTH_TOPIC_URL value
through REST API



Maxwell,



The search endpoint does not implement the “include” param. It always
returns a fixed set of standard attributes (prefLabel, synonyms,
definitions 
).



To return the “properties” you need to do an additional class call for
each class item in the search results. For example:



http://data.bioontology.org/ontologies/COSTART/classes/http%3A%2F%2Fpurl.b
ioontology.org%2Fontology%2FCST%2FANOMALY%2BHEART?include=properties



That would be the call for the first hit of the search results for your
query.



Manuel







On Nov 7, 2013, at 1:31 PM, Maxwell Neal <mneal at u.washington.edu> wrote:





Hi Manuel,



Thanks for your help retrieving all property values for an ontology class
using the REST services. However, I'm trying to retrieve these properties
using REST *search* calls and it doesn't seem to work as expected.



For example, I want to search the FMA for "heart" and include all the
values for the FMAID property in the results. I've tried this:



http://data.bioontology.org/search?q=heart
<http://data.bioontology.org/search?q=heart&ontology=FMA?include=prefLabel
,synonyms,definitions,properties>
&ontology=FMA?include=prefLabel,synonyms,definitions,properties



but it doesn't return the FMAIDs.



Any help would be greatly appreciated. Thanks!



M



---------------------------------

Maxwell Neal



Post-doctoral researcher

Department of Bioengineering

University of Washington

mneal at uw.edu

---------------------------------















On Nov 1, 2013, at 6:46 PM, manuelso wrote:





Hi Carlos,



The default REST class call does not return all the properties attached to
a term. If you want to see all properties you can add the following
parameter to your call:



?include=prefLabel,synonyms,definitions,properties



something like this would work:



http://data.bioontology.org/ontologies/MEDLINEPLUS/classes/http%3A%2F%2Fpu
rl.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31?include=prefLabel,synonym
s,definitions,properties



Manuel





On Nov 1, 2013, at 6:14 PM, Carlos Luis Sánchez Bocanegra
<carlosl.sanchez at gmail.com> wrote:





Hi everyone,



I´m diving on the bioontology REST API, try to exploit all their
possibilities including on this API.



I take some time to adapt and get manual results and finally I think I can
manage with the API. I need to access to the MP_HEALTH_TOPIC_URL value on
the Class Medicine (for example)
http://bioportal.bioontology.org/ontologies/MEDLINEPLUS?p=classes
<http://bioportal.bioontology.org/ontologies/MEDLINEPLUS?p=classes&concept
id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31#details
>
&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31
#details



But REST API does not give me this value:
<http://data.bioontology.org/ontologies/MEDLINEPLUS/classes/http%3A%2F%2Fp
url.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31>
http://data.bioontology.org/ontologies/MEDLINEPLUS/classes/http%3A%2F%2Fpu
rl.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31 :
<http://purl.bioontology.org/ontology/MEDLINEPLUS/31>
http://purl.bioontology.org/ontology/MEDLINEPLUS/31



In the rest result I can´t find MP_HEALTH_TOPIC_URL.



Thank your for helping me.



C.

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