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[bioontology-support] Access MP_HEALTH_TOPIC_URL value through REST API

manuelso manuelso at stanford.edu
Thu Nov 7 12:06:33 PST 2013


On Nov 6, 2013, at 2:28 AM, Carlos Luis Sánchez Bocanegra <carlosl.sanchez at gmail.com> wrote:

> Hi again,
> 
> 
> 2013/11/6 manuelso <manuelso at stanford.edu>
> Hi Carlos,
> 
> So our mapping dataset does not contain the information you are looking for.
> 
> You probably need to traverse ontology classes looking for links that can resolve to Web documents because definitely not all classes in BioPortal have links to external references.
> Other question, when you mention "to traverse ontology classed", are you thinking on mapping the node? just only to confirm that.

No I mean the /classes/ endpoint. The classes endpoint returns paginated results that can be traversed.

http://data.bioontology.org/ontologies/BRO/classes (by default first page)
http://data.bioontology.org/ontologies/BRO/classes?page=2

The returned JSON will tell how many pages are in the ontology. Then for each class in each page for a given ontology you can request the properties and look for external references. This, of course, would be a long time running process. 

Manuel


> 
> Thank for your attention.
> 
> Best,
> 
> Manuel
> 
> 
> 
> On Nov 5, 2013, at 3:26 AM, Carlos Luis Sánchez Bocanegra <carlosl.sanchez at gmail.com> wrote:
> 
>> Dear all and Manuel,
>> 
>> First, thanks for your great support.
>> 
>> My research is focussing on the semantic web in health sector, how to exploit there references/terms and to analyze them. When I say external references I mentioned the source of the obtained concept, mainly to retrieve information a patient from a trusted health information -not only a description or term. As an example MEDLINEPLUS collects a set of web page that explains the concept.
>> 
>> I don´t know If I explaind crearly, my apologize. I hope it would be better explained.
>> 
>> Best regards
>> C. 
>> 
>> 
>> 2013/11/4 manuelso <manuelso at stanford.edu>
>> Carlos,
>> 
>> Answers inlined below …
>> 
>> 
>> On Nov 2, 2013, at 4:20 AM, Carlos Luis Sánchez Bocanegra <carlosl.sanchez at gmail.com> wrote:
>> 
>>> Dear all,
>>> 
>>> The following class: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C2985?include=prefLabel,synonyms,definitions,properties
>>> 
>>> Consult another OWL files from the NCIT Ontology. Surprisely I found no external links on their description (remembering the MP_HEALTH_TOPIC_URL on MEDLINEPLUS Onto). That means that no all Class contain links in their properties, doesn´t it?.  Is there any way to deep in the class for obtaining external information? (mapping possible?).
>> 
>> You might want to look at our mapping dataset:
>> 
>> http://bioportal.bioontology.org/mappings
>> 
>> Though I am not sure if this is what you need. I am not sure what are external references in this context.
>> 
>>> 
>>> In this case which Ontologies are supporting external references?.
>> 
>> Carlos, can you explain a bit your use case and what you mean by external references ?
>> 
>> Thanks,
>> 
>> Manuel
>> 
>>> 
>>> My apologizes for these stupid queries, but i´m begining on this thread.
>>> 
>>> Thank you in advance.
>>> 
>>> 
>>> 2013/11/2 Carlos Luis Sánchez Bocanegra <carlosl.sanchez at gmail.com>
>>> Thanks Manuel!
>>> 
>>> Other question I have on my mind is the Category. What is the use of it? How can I manage over my queries?
>>> 
>>> Thanks a lot.
>>> C.
>>> 
>>> 
>>> 2013/11/2 manuelso <manuelso at stanford.edu>
>>> 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%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31?include=prefLabel,synonyms,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&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%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2F31 : 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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>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> 
>>> 
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>> 
>> 
> 
> 

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