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[bioontology-support] OLD Rest API

Alejandro Barahona abarahona at infomed.dia.fi.upm.es
Thu Oct 9 03:22:19 PDT 2014


Hi Paul

I want to know if you knew what the old api returns on the field contents
of the search bioportal (uri: ./search/?query={uri-encoded
query}[&{optional args}]&apikey={YourAPIKey}) .
I search in the example on the wiki but it is for a query of 1 word and i
have no idea what to do with the field "contents" when the term match with
more than 1 word on the query.

Regards,
Alejandro.

2014-10-03 20:51 GMT+02:00 Paul R Alexander <palexander at stanford.edu>:

> Sorry, we do not have examples of the old REST response formats. You will
> have to reverse engineer it from your tool’s code or update to use the new
> REST API.
>
> Paul
>
>
> On Oct 3, 2014, at 12:22 AM, Alejandro Barahona <
> abarahona at infomed.dia.fi.upm.es> wrote:
>
> Paul,
>
> I know it is now deprecated but i need to know what it returns because i
> need to make a similar document so our tool could read it as it does before
> it was deprecated
>
> 2014-10-02 19:24 GMT+02:00 Paul R Alexander <palexander at stanford.edu>:
>
>> Alejandro,
>>
>> The REST API available at rest.bioontology.org is now deprecated. You
>> will need to use the calls that I indicated that are available at
>> data.bioontology.org. Documentation on using the new API is here:
>> http://data.bioontology.org/documentation
>>
>> Paul
>>
>>
>> On Oct 2, 2014, at 12:06 AM, Alejandro Barahona <
>> abarahona at infomed.dia.fi.upm.es> wrote:
>>
>> Hi paul
>>
>> What i want to know is if exists any example of the xml result of making
>> that call (" http://rest.bioontology.org/bioportal/virtual/rootpath/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional
>> args}]"), i search for it at wiki but the example returns:
>>
>> <errorStatus>
>> <accessedResource>/bioportal/virtual/rootpath/1032/C3224
>> </accessedResource>
>> <accessDate>2014-10-02 00:05:39.735 PDT</accessDate>
>> <shortMessage>Internal Server Error</shortMessage>
>> <longMessage>
>> White spaces are required between publicId and systemId.
>> </longMessage>
>> <errorCode>500</errorCode>
>> </errorStatus>
>>
>>
>> Alejandro
>>
>> 2014-10-02 2:03 GMT+02:00 Paul R Alexander <palexander at stanford.edu>:
>>
>>> Alejandro,
>>>
>>> There are two things that could be useful to replace that call. The
>>> first is getting ancestors for a given class:
>>>
>>> http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224/ancestors
>>> <http://data.bioontology.org/ontologies/NCIT/classes/http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224/ancestors>
>>>
>>> The second would be the tree representation:
>>>
>>> http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224/tree
>>> <http://data.bioontology.org/ontologies/NCIT/classes/http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224/tree>
>>>
>>> The second is really only useful for drawing a tree for a UI because if
>>> there are multiple paths between the given class and the root node then it
>>> just selects one. Ancestors should give you all the paths.
>>>
>>> Paul
>>>
>>>
>>> On Oct 1, 2014, at 12:29 AM, Alejandro Barahona <
>>> abarahona at infomed.dia.fi.upm.es> wrote:
>>>
>>> Hi
>>>
>>> Im a developer and i was fixing a tool with the new api, but it uses the
>>> old api and i have to return some thigs like it does, i have one question:
>>> Is there any example result of the query,
>>> http://rest.bioontology.org/bioportal/virtual/rootpath/1032/C3224?apikey=YourAPIK
>>> <http://rest.bioontology.org/bioportal/virtual/rootpath/1032/C3224?apikey=YourAPIKey>, maked
>>> with the old api???
>>>
>>> Regards,
>>> Alejandro.
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>>
>>
>>
>
>
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