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[bioontology-support] New Bioportal API, searching ontology classes by acronym and accession

Marco Brandizi brandizi at ebi.ac.uk
Wed Oct 22 02:52:34 PDT 2014


Hi Paul,

thanks for your clarifications. If /search?q=<URI> is guaranteed to 
return only the classes identified by the parameter, and not, for 
example, other classes linking the URI, that would be good enough for 
me, ie, I will add the specific functionality of searching a class by 
URI to my little client code.

Cheers,
Marco.



On 22/10/2014 00:51, Paul R Alexander wrote:
> Thank you for the sample code, we’ll make sure to point people to it for similar problems.
>
> As for resolving a class based on URI, it actually won’t be possible to do that and guarantee a single result. Because ontologies can import classes from other ontologies, the same class could exist in multiple ontologies and without knowing which ontology you are interested in we have no way to guarantee a single result or even a way or knowing which ontology originated the class.
>
> The search you indicate will do the next best thing, IE give you all class/ontology pairs with that URI and you will need to decide how to handle them.
>
> Paul
>
>
> On Oct 10, 2014, at 4:14 AM, mbrandizi <brandizi at ebi.ac.uk> wrote:
>
>> Again on this issue, for the moment I'm solving it this way:
>>
>> https://github.com/EBIBioSamples/bioportal-client/blob/master/src/main/java/uk/ac/ebi/bioportal/webservice/client/BioportalClient.java#L212
>>
>> and I computed the list of pre-configured acronym/URI mappings by means of
>> this loop:
>> https://github.com/EBIBioSamples/bioportal-client/blob/master/src/test/java/uk/ac/ebi/bioportal/webservice/client/GetOntoPrefixesTest.java
>>
>> It's an approach less than ideal, but for the moment it works and I look
>> forward to the new APIs explicitly providing the functionality above.
>>
>> Another similar issue I've realised is that there is no straight way to get
>> the details about a term using only its URI, ie, we only have the method
>> /ontologies/:ontology/classes/:cls, which requires the :ontology parameter,
>> even though you cannot know it from the URI. Actually you can do something
>> via
>> http://data.bioontology.org/search?q=http://www.ebi.ac.uk/efo/EFO_0000270,
>> but you have to go through the results and that's not what I mean.
>>
>> As you can see, my code above is part of a new small Bioportal library:
>> https://github.com/EBIBioSamples/bioportal-client
>>
>> in case anyone need a simple solution. I haven't done intensive testing of
>> it, but I've done a few and it seems to work fairly well.
>>
>>
>>
>>
>> --
>> View this message in context: http://ncbo-support.2288202.n4.nabble.com/New-Bioportal-API-searching-ontology-classes-by-acronym-and-accession-tp4653417p4653462.html
>> Sent from the NCBO Support mailing list archive at Nabble.com.
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>

-- 

===============================================================================
Marco Brandizi, PhD brandizi at ebi.ac.uk, http://www.marcobrandizi.info

Functional Genomics Group - Sr Software Engineer
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European Bioinformatics Institute (EMBL-EBI)
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