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

mbrandizi brandizi at ebi.ac.uk
Fri Oct 10 04:14:20 PDT 2014


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.




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