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

Paul R Alexander palexander at stanford.edu
Tue Oct 21 15:51:15 PDT 2014


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.
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