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

Paul R Alexander palexander at stanford.edu
Wed Oct 1 17:12:08 PDT 2014


Marco,

Indeed, the revision of our API has purposefully removed lookup using the accession id, or what we used to call the “short id”, in favor of the full class URI. We found these short ids to be unpredictable across ontologies and they map very poorly to the class URIs in many cases.

The working example you have with the efo namespace is an accidental side effect of something else and could stop working at any point. As a more permanent fix, I think we could enable our search service to allow for partial matching on the class id, which allow for lookup based on the ‘short id’.

I’m creating an issue for our team to investigate. Sorry I don’t have a better solution right now.

Paul


On Sep 30, 2014, at 11:53 AM, mbrandizi <brandizi at ebi.ac.uk> wrote:

> Hi all,
> 
> I'm trying to use the new Bioportal API, but I don't get one thing. I have
> ontology terms which are specied by means of ontology acronym + term
> accession, like in: EFO + EFO_0000270. In the past, I was able to fetch term
> details by using these two parameters (OK, it required to resolve the
> ontology acronym to an internal Bioportal ID, but that wasn't a big deal).
> 
> How can I do the same now?
> 
> The examples I've seen so far use the term full URI, like in:
> http://data.bioontology.org/ontologies/EFO/classes/http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000270
> 
> The problem is I don't have the URI prefix. Is there a way to get it from
> the ontology reference? I understand this is difficult with OWL ontologies,
> but I was hoping some mapping has been defined at least for common cases.
> 
> I've tried:
> http://data.bioontology.org/ontologies/EFO/classes/efo:EFO_0000270 and this
> actually works, but then these don't: 
> http://data.bioontology.org/ontologies/GO/classes/go:GO_0015219
> http://data.bioontology.org/ontologies/GO/classes/GO:GO_0015219
> http://data.bioontology.org/ontologies/GO/classes/go:0015219
> http://data.bioontology.org/ontologies/GO/classes/GO:0015219
> 
> while this works with the lower-case prefix:
> http://data.bioontology.org/ontologies/BRO/classes/BRO:Ontology_Development_and_Management
> 
> so, it sounds like the APIs are using some internal namespace prefixes, but
> there isn't a way to map them to the ontologies.
> 
> Anyone who can help?
> 
> Thank you in advance,
> Marco.
> 
> 
> 
> 
> 
> --
> View this message in context: http://ncbo-support.2288202.n4.nabble.com/New-Bioportal-API-searching-ontology-classes-by-acronym-and-accession-tp4653417.html
> Sent from the NCBO Support mailing list archive at Nabble.com.
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