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[bioontology-support] moving from the old Api to the new Api

Ray Fergerson ray.fergerson at
Fri Dec 20 10:57:01 PST 2013



We understand the source of this problem. Unfortunately it will take some
time to fix. The count is correct but the mappings are not reliably
returned. As a workaround, suggest you iterate though the terms in the
smaller of the ontologies and ask for mappings between each term and any
term in the other ontology.


This workaround is painful and slow but it should work. It is about all
that we can offer until we have addressed the underlying problem.




From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of Paul
R Alexander
Sent: Friday, December 20, 2013 9:53 AM
To: Trish Whetzel
Cc: Maria Angeles Sanguino Gonzalez; support at Support
Subject: Re: [bioontology-support] moving from the old Api to the new Api


This is a bug. We'll be looking into it. Thanks for reporting.





On Dec 19, 2013, at 3:09 PM, Trish Whetzel <plwhetzel at> wrote:

Is the call:,FMA
y> &apikey=YourAPIKey  intended to return all 1,937 mappings between FMA
and NCIt? Only 1 mapping pair is returned. 

On the BioPortal mappings page, after selecting NCIt the page lists a
count of 1,937 mappings, but when clicking on the link for FMA only 1
mapping pair is displayed.




On Thu, Dec 19, 2013 at 10:00 AM, Paul R Alexander
<palexander at> wrote:



We will update the documentation with mappings examples, thank you for
pointing out that there are none.


The specific call that would replace the one you were using is this:,FMA





On Dec 19, 2013, at 3:22 AM, Maria Angeles Sanguino Gonzalez
<maria.sanguino at> wrote:


Dear Biportal support team,


I've receive an email suggesting moving any code that accesses the old API
to the new API. I'm particularly interested in the mappings resources and
I was wondering:

-          When de new API (
<> concretely) will provide some
examples of use.

-          And which is the equivalent method to the old method in charge
of provide mappings (unidirectional o bidirectional) between two
ontologies (an example of the old method)



Many thanks for the excellent work and thanks for the suggestion.




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