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

Trish Whetzel plwhetzel at gmail.com
Fri Dec 20 11:12:29 PST 2013


Thanks Ray. I don't need updated mapping data yet, but was looking to see
if the mappings now more easily include how they were generated, e.g. LOOM,
BioPortal UI, dbxref, etc. and stumbled upon this issue.

Is the type of process that generated the mapping included in the output
from this call:
http://data.bioontology.org/mappings?ontologies=NCIT,FMA

Trish


On Fri, Dec 20, 2013 at 10:57 AM, Ray Fergerson
<ray.fergerson at stanford.edu>wrote:

> Trish,
>
>
>
> 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.
>
>
>
> Ray
>
>
>
> *From:* bioontology-support-bounces at lists.stanford.edu [mailto:
> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *Paul R
> Alexander
> *Sent:* Friday, December 20, 2013 9:53 AM
> *To:* Trish Whetzel
> *Cc:* Maria Angeles Sanguino Gonzalez; support at bioontology.org 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.
>
>
>
> Paul
>
>
>
>
>
> On Dec 19, 2013, at 3:09 PM, Trish Whetzel <plwhetzel at gmail.com> wrote:
>
>
>
> Is the call:
> http://data.bioontology.org/mappings?ontologies=NCIT,FMA&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.
>
> Trish
>
>
>
>
>
> On Thu, Dec 19, 2013 at 10:00 AM, Paul R Alexander <
> palexander at stanford.edu> wrote:
>
> Nines,
>
>
>
> 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:
>
> http://data.bioontology.org/mappings?ontologies=NCIT,FMA
>
>
>
> Paul
>
>
>
>
>
> On Dec 19, 2013, at 3:22 AM, Maria Angeles Sanguino Gonzalez <
> maria.sanguino at atos.net> 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 (http://data.bioontology.org/metadata/Mapping 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)
>
> o
> http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceontology=1032&targetontology=1053&pagesize=500&pagenum=1&apikey=8b8e7850-0dbb-43ba-b29d-b5ed5719532c
>
>
>
> Many thanks for the excellent work and thanks for the suggestion.
>
> Regards,
>
> Nines
>
>
>
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