Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Ray Fergerson ray.fergerson at stanford.edu
Fri Dec 20 15:09:09 PST 2013


Trish,

 

The source of the mapping is stored in an object attached to the mapping
called a "process". The name of the "process" is what you are looking for,
e.g. "loom".

 

As an example of a single loom mapping, look at:

 

http://data.bioontology.org/mappings/http%3A%2F%2Fdata.bioontology.org%2Fm
etadata%2Fmapping%2F6b85bf019af4b67e8120e682eb238c2c198b7fea

 

Ray

 

From: Trish Whetzel [mailto:plwhetzel at gmail.com] 
Sent: Friday, December 20, 2013 11:12 AM
To: Ray Fergerson
Cc: Paul R Alexander; Maria Angeles Sanguino Gonzalez;
support at bioontology.org
Subject: Re: [bioontology-support] moving from the old Api to the new Api

 

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
<http://data.bioontology.org/mappings?ontologies=NCIT,FMA&apikey=YourAPIKe
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.

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>
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?sourceo
ntology=1032&targetontology=1053&pagesize=500&pagenum=1&apikey=8b8e7850-0d
bb-43ba-b29d-b5ed5719532c>
http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceon
tology=1032&targetontology=1053&pagesize=500&pagenum=1&apikey=8b8e7850-0db
b-43ba-b29d-b5ed5719532c

 

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

Regards,

Nines

 

------------------------------------------------------------------
This e-mail and the documents attached are confidential and intended 
solely for the addressee; it may also be privileged. If you receive 
this e-mail in error, please notify the sender immediately and destroy it.

As its integrity cannot be secured on the Internet, the Atos 
group liability cannot be triggered for the message content. Although 
the sender endeavours to maintain a computer virus-free network, 
the sender does not warrant that this transmission is virus-free and 
will not be liable for any damages resulting from any virus transmitted. 

Este mensaje y los ficheros adjuntos pueden contener informacion
confidencial 
destinada solamente a la(s) persona(s) mencionadas anteriormente 
pueden estar protegidos por secreto profesional. 
Si usted recibe este correo electronico por error, gracias por informar 
inmediatamente al remitente y destruir el mensaje. 
Al no estar asegurada la integridad de este mensaje sobre la red, Atos 
no se hace responsable por su contenido. Su contenido no constituye ningun

compromiso para el grupo Atos, salvo ratificacion escrita por ambas
partes. 
Aunque se esfuerza al maximo por mantener su red libre de virus, el emisor

no puede garantizar nada al respecto y no sera responsable de cualesquiera

danos que puedan resultar de una transmision de virus. 

------------------------------------------------------------------
_______________________________________________
bioontology-support mailing list
 <mailto:bioontology-support at lists.stanford.edu>
bioontology-support at lists.stanford.edu
 <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131220/11d05408/attachment-0001.html>


More information about the bioontology-support mailing list