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[bioontology-support] view extractor in bioontology

Natasha Noy noy at stanford.edu
Wed Mar 24 18:41:47 PDT 2010


Eugene,

Apologies for this! We normally try to give people a few days' notice  
but the change this afternoon was an emergency on our side.

In this particular case, for a while now CHD and SubClass were  
duplicating each other. SubClass is there for ontologies in all  
formats so this is definitely the one to use. So, we remove CHD  
because it was there only for some ontologies and was just doubling  
the size of our class beans while providing zero additional information.

By the way, are you on the bioportal-announce mailing list? We try to  
send these types of announcements there (although didn't today because  
of an emergency).

The upside is that now your downloads should be much smaller and  
faster :) at least for some ontologies.

Natasha


On Mar 24, 2010, at 6:37 PM, Eugene wrote:

> Nigam,
>
> Thanks.
>
> I have one question. Do you guys keep changing the XML schema? I am  
> aware the child concepts was used to be indicated in XML tag  
> <string>CHD</string>. But this later afternoon, it is changed to  
> <string>SubClass</string>.
>
> It’s ok to change on the fly. But if we are not notified, we will  
> need to do find out why it is used to work but it don’t work  
> anymore. The issue if the change occurs when we are in the middle of  
> downloading. Also, sometimes we need to emergently fix something  
> without much time to figure out why it doesn’t work.
>
> Thanks
>
> Eugene
>
> From: drnigam at gmail.com [mailto:drnigam at gmail.com] On Behalf Of  
> Nigam Shah
> Sent: Wednesday, March 24, 2010 11:11 AM
> To: Eugene
> Cc: support at bioontology.org
> Subject: Re: view extractor in bioontology
>
> Yes. C000304 is not an ID from MSH. You are using a CUI, those are  
> assigned by the UMLS metathesaurus .. MSH ids are of the form  
> D008545 (e.g. for Melanoma). So the call would be http://rest.bioontology.org/bioportal/virtual/ontology/1351/D008545?email=example@example.org
>
> --Nigam.
>
> On Wed, Mar 24, 2010 at 11:04 AM, Eugene <eugene at nextbio.com> wrote:
> Hi,
>
> I have a question.
>
> The following url is working for SnoMed CT ontology.
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1353/2704003?email=example@example.org
>
> However, I am changing to use MeSH to the following:
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1351/C0003047?email=example@example.org
>
> 1351: MeSH ontology id
> C0003047: “animal disease” concept id.
>
> Now, it doesn’t work. Is the parameter wrong?
>
> Thanks
>
> Eugene
>
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