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[bioontology-support] "leafpath" query on ontology 1352 (National Drug File)

Adrian Bivol ABivol at buckinstitute.org
Mon Jun 25 09:47:38 PDT 2012


Hi Trish,

Thank you for the clarification.

In this case, I was able to obtain a mapping between the two types of identifiers by using the .owl file.
Example:

<owl:Class rdf:ID="N0000010584">
<rdfs:label>B [Preparations]</rdfs:label>
<code>C288628</code>

Thank you,
Adrian Bivol.


________________________________________
From: Trish Whetzel [whetzel at stanford.edu]
Sent: Friday, June 22, 2012 2:52 PM
To: Adrian Bivol
Cc: support Support; Darcy Davis
Subject: Re: [bioontology-support] "leafpath" query on ontology 1352 (National Drug File)

Hi Adrian,

This is particularly confusing for the National Drug File since the different versions have different term identifiers, a change in content confirmed by our collaborators at Mayo.

The "Get Term" and "Search" Web services use the latest version of the ontology in BioPortal which has the ontology version id=47101 and term id=N0000010584 for the term "B [Preparations]":
http://bioportal.bioontology.org/ontologies/47101/?p=terms&conceptid=N0000010584

However, the Hierarchy database does not necessarily contain the latest version of the ontology present in BioPortal and in this case contains the version of the National Drug File with ontology version id=40402, which has term id=C288628 for "B [Preparations]". Therefore, the Hierarchy web services [1], such as the "leafpath" call, use this term identifier. To see which ontology versions have been processed for use with the Hierarchy Services, check http://rest.bioontology.org/obs/ontologies?apikey=YourAPIKey for ontologies with STATUS=28.

Trish

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Hierarchy_Services



On Jun 21, 2012, at 10:56 AM, Adrian Bivol wrote:

> Hi Trish,
>
> Thank you for your help. The query does work with the term identifier you specified.
>
> But I do not know where this identifier comes from? It is not the concept id.
> For instance, the concept id for the "B [Preparations]" term in "National Drug File" is listed as "N0000010584", here:
> http://rest.bioontology.org/bioportal/search/?query=B%20[Preparations]&ontologyids=1352&isexactmatch=1&objecttypes=class,individual&apikey=XXX
> http://bioportal.bioontology.org/ontologies/47101/?p=terms&conceptid=N0000010584
>
> The "leafpath" API takes a "conceptId" as parameter:
> "Signature: ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?apikey={YourAPIKey}&{optional args}] "
>
> My point is that this does not seem to apply for "National Drug File", and I cannot obtain the term identifiers that you mentioned (like C288628).
> Am I missing something?
>
> Thank you,
> Adrian Bivol.
>
>
> ________________________________________
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Thursday, June 21, 2012 10:02 AM
> To: Adrian Bivol
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] "leafpath" query on ontology 1352 (National Drug File)
>
> Hi Adrian,
>
> The term identifier in this case is: C288628 and when used in the "leafpath" web service call it does return results.
>
> Trish
>
>
> On Jun 20, 2012, at 6:05 PM, Adrian Bivol wrote:
>
> Hi,
>
> I am trying to run "leafpath" queries on ontology 1352 (National Drug File).
> All my queries are returning Internal Server Error (500); for example:
> http://rest.bioontology.org/bioportal/virtual/leafpath/1352/N0000010584?apikey=XXX
>
> My goal is to obtain all the children nodes of "Pharmaceutical Preparations", concept id: N0000000001. (gives the same error)
>
> Can you advise on this issue?
>
> Thank you,
> Adrian Bivol.
> _______________________________________________
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> http://www.bioontology.org
>
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