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[bioontology-support] [BioPortal] Feedback from Abhi

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Sep 26 18:11:28 PDT 2016


Hi Abhi,


On Sep 26, 2016, at 10:27 AM, Abby Sawarkar <absawarkar at gmail.com<mailto:absawarkar at gmail.com>> wrote:

Hi Jennifer,

Two questions about the mapping -
1. Does the mapping use only MeSH descriptors or does it use the qualifiers and the supplemental records as well?


I don’t know off the top of my head - mostly because I’m not a MeSH expert and I don’t know the difference between descriptors, qualifiers, and supplemental records.  Do you have an example of a supplemental record?  If it’s something that appears as a term in the tree structure that BioPortal displays to represent the MeSH hierarchy, then it would be used in the mappings.


2. Is there a way to download the MeSH to MedDRA mapping from the Bioportal for research purposes?


I’m not aware of any BioPortal service that allows a download of mappings.  We do offer access to mapping data between ontologies via our REST endpoint.  To retrieve mappings between MeSH and MedDRA, you would use this call:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA

Our REST endpoint is documented here:

http://data.bioontology.org/documentation

You need an API key to use the REST endpoint, which you can get by registering for an account on the BioPortal website: http://bioportal.bioontology.org/.

Kind Regards,
Jennifer




Thanks
Abhi



On Tue, Aug 30, 2016 at 7:23 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Abhi,


On Aug 30, 2016, at 4:00 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Abhi

Email: absawarkar at gmail.com<mailto:absawarkar at gmail.com>

Location: http://bioportal.bioontology.org/ontologies/MESH

Feedback:

Hi
Is there a way to tell which version/release of the ontology/terminology was used in the mapping exercise?
I am interested in the MeSH - MedDRA mapping

Mappings are generated by our system each time a new version of an ontology is submitted.

The most current MeSH and MedDRA versions were imported into BioPortal from the UMLS 2015AB release.  According to the UMLS website, release 2015AB contains MeSH version MSH2016_2015_08_18 [1], and MedDRA version MDR18_0 [2].

Jennifer

[1] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH/metadata.html
[2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html




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