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[bioontology-support] [BioPortal] Feedback from sharat.sinha

Michael Dorf mdorf at stanford.edu
Tue Jun 16 13:44:07 PDT 2020


Hi Sharat,

Thank you for contacting support.  Depending on how you identify an adverse event (based on its Preferred Label, Notation, or CUI), you can find the info you need using the BioPortal REST API in one of these two ways:

1. Using the /classes endpoint, you can paginate over ALL classes in MEDDRA, selecting those that meet your criteria (by examining the property of the class that defines it as being an adverse event):

https://data.bioontology.org/ontologies/MEDDRA/classes?no_links=true&no_context=true&display=prefLabel,synonym,submission,definition,cui,semanticType,obsolete,properties&page=1

By default, each page contains 50 classes. You can iterate over all classes by incrementing the &page=1 number.

2. Using the /search endpoint:

If ALL adverse events are contained within a branch, you can get ALL classes within that branch by executing a sub-tree search:

http://data.bioontology.org/search?ontology=MEDDRA&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10005908<http://data.bioontology.org/search?ontology=MEDDRA&subtree_root_id=http://purl.bioontology.org/ontology/MEDDRA/10005908>

Where the “subtree_root_id” is the URL encoded ID of the branch root class.

OR

If you know the labels of the classes that classify as adverse events, you can execute a search for each label you have:

http://data.bioontology.org/search?q=adverse%20event&ontologies=MEDDRA

Hope one of these methods works for you. Be sure to append your BioPortal API key to the above REST calls: &apikey=yourapikey

Let us know if you require further assistance.

Michael






----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jun 16, 2020, at 12:09 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: sharat.sinha

Email: sharat.sinha at excelra.com<mailto:sharat.sinha at excelra.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMEDDRA%3Fp%3Dwidgets

Feedback:

Is there a way to download meddra code for all adverse events listed?

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