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[bioontology-support] [BioPortal] Feedback from Samantha Walkow

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Mar 30 14:46:28 PDT 2016


Hi Samantha,


On Mar 30, 2016, at 12:28 PM, Samantha Walkow <swalkow at cfri.ca<mailto:swalkow at cfri.ca>> wrote:

Hi Jennifer,

Thanks for getting back to me. Sorry, I should have been more clear. I don’t have a lot of experience with ontologies, so I may be way off base with what I’m asking!

There is no DSM (Diagnostic and Statistical Manual of Mental Disorders) ontology that I can find, but I was wondering if Bio Portal is able to create an ontology and add a DSM ontology . Is that something Bio Portal can do?


BioPortal is a read-only application in the sense that we don’t provide an ontology editing environment where people can create and edit ontologies.  To do something like that, the Protege ontology editing tool would be more appropriate:

http://protege.stanford.edu/

People generally use BioPortal to upload ontologies that already exist in one of the standard ontology languages, e.g., OWL or OBO.  There is one exception that I can think of in that we do make UMLS terminologies available in BioPortal.  The UMLS provides their data to the public in relational database format, and we have an internal process whereby we convert the database contents to RDF ontology files that can then be imported into the BioPortal application.

I’ve spoken just now to a member of the Protege team that has a lot of experience with biomedical ontologies, and he was not aware of the existence of a DSM ontology.  He did mention one ontology in BioPortal called ADAR:

http://bioportal.bioontology.org/ontologies/ADAR

This is an instance where a researcher represented some DSM diagnostic criteria pertaining to autism in ontology format.  However, this is not a complete representation of all DSM criteria.

Alternatively, he also mentioned that you might be referring to the ICD-9-CM or ICD-10-CM codes for DSM diagnosis (http://www.dr-bob.org/tips/dsm5a.html)?  If that’s the case, we already have those ontologies available in BioPortal:

http://bioportal.bioontology.org/ontologies/ICD10CM
http://bioportal.bioontology.org/ontologies/ICD9CM

Hope that information helps.

Jennifer

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