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[bioontology-support] New triple-store backend

Ray Fergerson ray.fergerson at
Wed Oct 2 13:46:37 PDT 2013

Previously we stored data in Protégé 3 database format and the LexEVS
database format. These were migrated to a triple store by reparsing the
original ontology files (we didn’t try to migrate the previous formats).
We were driven to make this change because we wanted a uniform way to
store things and wanted to be able to provide a SPARQL based access to the
underlying ontologies and metadata.


From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of Lee
Sent: Tuesday, October 01, 2013 11:13 AM
To: support at
Subject: [bioontology-support] New triple-store backend

I'm interested to know what you used for your "new triple-store backend
storage system" and what was involved in migrating from triples stored in
a relational database (which is what I'm guessing you used previously?),
and what drove you to make the change.




Lee Watkins, Jr.

Director of Bioinformatics & IT

Center for Inherited Disease Research

McKusick-Nathans Institute of Genetic Medicine

Johns Hopkins University School of Medicine

333 Cassell Drive, Triad 2000

Baltimore, MD 21224

410-550-6702 w | 410-903-2989 c [urgent_only]

lee.watkins at |

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