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[bioontology-support] New triple-store backend

Ray Fergerson ray.fergerson at
Wed Oct 2 14:25:45 PDT 2013

We are using 4store and, so far are quite happy with it. At the moment we
are spending all our time fixing some stuff that we have, knowingly or
unknowingly, broken.


From: Lee Watkins [mailto:lee.watkins at]
Sent: Wednesday, October 02, 2013 2:24 PM
To: Ray Fergerson
Cc: support at
Subject: Re: [bioontology-support] New triple-store backend

Thanks!  So what triplestore are you using now?  TDB or something like
SparkleDB or maybe a graph database?  How you reparsed the ontology files
may have decided that for you, I guess.  Since this is fairly esosteric
knowledge and something very few people have actually done, a technical
report on it would be very informative to people like me who are trying to
come to grips with this whole domain.  Not that you need more work to do,
I’m sure...Lee

On 10/2/13 4:46 PM, "Ray Fergerson" <ray.fergerson at> wrote:

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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