Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] New triple-store backend

Lee Watkins lee.watkins at jhmi.edu
Wed Oct 2 15:06:51 PDT 2013


I’ll bet. Thanks again!



On 10/2/13 5:25 PM, "Ray Fergerson" <ray.fergerson at stanford.edu> wrote:

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.

Ray


From: Lee Watkins [mailto:lee.watkins at jhmi.edu]
Sent: Wednesday, October 02, 2013 2:24 PM
To: Ray Fergerson
Cc: support at bioontology.org
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 stanford.edu> 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.

Ray


From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Lee Watkins
Sent: Tuesday, October 01, 2013 11:13 AM
To: support at bioontology.org
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.
Thanks,
Lee



---

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 jhmi.edu | http://www.cidr.jhmi.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131002/847e889f/attachment.html>


More information about the bioontology-support mailing list