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

manuelso manuelso at stanford.edu
Wed Oct 2 15:17:57 PDT 2013


Hi Lee,

As triple store we use 4store [1]. We documented how we transitioned to a RDF/SPARQL backend in [2]. You might also want to look at [3] were we documented some of the pros and cons of using SPARQL to query Biomedical ontologies.

Best,

Manuel

[1] http://4store.org/
[2] BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF.
     http://www.semantic-web-journal.net/sites/default/files/swj278_4.pdf
[3] Using SPARQL to Query BioPortal Ontologies and Metadata
     http://iswc2012.semanticweb.org/sites/default/files/76500177.pdf
     http://www.slideshare.net/manuelso/using-sparql-to-query-bioportal-ontologies-and-metadata


On Oct 2, 2013, at 2:23 PM, Lee Watkins <lee.watkins at jhmi.edu> wrote:

> 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
>> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131002/0840cc92/attachment.html>


More information about the bioontology-support mailing list