Home

pellet

NMR SPARQL search problem solved

Fri, 2010-02-19 22:20 | by saml

The problem I've had, to find a working SPARQL query for doing similarity search for spectra, according to a list of peak shift values (documented on this blog: post1, post 2 and on semanticoverflow) is now finally solved, thanks to helpful advice from Brandon Ibach on the [pellet-users] mailing list.

Tags:

[solved] User defined datatypes not working in OWL 1.X

Mon, 2009-12-07 11:43 | by saml

I seemingly ran into the trouble that user-defined datatypes does not work in OWL 1.X (which is seemingly what the version of Pellet used in Bioclipse does support?

File based RDF storage in Pellet, first tests

Tue, 2009-11-24 17:32 | by saml

As reported in a previous blog post, I ran into java stacksize errors when importing large amounts of data into pellet. Pellet was using just the in-memory Jena RDF store, which obviously puts limits on the amount of data it can handle.

Jena offers other options for RDF storage though, including SDB for SQL backends, and TDB for a pure Java file based storage.

Initial performance comparison: Pellet vs Prolog in Bioclipse

Mon, 2009-11-23 11:41 | by saml

I started with some initial performance testing for RDF data, between pellet an prolog, which are now both available integrated in Bioclipse.

Nice intro to RDF in Prolog (by Pellet author)

Wed, 2009-11-04 11:00 | by saml

I found a nice introduction to the use of RDF in Prolog (SWI-Prolog). It contains short primers for both RDF and Prolog, so it should be accessible to anyone with a minimal programming background:

Tags:

Pondering over strategies for evaluating BLIPKIT vs Pellet for use with NMRShift data

Tue, 2009-11-03 10:48 | by saml

As a subproject, I'm now focusing on doing some comparison between reasoning in Prolog and Pellet, using example data from NMRShiftDB.org. Below I'm documenting my planning, + any new findings while I'm digging in to this subpeoject.

Reading tip: Quick overview of Prolog and it's role in Semantic Web

Tue, 2009-10-06 21:34 | by saml

I Just read this paper on using thea for OWL (Web Ontology Language) reasoning from within Prolog.

Tags:

Description Logic vs Prolog

Sun, 2009-10-04 03:53 | by saml

Pellet, the reasoning system already integrated in Bioclipse, is based on so called "Description Logics".