Rdfio on Living Systems_

Compiling RDFHDT C++ tools on UPPMAX (RHEL/CentOS 7)

Wed, 13 Sep 2017 18:04:00 +0200

At pharmb.io we are researching how to use semantic technologies to push the boundaries for what can be done with intelligent data processing, often of large datasets (see e.g. our paper on linking RDF to cheminformatics and proteomics , and our work on the RDFIO software suite ). Thus, for us, RDFHDT opens new possibilites. As we are heavy users of the UPPMAX HPC center for our computations, and so, we need to have the HDT tools available there. This post will outline the steps to compile the C++ HDT commandline tool suite from source.

New paper on RDFIO for interoperable biomedical data management in Semantic MediaWiki

Mon, 11 Sep 2017 15:57:00 +0200

As my collaborator and M.Sc. supervisor Egon Willighagen already blogged , we just released a paper titled: “RDFIO: extending Semantic MediaWiki for interoperable biomedical data management ”, with uses cases from Egon and Pekka Kohonen , coding help from Ali King and project supervision from Denny Vrandečić , Roland Grafström and Ola Spjuth .

See the picture below (from the paper) for an overview of all the newly developed functionality (drawn in black), as related to the previously existing functionality (drawn in grey):

RDFIO VM

Tue, 13 Jan 2015 20:43:00 +0100

The old Virtual Machine still available

The old virtual machine from June 25, 2014, based on Ubuntu 14.04, and RDFIO 2.x can be found here