Skip to main content

gen2phen

GEN2PHEN Semantic Web Labs

Contributed by:Pedro Lopes
Originally posted:21st October 2010: 9:22 am
Last updated:21st October 2010: 9:50 pm
Short URL:http://gen2phen.org/node/29087
Interest group icon Semantic Web in GEN2PHEN
Public document Public - anyone can view

During my stay in Leicester I analyzed some of the available tools and strategies to integrate existing systems in a Semantic Web environment. My accomplishments are reported in the attached document. Analyzed tools:

There are also two application demos available:

Tag & categorise
Tags: 
semantic web
Tags: 
gen2phen
Tags: 
sparql
Tags: 
mashup
Tags: 
federation
Tags: 
federated querying
Tags:

MOLGENIS and D2R

Contributed by:Pedro Lopes
Originally posted:21st October 2010: 9:18 am
Last updated:21st October 2010: 9:53 pm
Short URL:http://gen2phen.org/node/29086
Interest group icon Semantic Web in GEN2PHEN
Public document Public - anyone can view

During my Leicester stay I did a deep analysis on the integration of D2R in Molgenis, which resulted in a short report. This report highlights D2R setup and details some custom enhancements that should be added to D2R mappings in order to create a richer Semantic Web platform from Molgenis instances. All my experiments were performed using the Pheno-OM data model, with a SQL dump from Tomasz.

I've attached the report, a short presentation on the subject, and two D2R mapping files (an auto-generated and a customized) for the Pheno-OM data model.

Tag & categorise
Tags: 
semantic web
Tags: 
gen2phen
Tags: 
molgenis
Tags: 
d2r
Tags: 
d2rq
Tags: 
mapping
Tags: 
pheno-om
Tags:

Researcher Identification Primer

A number of ostensibly separate initiatives, with diverse objectives, have begun considering the risks, benefits, and practicalities of unambiguously identifying researchers as they use and contribute to biomedical data sources on the Internet. The GEN2PHEN project is one such initiative, given its general aim of helping to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data.

Tags:

Partners

The GEN2PHEN Consortium constitutes a talented pool of European research groups and companies that are interested in the G2P databasing challenges. A few non-EU participants have been included to bring extra capabilities to the initiative.

The GEN2PHEN Strategy

The GEN2PHEN project has the overall ambition of unifying human and model organism genetic variation databases, and doing this in such a way that the resulting holistic view of G2P data can be blended with all other biomedical database domains via one or more central genome browsers.

Project Summary and Objectives

The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. The project will establish the technological building-blocks needed for the evolution of today’s diverse G2P databases into a future seamless G2P biomedical knowledge environment, by the projects end.

General Information

HEALTH theme - contract no. 200754.
Duration: 60 months.
Start date: 1-Jan-2008.
Funding: 11.889.367 €

Participating institutions:

  • University of Leicester, UK
  • European Molecular Biology Laboratory, Germany
  • Fundació IMIM, Spain
  • Leiden University Medical Center, Netherlands
  • Institut National de la Santé et de la Recherche Médicale, France
  • Karolinska Institutet, Sweden
  • Foundation for Research and Technology – Hellas, Greece
  • Commissariat à l’Energie Atomique, France
  • Erasmus University Medical Center, Netherlands
  • Institute for Molecular Medicine Finland, University of Helsinki, Finland
  • University of Aveiro – IEETA, Portugal
  • University of Western Cape, South Africa
  • Council of Scientific and Industrial Research, India
  • Swiss Institute of Bioinformatics, Switzerland
  • University of Manchester, UK
  • BioBase GmbH, Germany
  • deCODE genetics ehf, Iceland
  • PhenoSystems SA, Belgium
  • Biocomputing Platforms Ltd Oy, Finland
  • University of Patras, Greece

 

FUNDING


GEN2PHEN is funded by the Health Thematic Area of the Cooperation Programme of the European Commission within the VII Framework Programme for Research and Technological Development.


G2P Knowledge Centre is part of GEN2PHEN and funded by the Health Thematic Area of the Cooperation Programme of the European Commission within the VII Framework Programme for Research and Technological Development.

© GEN2PHEN 2011