giovedì 13 settembre 2012

Announcing the first list of tutorials at SWAT4LS 2012

We are pleased to announce the first list of tutorials that will be provided at SWAT4LS in the 2012 edition.
With more tutorials still in discussion, we are planning of having two parallel tutorials sessions on Thursday, November 29th.

Interconnecting Linked Open Data and R with the SPARQL package for Linked Science

The openly available R package SPARQL allows to directly connect to Linked Data and use the SPARQL querying language for selecting interesting part of data for analysis. Thus it enables to meet massive and rich data sets with the analytical power of the R language and environment.
This approach and tools contribute to Linked Science and Open Science movements to support transparency of science and helps to conduct transdisciplinary research.
In this tutorial we will introduce the idea and concepts about Linked Science, and show via illustrative examples about how to practically query and analyze Linked Data from within R environment for statistical analysis.
The website for the tutorial will include all the tutorial materials (

The tutorial will be presented by Tomi Kauppinen (

Biological Pathways and the Semantic Web 
This tutorial will address exposing Biological Pathways to the semantic web. In this tutorial WikiPathways ( will be core. We recently exposed WikiPathways content as linked open data now available through a Sparql endpoint (

The tutorial will cover the following topics:
How to edit pathways at WikiPathways
How to convert pathway content to RDF and link it to other semantic web resources
How to perform common semantic queries on pathways
How to build tools around semantic pathway resources
How to use Open PHACTS ( with pathway content

The tutorial is proposed by Andra Waagmeester (BiGCaT@andrawaag ), Martina Kutmon (BiGCaT), Egon Willighagen (BiGCaT, @egonwillighagen), Chris Evelo (BiGCaT, @Chris_Evelo) and Alex Pico (

Using SPARQL to Query BioPortal Ontologies and Metadata

BioPortal is a repository of biomedical ontologies, with more than 300 ontologies to date. This set includes ontologies developed in OWL, OBO format, as well as a large number of medical terminologies that the US National Library of Medicine distributes in its own proprietary format. We have published the RDF based serializations of all these ontologies and their metadata at This dataset contains 203M triples, representing both content and metadata for the 300+ ontologies; and 9M mappings between terms. This endpoint can be queried with SPARQL, which opens new usage scenarios for the biomedical domain. This tutorial will present an overview of the SPARQL endpoint, commonly used queries, and lessons learned from having redesigned several applications that today use this SPARQL endpoint to consume ontological data.

The tutorial will be presented by Trish Whetzel, Ph.D,  Outreach Coordinator at the National Center for Biomedical Ontology (NCBO). 

Drug-discovery knowledge integration and analysis using OWL and reasoners
Biology relies on various classifications and databases to organize and explain the living world. These resources are traditionally disparate but can nowadays be expressed with the Web Ontology Language (OWL) in order to be more easily combined and queried. In this tutorial we will go beyond RDF/SPARQL and will explore the advantages of using OWL and reasoners for knowledge integration and analysis in life science.
The tutorial is composed of a theoretical part around OWL modelling for biology featuring hands-on exercises using Protégé and the OWL-API. Then follow a practical session, where the attendees will integrate the information coming from different sources (Gene Ontology, Uniprot and DrugBank) into an OWL knowledgebase. The integrated data will be queried using OWL constructs and is capable of answering drug-discovery questions such as finding new protein targets to treat a disease via reasoning.
The attendees are expected to have some general knowledge around Semantic Web and Java. During the tutorial, the participants will learn how to integrate and leverage the information present in various repositories using OWL. They will understand how to formulate biomedical questions in Description Logic and retrieve hidden knowledge with the help of a reasoner.

The tutorial will be presented by Samuel Croset ( and Dietrich Rebholz-Schumann (

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