venerdì 21 settembre 2012

SWAT4LS 2012 Special issue and new approach to peer review

Papers accepted for this year's SWAT4LS will be invited to submit revised and extended versions of their work to the BMC Journal of Biomedical Semantics (it will appear as a regular paper in the SWAT4LS/CSHALS thematic series, to be launched soon).

To foster the role of the workshop as a key venue for discussions and for improving the research quality, we are going to pilot a new review process by which participants' feedback on the workshop presentations will be considered as part of the formal review of an eventual journal publication. All participants will be invited to provide feedback using a review form after the presentations: this will be aken into consideration during the review process to improve the manuscript's quality.

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 (

mercoledì 12 settembre 2012

SWAT4LS 2012 is in cooperation with ACM

This year edition will be organized in co-operation with ACM (Bioinformatics Interest Group).
Proceedings will not be published in ACM, but in CEUR, following concerns of last year's participants (and reviewers) on copyright restrictions.

lunedì 10 settembre 2012

SWAT4LS 2012 Keynotes

We are happy to announce the SWAT4LS 2012 Keynotes.

Mark A. Musen, M.D., Ph.D
Director, Stanford Center for Biomedical Informatics Research

Principal Investigator, The United States National Center for Biomedical Ontology
Stanford University School of Medicine
Stanford, California  USA

Semantic Technology Goes Mainstream: The NCBO Experience
The National Center for Biomedical Ontology (NCBO) is one of seven National Centers for Biomedical Computing in the United States supported by the National Institutes of Health.  As workers in biomedicine recognize the importance of creating structured representations of the entities and the relationships among entities in experimental domains, the NCBO is developing the semantic technologies to use those representations to drive in a wide range of applications in data annotation, data integration, information retrieval, natural-language processing, and decision support.  The NCBO is creating Web-based software to facilitate the archiving, peer review, and application of ontologies by workers in biomedicine.  In recent years, the use of NCBO resources has been growing exponentially.  Currently, more than 65,000 visitors browse the BioPortal ontology repository each month, many of whom seem to visit the site nearly every day.  Each month, the NCBO handles more than 3 million Web service calls.  Learning what all these users are doing with NCBO technology provides an opportunity to track the requirements of the Semantic Web community in health care and the life sciences.  The NCBO continues to explore methods to obtain more information about these users and their needs in an attempt to anticipate trends in the work of biomedical scientists who are embracing semantic technology.

Dr. Musen is Professor of Biomedical Informatics at Stanford University, where he is Director of the Stanford Center for Biomedical Informatics Research.  He holds an MD from Brown University and a PhD from Stanford.  
Dr. Musen conducts research related to intelligent systems, the Semantic Web, reusable ontologies and knowledge representations, and biomedical decision support.  His long-standing work on a system known as Protégé has led to an open-source technology now used by thousands of developers around the world to build intelligent computer systems and new computer applications for e-science and the Semantic Web.   He is known for his research on the application of intelligent computer systems to assist health-care workers in guideline-directed therapy and in management of clinical trials.  He is principal investigator of the National Center for Biomedical Ontology, one of the eight National Centers for Biomedical Computing supported by the U.S. National Institutes of Health.  He chairs the Health Informatics and Modeling Topic Advisory Group for the World Health Organization’s revision of the International Classification of Diseases (ICD-11).  He is a member of the National Advisory Council of the National Institute for Biomedical Imagine and Bioengineering of the U.S. National Institutes of Health.
Early in his career, Dr. Musen received the Young Investigator Award for Research in Medical Knowledge Systems from the American Association of Medical Systems and Informatics and a Young Investigator Award from the National Science Foundation.  In 2006, he was recipient of the Donald A. B. Lindberg Award for Innovation in Informatics from the American Medical Informatics Association.  He has been elected to the American College of Medical Informatics and the Association of American Physicians.  Dr. Musen sits on the editorial boards of several journals related to biomedical informatics and computer science.  He is co-editor of the Handbook of Medical Informatics (Springer-Verlag, 1997) and co-editor-in-chief of the journal Applied Ontology.  

C. Michael Gibson, M.S., M.D., FRCP, FAHA, FSCAI, FACC
Chairman, PERFUSE Study Group
Founder & Editor-In-Chief (An Open Source Textbook of Medicine with 6,800 Contributors Viewed 160 Million Times A Year)

Interventional Cardiologist, Beth Israel Deaconess Medical Center, an Affiliate of Harvard Medical School

The World is Flat, but the Earth is Round
One of the tenets of Friedman's "The World is Flat" is that Innovation increases as open access to information increases.  Although the wisdom of the crowd literally argued that the "World is Flat" several centuries ago, a select number of "experts" demonstrated the world is in fact round.  With the vast amount of medical information on the internet, how do we harness the "Wisdom of the Crowds" yet vet it through experts, and drive traffic to credible sites with the most relevant content? How can we streamline the process so that greater numbers of individuals and websites can participate in

C. Michael Gibson, M.S., M.D. is an interventional cardiologist, cardiovascular researcher and educator at Harvard Medical School and Duke. Dr. Gibson is Founder and Chairman of the Board of WikiDoc Foundation (a 509 (a)(1) Charitable Organization). This is the world's largest medical textbook / encyclopedia. There are currently over 400,000 page views daily of over 175,000 chapters of content contributed and edited over 619,000 times by over 6,910 registered users. Dr. Gibson has personally made over 69,000 edits to WikiDoc. The site is viewed 160 million times each year.   Gibson was one of the co-creators of a schema that allows webmasters and content publishers to mark up health and medical content on the web. 

Christine Golbreich, Ph.D
Professor in Computer Science at the University of Versailles Saint-Quentin

Formal ontologies for the Semantic Web ?
Ontologies are widely considered as a foundational technique of the Semantic Web, in which meanings of terms are defined by formal ontologies and semantic annotations facilitate the access to Web content. This view has led to the standardization of the Web Ontology Language OWL 2. In this talk, we will reflect on the usefulness of OWL 2 ontologies for Life Sciences. We will do this by presenting a number of advantages of OWL 2 ontologies: interoperability, semantics, reasoning services. But we will also notice that it is often the case that applications only ever use terms, e.g., the classical utilization of SNOMED-CT is to use its catalogue and codes to index medical records. We will discuss a new approach reconciling ontologies and terminologies. We propose to use an OWL 2 ontology for clear semantics and reasoning, and to derive from it a lightweight terminology (or perhaps something like an OWL 2 QL ontology) for applications such as resources indexing and search. For large vocabularies, the underlying rich ontology is essential to ensure that the lightweight derived terminology is quality-controlled. Reliability is particularly important for Health Care and Life Sciences applications where safety is critical. I will illustrate this by examples, including the semantic annotation of brain MRI images (IEEE Transactions on Medical Imaging 2009), the Foundational Model of Anatomy in OWL 2 and its use for a European Portal of Health terminologies dedicated to resources indexing (AIIM 2012 under press).

Christine Golbreich is a Professor in Computer Science at the University of Versailles Saint-Quentin. She was pioneer in France in promoting the Semantic Web for life sciences and formal ontologies in biomedicine - initiating in 2003 the first workshops in France and at the Medical Informatics Europe Conference. She managed several projects on representing large biomedical ontologies in OWL, such as the MeSH in OWL (KR-MED 2004), the Foundational Model of Anatomy in OWL (Journal of Web Semantics 2006), OBO and OWL (ISWC 2007). She was responsible of a number of projects on semantic integration, for example for a system integrating transplantation and dialysis data from different medical centers in France. Her recent works were devoted to the semantic annotation of brain MRI images (IEEE Transactions on Medical Imaging 2009), and to the Foundational Model of Anatomy in OWL 2 and its use for a European Portal of health terminologies dedicated to resources indexing (AIIM 2012).
She was a member of the W3C OWL Working Group and editor of the OWL 2 Web Ontology Language: New Features and Rationale document (W3C Recommendation, 2009). She advocated the needs to extend OWL by a rule formal language at RuleML 2004 (LNCS 3323), presented a number of use cases for the RIF, which is now a W3C recommendation, and achieved the first Protégé plugin, SWRLJessTab, to reason with ontology and rules.
Christine Golbreich has a pluri-disciplinary expertise: she is Engineer of Ecole Nationale Supérieure des Mines de Paris, has a PhD and Habilitation in Computer Sciences from University Paris 11, a research master in Logics, in Biomathematics, and a professional master in Clinical Psychology.