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SWAT4LS Workshop

Semantic Web Applications and Tools for Life Sciences

December 10th, 2010
Berlin, Germany

Home Call for Papers Scientific Programme Registration Useful Info Organization

Scientific Programme

Wednesday 8th December 2010 (Tutorial/hackathon day)

Location: Free University of Berlin
Königin-Luise-Straße 24-26
room SR 016 (Morning) and SR 017 (Afternoon)
9.00-9.30Welcome and registration
9.30-13.30 (30' break) Tutorial: Semantic Web meets Cloud Computing
Presenter: Jonas Almeida (Univ. Texas MDAnderson Cancer Center, Huston, USA)
This hands-on tutorial is conceived with reference, and anticipation of the Keynote lecture. Two goals as proposed: a) Explore and engage the attendants in the use of browser-based application development tools; and b) put to discussion, and experimentation, the use of cloud computing Map-Reduce resources for application deployment. Specifically, in this hands-on exploration of the client-side we'll use javascript development tools native to the browser (Chrome and IE) or made available via add-on (Firefox). The server side will be a NOSQL platform, couchDB. Throughout the exercise we will be arguing for the need for higher level semantic web abstractions if the resulting applications are to be scalable.
13.30-14.30Lunch break
14.30-18.30Free Hackathon

Thursday 9th December 2010 (Tutorial day)

Location: Harnak Haus
Ball room (registartions) and Vogt Saal

8:30-9:00Welcome and registration
9.30-13.00 (30' break) Tutorial: Interoperable Semantic Web services
Presenters: Jon Ison (EMBL-EBI, Hinxton, U.K.), Matus Kalas (Bergen Center for Computational Science, Bergen, Norway)
Life-scientific Web services are increasingly available and diverse. Their semantic interoperability is crucial to enable automated workflow construction and efficient searching for the right service. At the same time, smooth programmatic access must be possible with all the main programming, scripting, or workflow languages. This tutorial will give an introduction to the SAWSDL standard for semantic annotation of Web services and XML Schemas; the EDAM ontology for describing bioinformatics tools; and BioXSD as a canonical data model for bioinformatics Web services. EDAM (EMBRACE Data And Methods) defines terms for annotating the service scope, functions and the types of input and output data. BioXSD defines an exchange format for common bioinformatics datatypes which are not covered by specialised standards. BioXSD is annotated with EDAM terms, thus serving as an example of XML Schema annotation and as a set of ready-made building blocks for Semantic Web service interfaces. The practical, combined approach of XML Schema and SAWSDL annotation, as recommended by EMBRACE, ensures maximum interoperability with both the Semantic Web and the common SOAP libraries. Most of the tutorial will be hands-on, with exercise on annotating Web services and custom Schemas and the use of the BioXSD types. Participants are encouraged to use their Web services in the exercise, or work with given examples.
13.00-14.00Lunch break
14.00-15.45 Tutorial: D2RQ
Presenters: Radoslaw Oldakowski (Free University of Berlin)
D2RQ is a complete solution to map and expose relational databases as RDF. More information can be found here.
16.00-17.45 Tutorial: Query Federation with SWObjects
Presenters: Eric Prud'hommeaux (W3C), Helena Deus (University of Texas ) and M. Scott Marshall (HCLS IG co-chair)
Query federation is a way to make use of distributed data sources on the Web, including many SPARQL endpoints as well as relational databases. SWObjects makes use of mapping rules represented as SPARQL Constructs to dynamically rewrite the terms and predicates of a SPARQL query into corresponding terms in another vocabulary and connect the resulting query with the appropriate service for answering the query. SWObjects can also rewrite SPARQL queries in SQL, effectively including relational databases alongside SPARQL endpoints in a linked data federation. The author of SWObjects, Eric Prud'hommeaux, is the W3C staff contact for the W3C Health Care and Life Sciences Interest Group (HCLS IG) and will give the tutorial via a teleconference connection, with assistance from Helena Deus and M. Scott Marshall (HCLS IG co-chair).
18.00-19.30 7th Berlin Semantic Web Meetup - Semantic Health Care and Life Sciences
Presentations from Meetup participants
19:30- SWAT4LS / Meetup Dinner + poster and demo session

Friday 10th December 2010 (Workshop day)

SWAT4LS Workshop (program is subject to minor modifications)
Location: Harnak Hause
Ball room (registartions) and Vogt Saal

8.30-9.00Welcome and registration
Jonas Almeida: Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).
10.00-10.15Coffe break
  • Matt Holford, James McCusker, Kei Cheung and Michael Krauthammer.
    Analysis Of Cancer Omics Data In A Semantic Web Framework (20')
  • Anna-Lena Lamprecht, Stefan Naujokat, Bernhard Steffen and Tiziana Margaria.
    Constraint-Guided Workflow Composition Based on the EDAM Ontology (15')
  • Rafael Berlanga, Ernesto Jimenez-Ruiz and Victoria Nebot Romero.
    Building conceptual spaces for exploring and linking biomedical resources (20')
  • Adrian Paschke and Zhili Zaho.
    Process Makna - A Semantic Wiki for Scientific Workflows (15')
  • Kenneth McLeod, Gus Ferguson and Albert Burger.
    Argudas: arguing with gene expression information (20')
  • Samuel Croset, Christoph Grabmüller, Chen Li, Silvestras Kavaliauskas and Dietrich Rebholz-Schuhmann.
    The CALBC RDF Triple Store: retrieval over large literature content (15')
Christopher Baker: A renaissance for the point mutation: from legacy data to semantic web service
14.00-14.15Cofee break
  • Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens and Katy Wolstencroft.
    Populous: A tool for populating ontology templates (20')
  • Sylvie Ranwez, Vincent Ranwez, Mohameth François Sy, Jacky Montmain and Michel Crampes.
    User Centered and Ontology Based Information Retrieval System for Life Sciences (15')
  • Alejandra Gonzalez-Beltran, Ben Tagger and Anthony Finkelstein.
    Ontology-based Queries over Cancer Data (20')
  • Abdelaali Briache, Kamar Marrakchi, Amine Kerzazi, Ismael Navas-Delgado, Jose F Aldana Montes, Badr D. Rossi Hassani and Khalid Lairini.
    YeastMed: an XML-Based System for Biological Data Integration of Yeast (15')
15.30-17.00Coffe break,
Demo/Poster session
Demo and Poster session will be held in parallel. The demo schedule will be finalized durting the workshop day
  • Theodore Dalamagas, Tryfon Farmakakis, Manolis Maragkakis and Artemis Hatzigeorgiou.
    FreePub: Collecting and Organizing Scientific Material Using Mindmaps (20')
  • Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi and Martin Kuiper.
    Benchmarking triple stores with biological data (20')
  • Jasmin Opitz, Bijan Parsia and Ulrike Sattler.
    Evaluating Modelling Approaches for Medical Image Annotations (20')
18.00-19.00Panel discussion:
Chris Baker, Jonas Almeida, Chris Bizer, Ulf Leser
19.00-(optional) social dinner


Christopher Baker: A renaissance for the point mutation: from legacy data to semantic web service
Experiments that construct or discover protein point-mutations and investigate their functional consequences represent a one of the cornerstones of biomedical investigation. And yet, despite the importance of these annotations, the interpretation and reuse of knowledge about their impacts remains a formidable task. This is due to a number of reasons including (i) the publishing of salient mutation impact descriptions in unstructured text, (ii) the existence of numerous boutique databases of mutation information which can have a many years of latency, and (iii) errors within manually populated mutation databases. In recent years the mining of mutations from scientific documents has emerged as a promising research theme resulting in automated methods for mutation extraction and denovo database creation. While such methods have shown good performance, this alone does not suffice in seamlessly integrating mutation annotations to other biological datatypes.
In this talk I demonstrate the challenges and innovations that have resulted in the deployment of semantic services that supply text-extracted mutation impact annotations on demand. These include; mutation grounding algorithms linking extracted mutations to the correct position on wild type protein sequences, the grounding of mutated protein properties to GO Molecular Function, rule based extraction of mutation impacts and impact direction, conceptualization and population of mutation impact ontology, graphical composition of SPARQL queries using mutation specific metadata, visualization of mutation impact annotations on protein structures, dynamic annotation of PubMed abstracts containing mutations mentions using the Semantic Assistant framework , and lastly SADI web service deployment facilitating queries that leverage mutation impact annotations integrated with multiple semantic web services, namely queries that select for mutations that impact specific protein properties, mutations that impact specific metabolic or signaling pathways, drugs that target mutated proteins, and literature describing mutations on proteins with a given nsSNP.

Christopher Baker is currently the Innovatia Research Chair and Associate Professor at the University of New Brunswick, Canada. Up until 2008 he was the head of the Semantic Technology Group at the Data Mining Department, I2R, (A-STAR) where his team developed KnowleSuite, now licensed from I2R by Knorex Pte Ltd, in Singapore. Chris has considerable experience in Biomedical Informatics and Semantic Technologies and was co-editor of the book Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences published by Springer in 2007. In 2005, his team won the Semantic Web Challenge (2nd prize) at the International Semantic Web Conference. He now serves on the Editorial Board of the Journal of Biomedical Semantics and is an invited expert for the W3C's Semantic Web in Health Care and Life Sciences Interest Group (HCLSIG). Chris holds a PhD in Microbiology from the University of Wales, Cardiff (1996).

Jonas Almeida: Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).
In response to the increasingly data intensive and increasingly heterogeneous sources involved in large scale biomedical initiatives, such as The Cancer Genome Atlas (TCGA), NCI's Specialized Programs of Research Excellence (SPOREs) and NHLBI's Proteomics Centers, we have had to move to abstract logical frameworks to develop applications that make use of more distributed computational resources. As a result, we embarked on a 6 year effort to increase the abstraction level of our data structures by relying on the diadic predicated nature of RDF (Wang 2005) to facilitate both our ability to represent fast changing biological data and to let the domain experts themselves participate in its constant re-definition (Almeida 2006). Fast forward to 2010 and a Knowledge Organization System, S3DB (Almeida 2010) is in place as a logical framework for a computational ecosystem assessable via SPARQL endpoints, such as In the process we found out, like many others, that the collaborative involvement of domain experts puts peculiar pressures on the software development environment. Specifically, that it clashes with the conventional stand alone executable application model we were used to. In response we moved to use code injection (javascript) and other distributed features of the modern web browser as a development platform, as in clinical trial initiatives such as and visualization of biomolecular data as in, and distributed computing in
I lead a graduate research team working on integrative bioinformatics applications. The current research is centered on the conjugation of semantic web abstractions and distributed cloud computing approaches. This work pulls together threads from past work on mathematical modelling and machine learning, at a time when these fields are challenged by the increasingly data driven nature of modern Biomedical research. Putting together the systemic puzzles of Biological processes increasingly requires integrative computational infrastructures that collaboratively articulate data management and data analysis and as integral part of the biomedical research effort. My own trajectory starts in the Biological Domain (Plant Biology, Univ. Lisbon, Portugal), then moves to Biochemical Engineering, Mathematical modelling, and then arcs back to the computational and clinical side of the Life Sciences through Biostatistics and Bioinformatics (Univ. Texas MDAnderson Cancer Center, Houston).

Accepted demos

  • M. Scott Marshall.
    The AIDA Toolkit - a tool for users and developers
  • Catherine Canevet, Artem Lysenko, Andrea Splendiani, Matthew Pocock and Christopher Rawlings.
    Analysis and visualisation of RDF resources in Ondex
  • Richard Huber, Kirsten Hantelmann, Alexandru Todor, Sebastian Krebs, Ralf Heese and Adrian Paschke.
    Use of semantic technologies for the development of a dynamic trajectories generator in a Semantic Chemistry eLearning platform
  • Luke McCarthy, Ben Vandervalk and Mark Wilkinson.
    SPARQL Assist Language-Neutral Query Composer

Accepted posters (confirmed)

  • Paul Boekschoten, Kees Burger, Barend Mons and Christine Chichester.
    Import of ENZYME data into the ConceptWiki and its representation as RDF
  • Adrian Groza and Radu Balaj.
    Using Semantic Wikis for Structured Argument in Medical Domain
  • Ernesto Jimenez-Ruiz, Bernardo Cuenca Grau, Rafael Berlanga and Dietrich Rebholz-Schuhmann.
    First steps in the logic-based assessment of post-composed phenotypic descriptions
  • Jerven Bolleman, Alain Gateau, Sebastien Gehant and Nicole Redaschi.
    Provenance and evidence in UniProtKB
  • Julia Dmitrieva and Fons Verbeek.
    Creating a new Ontology: a Modular Approach
  • Halit Erdogan, Umut Oztok, Yelda Erdem and Esra Erdem.
    Querying Biomedical Ontologies in Natural Language using Answer Set Programming
  • Christian Pich and Douglas Howe.
    Ontology Usage at ZFIN
  • Adrian Paschke and Zhili Zhao.
    The Rule Responder eScience Infrastructure
  • Ning Kang, Rogier Barendse, Zubair Afzal, Bharat Singh, Martijn J. Schuemie, Erik M. van Mulligen and Jan A. Kors.
    A Concept Annotation System for Clinical Records
  • Iker Huerga, Ainhoa Serna and Jon Kepa Gerrikagoitia.
    Fundamentals of Semantic Web Technologies in Medical Environments: a case in breast cancer risk estimation
  • Thomas Bandholtz, Maria Rüther and Antoine Logean.
    Linked Environment Data and the Life Sciences
  • Pablo López-García.
    Are SNOMED CT Browsers Ready for Institutions? Introducing MySNOM
  • María Pérez, Rafael Berlanga and Ismael Sanz.
    A semantic approach for the requirement-driven discovery of web services in the Life Sciences
  • Pedro Almeida, António Dourado, Paulo Gomes and Francisco Sales.
    Knowledge Management System on Epilepsy and Epileptic Seizures
  • Alexandru Todor, Adrian Paschke and Stephan Heineke.
    ChemCloud - The Chemical e-Science Information Cloud
  • Falko Krause, Marvin Schulz, Timo Lubitz and Wolfram Liebermeister.
    semanticSBML 2.0 - A Collection of Online Services for SBML Models
  • He Tan.
    A study on the relation between linguistics-oriented and domain-specific semantics
  • Eric Leclercq and Marinette Savonnet.
    Scientific Collaborations: principles of WikiBridge Design


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SWAT4LS 2010 is endorsed by:
    National Center for Biomedical Ontologies

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