All tutorials are FREE!!! See registration


Tutorials Schedule

8:30am
start
10:15am - 10:45am
coffee break
12:00pm - 1:30pm
lunch
3:15pm - 3:45pm
coffee break
5pm
end


ICBO Tutorials:


ICBO 1
OBO Foundry
Sunday full-day
ICBO 2
Referent Tracking Sunday half-day PM
ICBO 3 OWL Sunday half-day AM
ICBO 4
SPARQL Sunday half-day PM
ICBO 5 Intro to Modeling Sunday half-day AM
ICBO 6
NCBO Tech Sunday half-day PM
ICBO 7
Bio2RDF Sunday half-day PM

1. OBO Foundry 101: Collaborative ontology development, tool support and semantic web
Link

Melanie Courtot, Melissa Haendel, Chris Mungall, Bjoern Peters, Alan         Ruttenberg, Barry Smith, Carlo Torniai and Jie Zheng.
Details []
Abstract
With the increase in use of ontologies, specifically in the biomedical domain, more and more resources are being developed ad-hoc rather than following a concerted action. This can result in resources that can be used only within a specific project, and will often die when funding runs out. The OBO Foundry is a consortium of ontology developers which aims to address this issue by implementing a set of best practices for ontology development, including open access, collaborative work, and technical resources supporting them.

This introductory tutorial will provide:
  1. a brief introduction to the rationale behind the OBO consortium effort, and a short update as to its status,
  2. a guideline of becoming a member of OBO foundry ontologies including OBO foundry ontology requirements and registration,
  3. an overview of the current best practices pertaining to development of OBO foundry ontologies such as ID policy, naming convention, deprecation policy, ontology metadata, importing selected terms from external resources using the Minimum Information to Reference an External Ontology Term (MIREOT) mechanism,
  4. an introduction to the use of Protege to build OWL format ontologies
  5. a description of tools that have been implemented to support OBO foundry resources, such as the unique URI generation tool (URIgen,) the obo2owl pipeline, the OBO Ontology Release Tool (OORT), the MIREOT web tool, OntoFox.
We will provide small exercises for attendees to follow along during the discussions. At the end of the tutorial, attendees will have a better understanding of the importance of collaborative and open development and will be aware of various tools available to support them in their daily activities.

Format
This is a full day event. Morning will consist in a theoretical session, aimed at people wanting to better understand the OBO Foundry and its place within the semantic web. Afternoon will be geared towards developers of resources with a practical session and hands-on exercises.

Tutorial Instructors (in alphabetical order)

Mélanie Courtot
BC Cancer Agency, Vancouver, BC
email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organized the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop. She chaired the workshop session at ICBO 2012 and participated in several of them.

Melissa Haendel
Oregon Health & Science University, Portland, OR
email: haendel@ohsu.edu
Dr. Haendel has co-lead several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI). She is currently working on the ontology driven eagle-i research resource discovery platform. Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

Chris Mungall
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA
email: cjmungall@lbl.gov
Chris Mungall is a computer scientist at LBNL with an interest in applications of biological ontologies. He is part of the Gene Ontology Consortium, where he leads the software group and works on the maintenance of the GO and the cell type ontology. He is also involved in a number of other Open Bio-Ontology (OBO) efforts, and with the organization of the OBO Foundry. His research is in applying phenotype ontology based algorithms for linking animal models to human diseases using a diversity of OBO ontologies. One aspect of this work was integrating multiple vertebrate anatomy ontologies through a bridging ontology (Uberon).

Bjoern Peters
La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
email: bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is Principal Investigator or Co-Investigator on multiple projects ranging from leading the bioinformatics component of the Immune Epitope Database to designing and analyzing clinical and basic studies of immune responses in the context of allergy, Dengue fever, Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO foundry, and is actively contributing to several other ontologies. He has led several workshops for users of the IEDB.

Alan Ruttenberg
University at Buffalo School of Dental Medicine, Buffalo, NY
email: alanruttenberg@gmail.com
Alan Ruttenberg’s research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.

Barry Smith
University at Buffalo Department of Philosophy, Buffalo, NY
email: phismith@buffalo.edu
Barry Smith is Professor of Philosophy, Neurology and Computer Science and Director of the National Center for Ontological Research at the University at Buffalo. He is also one of the principal scientists of the National Center for Biomedical Ontology (NCBO), an NIH Roadmap National Center for Biomedical Computing, a member oft he Scientific Advisory Board of the Gene Ontology Consortium, and a PI of the Protein Ontology and Infectious Disease Ontology projects. He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in Basic Formal Ontology and the Ontology for General Medical Science, the Environment Ontology, and the Plant Ontology initiatives.

Carlo Torniai
Oregon Health & Science University, Portland, OR
email: torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

Jie Zheng
Penn Center for Bioinformatics, Philadelphia, PA
email: jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

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2. Referent Tracking: How to Represent Anything with Ontologies
William Hogan and Werner Ceusters.
Details []
ABSTRACT
WC has developed with Barry Smith the paradigm of referent tracking (RT) for recording data about particulars in a coherent manner and using standard ontologies to ensure the data are interoperable (Ceusters & Smith, 2006). WC and WH have collaborated for over 3 years on the further development of RT and the creation of RT systems (RTSs) that meet particular use cases. These use cases include representing web sites (Ceusters & Manzoor, 2009), managing adverse events (Ceusters, Capolupo, Moor, Devlies, & Smith, 2011), optimizing corporate memories (Ceusters & Smith, 2007), healthcare encounters, diagnoses (Hogan, 2010), that on the side of reality which demographic data are about (Hogan, Garimalla, & Tariq, 2011), and local identifiers (Hogan, Garimalla, Tariq, and Ceusters, 2011). In this tutorial, we will introduce participants to RT and show (1) how it is faithful to reality, (2) how with a base set of fewer than 10 templates, it has been able to represent a diversity of entities in reality, and (3) how it represents reality in an interoperable fashion. Participants will learn the theory and learn from practical demonstrations of RTS software how to start creating their own RTS applications.

RATIONALE
The rationale for this half-day tutorial is that the literature on RT and its applications discusses the theory of RT and evaluations of its applications. But it does not discuss how to get started with RT practically. Therefore a tutorial is the ideal format for individuals to learn how to take the theory in put it into practice in a similar manner as published applications of RT.

PRIOR WORKSHOPS
The authors presented a similar tutorial at ICBO 2011, entitled “Improving Structured Electronic Health Record Data through Ontological Realism”.
Other tutorials by WC include;
  •  Meeting Meaningful Use Criteria through Referent Tracking. Pre-conference workshop on Utilization of EHRs/EMRs to Further Drug and Disease Related Research, associated with Bio-IT World 2011, April 12, 2011, Boston, MA
  • Spatiotemporal Reasoning in Referent Tracking Systems: Why Is It So Hard? Spring 2011 Colloquia of the UB Center for Cognitive Science, University at Buffalo, February 16, 2011
  • Keeping Track of Data and What the Data are About: An Exploration in Realism-Based Ontology for Translational Research. BIO-IT World Europe Conference & Expo 2010, October 5-7, Hannover, Germany.
  • The Next Generation of Electronic Health Records. Hauptman-Woodward Institute, Buffalo NY, September 22, 2010
  • Referent Tracking: why Big Brother was just a little baby. Lecture series at the Free University of Brussels as Distinguished Visiting Professor - Honorary Chair 2009-2010 (“VUB Leerstoel”), May 17-21, 2010, Brussels, Belgium
  • Sharing Data while Keeping Control. (BIO-IT World Conference & Expo 2010, April 22, Boston MA. slides)
  • Principles of Referent Tracking and its application in biomedical informatics. Rochester Clinical & Translational Research Curriculum Seminar Series (RCTRC), University of Rochester Medical Center, NY – October 20, 2009.
In addition, WC is scheduled to give a workshop entitled “Workshop on Biomedical Ontology and Referent Tracking: Introduction to Basic Principles” at the International Association for Dental Research 2013 meeting on March 20, 2013 with his collaborator Dr. Richard Orbach.

ADVERTISEMENT
Are you looking for an application platform that can capture data on just about anything (and everything) and that is flexible, extensible, and interoperable using standard ontologies? Then attend this tutorial to find out why Referent Tracking is currently the best platform that meets these requirements. You will also learn how to do things with Referent Tracking Systems, accessing practical demonstrations.

PROPOSED FORMAT
Tutorial.
Proposed agenda:
  • Introduction and welcome: WH
  • Basics of RT Theory: WC
  • Demonstrations of RT for demographics, encounters, and diagnoses: WH
  • Demonstration of RT use in the Ontology for painrelated disablement, mental health and quality of life project

REQUIREMENTS
  • Attendees should bring a laptop with internet access and a browser (Chrome or Firefox preferable)
  • The conference venue must have WiFi freely available to participants

DELIVERABLES
  • The proposers will provide a final, detailed agenda
  • The proposers will provide a list of recommended reading
  • The proposers will create slide decks for presentations
  • The proposers will provide links to web-accessible demonstration applications

PROPOSERS
Contact Information

William R. Hogan

MD, MS Associate Professor and Chief Division of Biomedical Informatics University of Arkansas for Medical Science
4301 W. Markham St., Slot 782 Little Rock, AR 72205, USA
hoganwr@gmail.com

Werner Ceusters

MD, PhD Institute for Healthcare Informatics University at Buffalo
923 Main Street Buffalo NY 14203, USA
ceusters@buffalo.edu

Short bio
William R. Hogan, MD, MS, is Associate Professor and Chief of the Division of Biomedical Informatics at UAMS. He has over 15 years experience with medical terminologies and ontologies. He has been collaborating with Werner Ceusters on Referent Tracking for 3 years. Currently he is principal investigator on a five-year, multiple-principalinvestigator grant from the National Institute for General Medical Sciences to develop an ontology of epidemic models. He helped to establish—and is the first and current Director of—the Clinical and Translational Science Ontology Affinity Group in the Clinical and Translational Science Award Consortium. Werner Ceusters studied medicine, neuro-psychiatry, informatics and knowledge engineering in Belgium. Since 1993, he has been involved in numerous national and European research projects in the area of Electronic Health Records, Natural Language Understanding and Ontology. Prior to coming to Buffalo, he was Executive Director of the European Centre for Ontological Research at Saarland University, Germany. He is currently Professor in the Psychiatry Department of the School of Medicine and Biomedical Sciences, SUNY at Buffalo NY, Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Director of Research of the UB Institute for Healthcare Informatics. Since 2009, he is key-function Director of the Ontology component of UB´s CTSA initiative. His research is focused on the application of Referent Tracking for data management and the requirements of ontologies and terminologies to be useful for annotation under this framework.

REFERENCES
  • Ceusters, W., Capolupo, M., Moor, G.D., Devlies, J., & Smith, B. (2011). An evolutionary approach to realism-based adverse event representations. Methods of Information in Medicine, 50(1), 62-73.
  • Ceusters, W., & Manzoor, S. (2009). Applying referent tracking to the use and evolution of websites. In M. Okada & B. Smith (Eds.), Interdisciplinary ontology; proceedings of the second interdisciplinary ontology meeting (interontology 2009), tokyo, japan, february 28 - march 1, 2009 (pp. 63-76). Tokyo.
  • Ceusters, W., & Smith, B. (2006). Strategies for referent tracking in electronic health records. Journal of Biomedical Informatics, 39(3), 362-378.
  • Ceusters, W., & Smith, B. (2007). Referent tracking for corporate memories. In P. Rittgen (Ed.), Handbook of ontologies for business interaction (pp. 34-46). New York and London: Idea Group Publishing. Hogan WR. To what entities does an ICD-9-CM code refer? A realist approach. In, Proceedings of Bio-Ontologies 2010, “Semantic Applications in Life Sciences.” 2010:60-63. http://www.bio-ontologies.org.uk/programme/Bio-Ontologies- 2010-Handout-Formatted.pdf
  • Hogan WR, Garimalla S, Tariq SA. Representing the reality underlying demographic data. Proceedings of the International Conference on Biomedical Ontology (July 28-30, 2011, Buffalo, NY):147-152. Available at: http://ceur-ws.org/Vol- 833/paper20.pdf.
  • Hogan WR, Garimalla S, Tariq SA, Ceusters W. Representing local identifiers in a referent-tracking system. In Proceedings of the International Conference on Biomedical Ontology (July 28-30, 2011, Buffalo, NY):252-254. Available at: http://icbo.buffalo.edu/ICBO-2011_Proceedings.pdf

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3. Knowledge manipulation using OWL and reasoners for                    drug-discovery
Samuel Croset.
Details []
Abstract
The development of a drug relies on the biomedical knowledge accumulated throughout the years, nowadays stored in databases or captured by ontologies. In order to benefit at best from this large amount of information, it becomes necessary to find smart ways to integrate and query it. The Web Ontology Language (OWL) can be used for such a task, as it provides the means to capture and integrate the logic between concepts spanning from the molecule up to the biological process. With the help of a reasoner, it becomes possible to ask questions with implicit answers, such as finding a new protein target for a particular condition.
The tutorial is composed of a theoretical part around OWL modelling for biology featuring hands-on exercises using Protégé. Then follow a practical session, where the attendees will integrate the information coming from different sources (Gene Ontology, Uniprot and DrugBank) into an OWL knowledge-base. The integrated data will be queried using a reasoner in order to identify some hypothetical new targets that could be investigated to treat the thrombosis.

Tutorial level
Introduction to the Web Ontology Language (OWL) and reasoners from a biomedical perspective.

Prior knowledge required
The attendees are expected to have some general knowledge around Semantic Web technologies as well as a basic understanding of the drug-discovery process.

Suitability
The tutorial abords OWL from a biological perspective, with a focus on large-scale data and reasoners in order to answer pragmatic biomedical questions. The participants will be able to understand the motivations behind OWL2 EL and the advantages provided by the language over relational databases and RDF. The tutorial has been already presented at SWAT4LS 2012 and has received some positive feedback. It was originally prepared to last two hours, but would certainly benefit to run over half a day in order to not overwhelm the participants. Attendees are advised to install the software Protege, but they could also perfectly just follow the slides and do the exercises later on as the content will be available online. The tutorial would ideally be video recorded and made available online.

Outline
● What is OWL and OWL2 EL?
● Why is it particularly interesting for life science?
● How to use OWL?
● How to integrate and query biomedical knowledge?

Biography
Samuel Croset
Biologist by formation, I am currently a PhD student at the European Bioinformatics Institute working with Dietrich Rebholz-Schumann and John Overington. I have over two years of experience working with OWL and reasoners to address drug repurposing questions. I previously ran some tutorials at the 2011 and 2012 editions of the workshop Semantic Web Applications and Tools for Life Sciences alongside Dietrich Rebholz-Schumann.

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4. Introduction to SPARQL Link
Jerven Bolleman.

6. NCBO Technology and the Development of Semantic Applications

Trish Whetzel.
Details []
Abstract
The National Center for Biomedical Ontology (NCBO) offers a range of Web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets for data annotation, and to recommend particular terminologies and ontologies that would be appropriate for data annotation tasks. The BioPortal ontology repository provides a Web-based interface that utilizes the NCBO Web services and allows users to visualize ontologies, to map terms between ontologies to one another, and to add comments on ontologies that can guide ontology developers and offer assistance to ontology users. The newly developed NCBO RDF store, currently released as beta, also provides access to the ontology content via SPARQL queries. The NCBO Web services are used to create a searchable ontology-based index of data records, to create UIMA components for concept recognition, and to create structured data entry interfaces. This tutorial will provide hands-on experience using the NCBO Web services and SPARQL endpoint. The tutorial will demonstrate the use of Web services provided by NCBO to perform tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management.

Tutorial level
Intermediate level

Prior knowledge required
REST Web services, XML, SPARQL Requirements Each participant will need a computer with Internet access, a Web browser, and integrated development environment (IDE) such as Eclipse or Emacs.
Documentation of the NCBO Web services is available at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services Documentation of the SPARQL endpoint is available at: http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal
Sample code examples are provided at: http://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook and https://github.com/ncbo/sparql-code-examples

Time required
Half-day session

Suitability with respect to timeliness, applicability, benefit
NCBO has a large and growing user base that routinely inquires about use of the NCBO Web services and SPARQL endpoint and requests demo sessions. The tutorial session will provide a hands-on opportunity to use NCBO Technology, which is best addressed in an interactive session. Presentations on NCBO Technology have been very well attended at previous ICBO and other semantic web-related conferences.

Outline
The tutorial format will consist of a half-day session appropriate for software developers, users of ontologies and ontology developers. The content will include a review and demonstration of BioPortal, the NCBO Web services, and the SPARQL endpoint. Use cases of how the NCBO Web services are incorporated in existing applications for ontology-based data integration, information retrieval, structured data entry, and knowledge management in both biological and clinical applications will be presented.

Brief bio - expertise, prior tutorial experience
Trish Whetzel is the Outreach Coordinator for the National Center for Biomedical Ontology. She has worked with biomedical ontologies over the last 10 years as an ontology developer and programmer within the biomedical domain and routinely presents at conferences and workshops on NCBO Technology. Dr. Whetzel regularly interfaces with software developers and researchers via individual WebEx sessions and the NCBO User Support mailing list to provide instruction on the use of the NCBO Web services and SPARQL endpoint. She performs quality assurance reviews of NCBO technology and develops sample code client examples based on user requests and therefore is thoroughly familiar with the NCBO Technology APIs.

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7. Generating, publishing and using Bio2RDF linked open data
Alison Callahan, Jose Cruz-Toledo and Michel Dumontier.
Details []
Abstract
The open-source Bio2RDF project (http://bio2rdf.org) uses Semantic Web technologies and a set of conventions to provide linked data for the life sciences, unifying the representation of diverse (molecules, enzymes, pathways, diseases, etc.) and heterogeneously formatted biological data (e.g. flat-files, tab-delimited files, SQL, dataset specific formats, XML etc.). Once converted to RDF, this biological data can be queried using the powerful SPARQL Protocol and RDF Query Language (SPARQL), which can be used to federate queries across multiple SPARQL-compliant databases. Key to the success and further development of Bio2RDF is its use by the scientific community. To this end, we propose a tutorial focused on developing core skills for generating, publishing and querying Bio2RDF linked open data.

Tutorial level
Intermediate

Time required
Half-day

Attendee requirements
Basic knowledge of/experience with RDF and SPARQL; basic programming experience. A laptop computer with PHP5 (or higher) and OpenLink Virtuoso version 6 (or higher).

The tutorial will focus on the following topics:
- Best practices for generating Bio2RDF linked data
- Bio2RDF database setup and loading using OpenLink Virtuoso
- Querying Bio2RDF data using SPARQL, performing federated queries across endpoints
- Configuring and hosting a Bio2RDF mirror; enabling search with the Bio2RDF webapp

Tutorial presenters
Alison Callahan and José Cruz-Toledo, Bio2RDF developers
Alison Callahan is a PhD candidate in the Department of Biology at Carleton University, under the supervision of Dr. Michel Dumontier. Her research focuses on hypothesis evaluation using Semantic Web technologies as well as data integration from large-scale biological data sources and scientific full text publications.
José Cruz-Toledo is a PhD candidate also working with Dr. Dumontier, and his current research is focused on predicting nucleic acid structure and nucleic acid small molecule interaction. José has also led the creation of the Aptamer Base, a collaboratively created knowledge base about aptamers on Freebase. As part of the Bio2RDF developer team, Alison and José design and implement best practices for Bio2RDF linked data, develop code to convert biological data for Bio2RDF, and maintain Bio2RDF datasets, code and servers.

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DILS Tutorials:


DILS 8
Bio2RDF
Friday half-day PM
DILS 9
SADI
Friday half-day PM

8. How to produce and consume Linked Data the Bio2RDF way 

François Belleau, Arnaud Droit and René Paradis
Details []
This half day tutorial will present methods that can be used to build a semantic mashup using two powerful open source software Talend ETL framework and OpenLinks Virtuoso triplestore.

Abstract
The Bio2RDF project aims to transform silos of life science data into a globally distributed network of linked data for biological knowledge discovery. Bio2RDF creates and provides machine understandable descriptions of biological entities using the RDF/RDFS/OWL Semantic Web languages. Using both syntactic and semantic data integration techniques, Bio2RDF seamlessly integrates diverse biological data and enables powerful new SPARQL-based services across it’s globally distributed knowledge bases. The project has released 28 public databases in RDF format, all available on the internet using a SPARQL endpoint or by fetching dereferencable URI.
Now with major data provider like NCBO, UniProt, KEGG, PDB and EBI who also expose their data as Linked Data, we need a framework to ease the buildup of mashup application and designing a workflow is a well-known approach to do so. The tutorial propose to use an open source professional ETL software, Talend, to help rdfization of existing data and to automate triples fetching to populate a mashup into the OpenLink Virtuoso triplestore.
How can we build a specific database to answer a very specialized question? How can we build a mashup by fetching linked data from the web? How can we merge our own lab results with the publicly available knowledge from the semantic web? Those are the questions we answer in the tutorial by proposing tools and methods to the participant. In this tutorial you will learn how to install and administer the Virtuoso triplestore, then we will show you how to load RDF triples directly from the web or from your own data you will have converted to RDF using an open source professional ETL software: Talend. Now that Life Sciences semantic web is a reality, we need to make it answer our questions
.
Audience and format
The tutorial will be targeted to a general audience; it will serve to introduce how to manipulate RDF and fetch Linked Data to new users. Attendees will acquire basic knowledge of Virtuoso triplestore, and Talend ETL software, enough to be able to transform an existing data source in RDF, load it in the triplestore and merge it to existing Linked Data from Bio2RDF by designing a simple mashup workflow with Talend.
The tutorial need little background, but attendee should be familiar with SPARQL queries and RDF n-triples file format. Participant will leave the tutorial with Virtuoso and Talend software installed and configured on their laptop. They will also have designed two Talend workflow a rdfiser workflow transforming data to RDF format and a mashup workflow to implement a “follow your nose” RDF crawling strategy.

Schedule
  • Presentation of Bio2RDF project and other RDF public data provider like NCBO, UniProt and KEGG. (15 minutes)
  • Virtuoso triplestore installation and administration (30 minutes)
    • Basic server configuration
    • Installing the facet browser
    • Loading RDF into the triplestore
    • Submitting SPARQL queries
  • Talend Open Studio installation and basic introduction (30 minutes)
    • Concept of JOB and Component
    • Java compilation and exporting package
    • How to access and transform data from SQL database or in, XML, JSON or text format
    • How to access the web and consume SOAP service
  • Hands on part of the tutorial (90 minutes)
    • Learning basic Talend technics
      • Fetching data from the web
      • Creating triple in n-triples format
      • Parsing a XML document
      • Accessing Virtuoso triplestore via JDBC API
  • Finally the attendee will:
    • Create a rdfiser workflow to transform its own data in RDF
    • Load RDF into the triplestore using Talend JDBC component
    • Fetch RDF by submitting SPARQL queries automatically locally or on the web.
What you need to participate
Faculty
François Belleau, Dr Arnaud Droit and René Paradis
Centre de recherche du CHUQ/CHUL, 2705 Boul. Laurier, Québec, Canada

Further information
Person interested to participate to the Bio2RDF project are invited to join its mailing list at https://groups.google.com/forum/?fromgroups=#!forum/bio2rdf
You may access Bio2RDF collection of SPARQL endpoint from our server http://bio2rdf.org

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9. Semantic Automated Discovery and Integration
Artjom Klein and Christopher Baker
Details []
Abstract
The SADI tutorial will begin with an overview of the project. We will then talk about what a SADI service "is", and the specific design patterns advocated by SADI. The hands-on component will then continue, with workshop participants being shown how to extend the template through building services of their own. In particular, participants will write, and deploy, two additional services that can be fed by data from existing services. Finally, participants will add these new services into the SPARQL queries they wrote earlier.

Tutorial Attendee Profile
The first half of the tutorial will be accessible to newbies wishing to learn the capabilities of and principles underlying the SADI framework. For the hands on part of the tutorial attendees are expected to be comfortable working in the in Linux environment (editor, terminal), and have working knowledge of Java, RDF/OWL, at least some familiarity with SPARQL, and the Protege Ontology Editor.

SADI Tutorial System Requirements
The following MUST be installed PRIOR to the tutorial.
Participants will receive a fully configured virtual machine image loaded with open source software and demo or free trial versions of proprietary software for practical SADI exercises (writing SADI services and running SPARQL queries). Participants must have 10GB of free space on their hard drive to uncompress the VM image.
Install VMWare player (Download for Windows and Linux here)
Participants who use Apple Computers: There is no version of VMware Player for OS X. Instead, there is a VMWare Fusion software for Mac. The 30-day trial can be downloaded here.  The price of the full version is $49.99. The tutorial presenters have tested the Ubuntu VM image on a Mac machine (Mac OS 10.8.2) with licensed VMWare Fusion (Full Version). All the programs were working fine. The only thing is the memory of Virtual machine must be set to 1GB or more in the VM Settings.
We strongly recommend to download and test your VMWare Player/Fusion with small image (http://www.trendsignals.net/vm/ubuntu1004t/).

SADI Instructor
Artjom Klein
Research Scientist, University of New Brunswick, Canada
Software Engineer, IPSNP Computing Inc, Saint John, Canada
www.linkedin.com/in/artjomklein
Artjom Klein is a computational linguist holding an MSc from Heidelberg, Germany, Semantic Technology researcher and software developer. He has worked, both in academic and industrial settings, on multiple projects involving combined use of semantic technologies and Natural Language Processing techniques and tools. He is has many years of hands on experience in Semantic Web techniques. Recent projects involved the provision of natural language query interfaces to semantic knowledge bases and deployment of text mining services in SADI Framework. Artjom was a core developer on the C-BRASS project (Canadian Bioinformatics Resources as Semantic Services) deploying more than 200 SADI services in Dr Chris Baker's lab at UNB, Saint John.

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Note: Unless otherwise instructed by tutorial instructors, all tutorials
will be held from

    08.30-12.00
    13.30-17.00

and will include at lease one 30 min coffee break.