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RE: messages to Data Integration in Life Sciences conf

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Mon, 16 Jun 2008 10:41:49 -0400
Message-ID: <AB349814F1ECB143A5D4CD29C7A6456902DC27BF@CCSEXB10.CUNET.CARLETON.CA>
To: <public-semweb-lifesci@w3.org>

Eric, 
I'll be attending DILS, which does indeed look to be very interesting from our perspective. Holger will also be attending. Together, we will certainly raise the issue of HCLS participation with relevant or potential semweb groups.

The work that we will be presenting describes our transformation of pubchem and drugbank into an OWL KB, whose representation follows more formal ontology. We show queries to both sources + dbpedia. The transformation of chemical data is done via a new OpenBabel plugin [1], which supports a transformation to our ontology, or to some arbitrary ontology. 
[1] http://code.google.com/p/semanticwebopenbabel/



You also asked about the Bio2RDF;
An HTML front end:
http://bio2rdf.org

A SPARQL endpoint using Virtoso:
http://bio2rdf.org:8890/sparql

the repository contents are listed here:
http://freebase.com/view/user/bio2rdf/default_domain/atlas



Cheers!

-=Michel=-


> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of Eric Prud'hommeaux
> Sent: June 12, 2008 1:16 AM
> To: public-semweb-lifesci@w3.org
> Subject: messages to Data Integration in Life Sciences conf
> 
> Ther's a conf call DILS (program link below:)
>   http://dils2008.lri.fr/index.php?option=com_content&task=view&id=16
> Of our lot, Michel and Holger might be going (Holger is trying, I
> haven't asked Michel). What messages do we have to deliver to
> A. the individual sessions
> B. the folks who will likely attend
> ?
> 
> Here are my notes from scanning the agenda (and regretting that I
> won't be there):
> 
>           BioWarehouse: Relational Integration of Eleven
>           Bioinformatics Databases and Formats
> 
>           Session 1: Annotation in scientific data
>           integration
> 
>             * Integrating Protein-Protein Interactions and
>               text Mining for protein Function Prediction,
>               Samira Jaeger, Sylvain Gaudan, Ulf Leser,
>     03:15     Dietrich Rebholz-Schuhmann
>     -
>     04:15   * Integrating Biological Data - The Distributed
>     pm        Annotation System, Andrew M Jenkinson, Mario
>               Albrecht, Ewan Birney, Hagen Blankenburg,
>               Thomas Down, Robert D Finn, Henning Hermjakob,
>               Tim JP Hubbard, Rafael C Jimenez, Philip Jones,
>               Andreas Kahari, Eugene Kulesha, José R Macias,
>     04:15     Gabrielle A Reeves and Andreas Prlic
> 
> This sounds to me like labeling a text string in HTML, Word, ... with
> something that allows them to unify based on that term. Relevent to
> Sudeshna's Scientific Collaboration Framework.
> 
>     -     Coffee
>     04:45  Flash Session
> 
>             * Analysing Experimental Data in the context of
>               Integrated Biological Networks, Jan Taubert,
>               Jochen Weile, Matthew Hindle, Artem Lysenko,
>               Keywan Hassani-Pak,Catherine Canevet, and Chris
>               Rawlings
> 
>             * Terminizier: An interactive web-based tool for
>               automated detection of ontological terms in
>               unstructured, free-text annotation, David
>               Hancock, Norman Morrison, Giles Velarde,
>               Douglas Kell, and Dawn Field
> 
> Perhaps like Therese Vachon (Novartis)'s UltraLink?
> 
>             * Semantic Mashups with BioXMash, Patrick
>               Ziegler, and Ela Hunt
> 
>             * Mixed queries for a functional genomics
>     04:45     warehouse, Frederic Lemoine, Bernard Labedan,
>     -         and Christine Froidevaux
> 
> How are the mixing their queries? Some meta-query lang that we can
> play with/map to?
> 
>     05:15   * Mapping the NRC dataflow model to the Open
>               Provenance Model, Natalia Kwasnikowska, and Jan
>               Van den Bussche
> 
>             * UniMed: Mapping of UniProt entries to disease
>               terminologies, Anais Mottaz, Yum L Yip, Julien
>               Gobeill, Patrick Ruch, and Anne-Lise Veuthey
> 
> Would be fun to get ahold of this data and RDF-ize it.
> 
>             * Using a metadata approach to manage
>               similarities and differences between clinical
>               datasets, Irene Papatheodorou, Charles Crichton
>               Lorna Morris, Peter Maccallum, James Brenton
>               and Carlos Caldas
> 
> Sounds like they're factoring out info we want for COI.
> 
>             * Semi-automatic composition of bioinformatics
>               Web services based on task and domain
>               ontologies, Nicolas Lebreton, Olivier Dameron,
>     06:00     Christophe Blanchet, and Julie Chabalier
> 
> How does this compare to Northampton or CWI's semweb service
> integration? Would like to show them SPDL.
> 
>      Thursday, June 26 (Evry)
>           Ontologies and data integration in biomedicine:
>           Success stories and challenging issues
> 
>     10:30 Session 2: Semantic Web for the life sciences
> 
>             * Analyzing the Evolution of Life Science
>               Ontologies and Mappings
>               Michael Hartung, Toralf Kirsten, and Erhard
>               Rahm
> 
> Could support us if their onto-mapping needs line up with SemWeb
> strengths (distributed ont development, monotonic interpretation)
> 
>     10:30   * Ontology Design Principles and Normalization
>     am -      Techniques in the Web
>     12:00     Xiaoshu Wang, Jonas S. Almeida, and Arlindo L.
>     pm        Oliveira
> 
>             * Exploiting Ontology Structure and Patterns of
>               Annotation to Mine Significant Associations
>               between Pairs of Controlled Vocabulary Terms
>               Woei-Jyh Lee, Louiqa Raschid, Hassan Sayyadi,
>     12:00     and Padmini Srinivasan
> 
> May provide techniques relevent to COI mapping use case (CTO queries
> over CPO data)
> 
>     -     Lunch
>     02:00 Session 3: Designing and evaluating architectures
>           to integrate biological data
> 
>             * Automatic Methods for Integrating Biomedical
>               Data Sources in a Mediator-Based System
>               Fleur Mougin, Anita Burgun, Olivier
>               Bodenreider, Julie Chabalier, Olivier Loréal
>     02:00     and Pierre Le Beux
>     -
>     03:30   * VisGenome and Ensembl: Usability of Integrated
>     pm        Genome Maps
>               Joanna Jakubowska, Ela Hunt, John McClure,
>               Matthew Chalmers, Martin McBride and Anna F.
>               Dominiczak
>             * An Entity Resolution Framework for
>               Deduplicating Proteins
>     03:30     Lucas Lochovsky and Thodoros Topaloglou
>     -     Coffee - Poster session 2 (to be announced soon)
>     04:30 Session 4: New architectures and experience on
>           using systems
> 
>             * Semantic Representation and Querying of caBIG
>               Data Services
>               E. Patrick Shironoshita, Ray M. Bradley,
>               Reginald Jean-Mary, Thomas J. Taylor, Michael
>               Ryan, and Mansur R. Kabuka
> 
> ooo, we need ears at this one!
> 
>     04:30   * SisGen: A CORBA--based data management program
>               for DNA sequencing projects
>               Georgios J. Pappas Jr., Robson P. Miranda,
>               Natalia F. Martins, Roberto C. Togawa and
>               Marcos M.C. Costa
> 
> what works for CORBA works for web services.
> 
>             * Bgee: Integrating and Comparing Heterogeneous
>               Transcriptome Data Among Species
>               Frederic Bastian, Gilles Parmentier, Julien
>               Roux, Sebastien Moretti, Vincent Laudet and
>               Marc Robinson-Rechavi
> 
>             * ENFIN - an integrative structure for Systems
>               Biology
>               Florian Reisinger, Manuel Corpas, John Hancock,
>               Henning Hermjakob, Ewan Birney and Pascal
>      05:50    Kahlem
> 
> Need to talk to them about SPASQL and semantic query federation.
> What's happening in ENFIN now?
> 
>      Friday, June 27
>           Session 5: New features of major resources for
>           biomolecular data
> 
>     09:30   * UniProtKB/Swiss-Prot: new and future
>     -         developments
>     10:30     Amos Bairoch
>     am
>             * EBI Proteomics Services
>               Henning Hermjakob
>     11:00 Data Integration in the Life Sciences: Fun,
>     12:00 Findings and Frustrations
> 
>     02:00 Session 6: Systems using technologies from the
>           Semantic Web for the life sciences
> 
>             * A System for Ontology-Based Annotation of
>               Biomedical Data
>               Clement Jonquet, Mark A. Musen, and Nigam Shah
> 
>             * Bio2RDF: A Semantic Web Atlas of post genomic
>               knowledge about Human and Mouse
>               Francois Belleau, Nicole Tourigny, Benjamin
>               Good and Jean Morissette
> 
> already RDF-y -- and I think Mark has a SPARQL endpoint.
> 
>             * OMIE: Ontology Mapping within an Interactive
>               and Extensible environment
>               Amel Bouzeghoub, Abdeltif Elbyed, and Fariza
>               Tahi
> 
>             * Chemical Knowledge for the Semantic Web
>               Mykola Konyk, Alexander De Leon, and Michel
>     03:20     Dumontier
> 
> Michel, can you give us a hint about this presentation?
> 
>           Session 7: Mining integrated biological data
> 
>             * Combining One-Class Classification Models Based
>     03:50     on Diverse Biological Data for Prediction of
>     -         Protein-Protein Interactions
>     04:50     José A. Reyes and David Gilbert
>     pm
>             * Semi supervised Spectral Clustering for
>               regulatory module discovery
>               Alok Mishra and Duncan Gillies
> --
> -eric
> 
> office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
> mobile: +1.617.599.3509
> 
> (eric@w3.org)
> Feel free to forward this message to any list for any purpose other than
> email address distribution.
Received on Monday, 16 June 2008 14:42:32 GMT

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