[BiO BB] Final Call: Data Integration in the Life Sciences, DILS04

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Mon Dec 1 06:53:32 EST 2003

oops... ;)

<quote who="Dan Bolser">
> Dear Sir/Madam,
> I am having trouble meeting the deadline, but I believe my paper is very relevant
> to the conference. I would like to ask if I can still send my paper in the next
> couple of days?
> Below I have reproduced the abstract.
> I would be very grateful if you could consider this paper for submission in a
> couple of days.
> Yours sincerely,
> Dan Bolser.
> Abstract
> A major challenge in the post-genomic era is the integration, classification and
> dissemination of of diverse sources of biological data. Data integration is
> attractive for several reasons, providing context for biological analysis,
> allowing different types of data to be cross-correlated, and providing a
> validation framework for different sources of experimentally and computationally
> derived data. Centralised data repositories have proven very effective at
> organising specific kinds of data, both helping to coordinate the research
> community and providing standards for the categorisation and distribution of the
> accumulated knowledge. However, the underlying conceptual complexity of data in
> the biological domain, as well as the continual development of new concepts, makes
> the task of producing a 'universal' data repository much more challenging. As a
> consequence many integrated databases have become arbitrarily complex, with no
> intrinsic classification value.
> Here, we emphasise a point which is not widely acknowledged by the database
> community, that data modelling in the scientific domain is equivalent to the
> scientific process itself. To this end we propose a 'distributed data model'
> framework for data integration in the scientific domain. Different sources of data
> to be integrated with will naturally have conceptual overlap (if they are to be
> integrated at all), but may have very complex conceptual and/or algorithmic
> associations. In this framework the burden of integration is put back on the
> domain expert (to implement or devise specific integration strategies), but the
> underlying issues of data access and subsequent distribution are made transparent
> via the data model framework. The advantage of integrating and distributing data
> within this framework is that new data and new concepts (produced as the result of
> integrative analysis for example) are naturally accommodated by specific
> extensions to the data models of the underlying data.
> Here we develop components of a high level data model relating to the principal
> axes of an integrated protein classification database (called the protein periodic
> table). Additionally we have developed conceptually clear ORM style models for
> integrated protein interaction data and metabolic pathway data (suitable for
> metabolic reconstruction). The the subsequent analysis of these models highlights
> several key areas for model development, and thus highlights areas for scientific
> research into specific integration and classification techniques.
> <quote who="DILS04">
>> Int. Workshop on Data Integration in the Life Sciences (DILS 2004)
>> Deadline: Nov. 30, 2003
>> Industrial exhibits welcome
>> Proceedings will be published in Springer LNCS
>> http://izbi.uni-leipzig.de/dils04
>> Workshop date: March 25-26, 2004, Univ. of Leipzig, Germany
>> -------------------------------------------------------
>> New advances in life sciences, e.g. molecular biology,
>> biodiversity, drug discovery and medical research,
>> increasingly depend on bioinformatics methods to manage
>> and analyze vast amounts of highly diverse data.
>> The volume of data is increasing at an unprecedented pace,
>> fueled by world-wide research activities producing publicly
>> available data, and new technologies, e.g. high-throughput
>> devices such as microarrays. Thus, data mining and analysis
>> require comprehensive integration of heterogeneous data,
>> that is typically distributed across many data sources
>> on the web and often structured only to a limited extent.
>> Despite new interoperability technologies such as XML and
>> web services, data integration is a highly difficult and
>> still largely manual task, especially due to the high
>> degree of semantic heterogeneity and varying data quality
>> as well as specific application requirements.
>> DILS 2004 aims at providing a new forum for
>> presenting novel research results and assessing
>> the state of the art in the field of data integration
>> for life sciences. It addresses researchers,
>> professionals, and industrial practitioners to
>> share their knowledge on this highly important
>> bioinformatics subject.
>> In an effort to bring together academics and industrial
>> practitioners, we solicit both research papers and
>> application / experience papers. It is planned to
>> publish accepted papers by Springer-Verlag in the
>> Lecture Notes in Computer Science (LNCS) series.
>> Topics of interest include, but are not limited to:
>> * Challenges for data integration in life sciences
>> * Architectures for data integration in life sciences
>> * Ontology-based data integration and analysis
>> * Metadata and annotation management
>> * Data quality and data cleaning
>> * Tool integration and experimental workflows
>> * Evaluation of data integration approaches in life sciences
>> * Data integration for specific applications
>> * Prototypes and commercial solutions
>> Authors are invited to submit original, previously
>> unpublished papers. All submitted papers will be
>> peer-refereed for quality, correctness, originality
>> and relevance. Accepted papers will be published in
>> the workshop proceedings which will be available
>> at the workshop.
>> Submissions must not exceed 15 pages and should be
>> formatted according to the LNCS guidelines under:
>>  http://www.springer.de/comp/lncs/authors.html
>> All submissions will be handled electronically.
>> Please send your submissions in PDF format to
>>    dils04 at izbi.uni-leipzig.de
>> Please also visit the workshop website for further
>> information http://izbi.uni-leipzig.de/dils04
>>    Paper submissions:     November 30, 2003
>>    Author notification:   January   8, 2004
>>    Camera-ready due:      January  28, 2004
>>    Workshop date:         March 25-26, 2004
>> Erhard Rahm, Univ. of Leipzig
>> Howard Bilofsky, GlaxoSmithKline, USA
>> Terence Critchlow, Lawrence Livermore National Laboratory, USA
>> Peter Gray, Univ. of Aberdeen, UK
>> Barbara Heller, Univ. of Leipzig, Germany
>> Ralf Hofestaedt, Univ. of Bielefeld, Germany
>> Jessie Kennedy, Napier Univ. Edinburgh, UK
>> Ulf Leser, HU Berlin, Germany
>> Bertram Ludäscher, San Diego Supercomputer Center, USA
>> Sergey Melnik, Microsoft Research, USA
>> Peter Mork, Univ. of Washington, Seattle, USA
>> Felix Naumann, HU Berlin, Germany
>> Frank Olken, Lawrence Berkeley National Laboratory, USA
>> Norman Paton, Univ. of Manchester, UK
>> Erhard Rahm, Univ. of Leipzig, Germany
>> Louiqa Raschid, Univ. of Maryland, USA
>> Kai-Uwe Sattler, TU Ilmenau, Germany
>> Steffen Schulze-Kremer, FU Berlin, Germany
>> Robert Stevens, Univ. of Manchester, UK
>> Sharon Wang, IBM Life Sciences, USA
>> Limsoon Wong, Institute for Infocomm Research, Singapore
>> Sponsors of the event can exhibit their software
>> and other products.
>> The workshop is organized by the Bioinformatics centre
>> of the University of Leipzig (www.izbi.de).
>> -------------------------------
>> Prof. Dr. Erhard Rahm
>> http://dbs.uni-leipzig.de
>> _______________________________________________
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