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Call for Papers: International Workshop on Knowledge Support for Deep Phenotyping

From: Hilmar Lapp <hlapp@nescent.org>
Date: Sat, 13 Jul 2013 20:25:51 -0400
Message-Id: <99ECFE98-C4E5-490B-B07C-A264B0AC5681@nescent.org>
To: HCLS HCLS <public-semweb-lifesci@w3.org>
Call for Papers: International Workshop on Knowledge Support for Deep Phenotyping
co-located with IEEE International Conference on Bioinformatics and Biomedicine
December 18 - 21, 2013
Shanghai, China
- Confirmed invited speaker: Dr. Dietrich Rebholz-Schuhmann (University of Zurich)
- Extended versions of all accepted full papers will be included in a Special Issue of
 the Journal of Biomedical Semantics.

Important Dates
- Paper Submission: Oct 5, 2013
- Notifications: Nov 1, 2013
- Camera-Ready Versions: Nov 18, 2013


The systematic description of variation has gained increasing importance since the discovery of the causal relationship between a genotype placed in a certain environment and a phenotype.  The triumvirate connection of a phenotype, genotype and its environment, plays an important role to enhance our knowledge in areas such as the origins of human genetic disorders, the evolution of species, species diversity and adaptability to environmental change. Effective use of phenotype data requires researchers to achieve a common mindset and build a shared conceptual view on the definition, representation and interoperability of phenotypes.

With the need for interoperability between large-scale experimental and clinical data sets we assert that knowledge support for Deep Phenotyping is currently of a particular relevance, yet it has not been tackled as a well-defined field in itself. Various research activities that attempt to understand the underlying domain knowledge exist, but they are rather restrictively applied and not very well synchronized. In this workshop we propose to trigger a comprehensive and coherent approach to studying (and ultimately facilitating) the process of knowledge acquisition and support for Deep Phenotyping by bringing together researchers and practitioners that include but are not limited to the following fields:
* Computational biology
* Genomics, clinical genetics, pharmacogenomics, healthcare
* Text/Data mining and knowledge discovery
* Knowledge representation and ontology engineering

Research topics

* Phenotype/environment representation as well as the connection between phenotype and environment
-- Standards and models for representing phenotypes in the environment, including behavioural 
-- Pre-composition(Pre-coordination) and post-composition(post-coordination) of phenotypes
* Phenotype/environment extraction / acquisition as well as relation extraction between genotype-
-- Natural Language Processing and text mining methods for phenotype extraction
-- Data Mining methods for phenotype discovery
* Phenotype alignment and interoperability (can include environmental aspects)
-- Alignment to phenotype standards
-- Cross-species phenotype alignment and interoperability
* Phenotype-driven decision support
* Inference and reasoning based on phenotypes (can include environment, behaviour)
* Tools and methods for phenotype-disorder, phenotype-genotype,  phenotype-drug, and phenotype-
genotype-environment discovery

Submission Information

We encourage researchers to submit full research papers (up to 8 pages), as well as Poster papers (up to 2 pages) reporting work in progress. All accepted papers will be included in the proceedings published by IEEE CPS and will be scheduled for presentation during the workshop.

Papers should be formatted using the IEEE Computer Society Proceedings Manuscript Formatting Guidelines:
* http://www.ieee.org/conferences_events/conferences/publishing/templates.html

Submissions are accepted as PDF, PS, and DOC/RTF files, however, authors are strongly encouraged to generate a PDF version of the submission if this has been prepared in Word.

Submission system:
* https://wi-lab.com/cyberchair/2013/bibm13/cbc_index.php

Extended versions of all accepted full papers will be included in a Special Issue of the Journal of Biomedical Semantics.

Workshop Organizers
* Nigel Collier, European Bioinformatics Institute, UK and National Institute of Informatics, Japan
* Anika Oellrich, Wellcome Trust Sanger Institute, UK
* Tudor Groza, The University of Queensland, Australia

Program Committee
* Kevin Cohen, University of Colorado, US
* Hong-Jie Dai , National Tsing Hua University, Taiwan
* Georgios V. Gkoutos, Aberystwyth University, UK
* Melissa Haendel, Oregon Health & Science University, US
* Eva Huala, Carnegie Institution for Science, US
* Jin-Dong Kim, The University of Tokyo, Japan
* Jung-Jae Kim, Nanyang Technological University, Singapore
* Hiroaki Kitano, Okinawa Institute of Science and Technology Graduate University, Japan
* Sebastian Koehler, Charite Medical University Berlin, Germany
* Hilmar Lapp, National Evolutionary Synthesis Center (NESCent), US
* Suzanna Lewis, Berkeley Lab, US
* Yves Lussier, The University of Chicago, US
* Jong Park , KAIST, Korea
* Paul N. Schofield, University of Cambridge, UK
* Nigam Shah, Stanford University, US
* Damian Smedley, Wellcome Trust Sanger Institute, UK
* Von-Wun Soo , National Tsing Hua University, Taiwan
* Toshihisa Takagi, The University of Tokyo, Japan
* Andreas Zankl, University of Sydney, Australia
* Xuezhong Zhou , Beijing Jiaotang University, China
Received on Sunday, 14 July 2013 00:26:23 UTC

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