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Phenotype Day

July 12, 2014

Call for Papers:
Phenotype Day – joint iniative with BioLink and BioOntologies SIG
12 July 2014
Boston, MA, co-located with ISMB 2014


– Confirmed invited speaker: Dr. Dietrich Rebholz-Schuhmann (University of Zurich)
– One other invited speaker TBA
– Special Issue of the Journal of Biomedical Semantics with selected accepted, extended publications.

Important Dates:
– Paper Submission: Apr 11, 2014
– Notifications: May 9, 2014
– Camera-Ready Versions: May 16, 2014

We cordially invite submissions from researchers and practitioners that include but are not limited to the following fields: (computational) biology, clinical genetics, pharmacogenomics, healthcare, text mining, and knowledge representation.

Phenotype Day will bring researchers together from different disciplines to share information about phenotype resources and issues as well as experiences with defining, representing, processing and using phenotype data.

The systematic description of phenotype variation has gained increasing importance since the discovery of the causal relationship between a genotype placed in a certain environment and a phenotype. It plays not only a role when accessing and mining medical records but also for the analysis of model organism data, genome sequence analysis and translation of knowledge across species. Accurate phenotyping has the potential to be the bridge between studies that aim to advance the science of medicine (such as a better understanding of the genomic basis of diseases), and studies that aim to advance the practice of medicine (such as phase IV surveillance of approved drugs).

The Phenotype day is a joint special day of the Bio-Ontologies and BioLINK Special Interest Groups. Selected submissions accepted for the phenotype day will be published as a special edition of the Journal of Biomedical Semantics.

Research topics:
Representation of phenotypes
– Controlled vocabularies
– Ontologies (pre- and post-composed)
– Data standards
Acquisition of phenotype descriptions
– NLP annotation tools and pipelines
– Tools and methods to support data curation for phenotypes
– Integration of textual data and controlled vocabularies/ontologies
– Phenotype discovery
– Collaborative development and peer-review
– Guidelines for phenotype data curation
– Quality control and evaluation
Application of phenotypes to real world problems
– Methods for phenotype alignment and interoperability
– Drug repurposing / development
– Genotype-environment/phenotype-genotype/phenotype-disorder relation discovery
– Personalised medicine

Submission Information:
We invite researchers to submit:
– full research papers (up to 8 pages): to present results of a study
– short (up to 4 pages) or poster (up to one page) paper: to present preliminary results of a study
– position papers (up to 2 pages): to raise discussion points and provide opinions (no results required)

Accepted papers will be scheduled for presentation during the workshop either as a talk or as a poster.

Papers should be formatted using the following templates:
– Full paper template: http://phenoday2014.bio-lark.org/PhenoDay-Full.dot
– Short / Position / Poster template: http://phenoday2014.bio-lark.org/PhenoDay_Short-Poster-Position.dott

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:

Phenotype Day Co-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
– Karin Verspoor, National Information and Communication Technology Australia (NICTA), Australia
– Nigam Shah, Stanford University, United States

Program Committee:
– Kevin Cohen, University of Colorado, US
– Hong-Jie Dai, Taipei Medical University, Taiwan
– Georgios V. Gkoutos, Aberystwyth University, UK
– Melissa Haendel, Oregon Health & Science University, US
– Eva Huala, Carnegie Institution for Science, US
– Hilmar Lapp, National Evolutionary Synthesis Center (NESCent), US
– Jin-Dong Kim, Database Center for Life Science, 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
– Suzanna Lewis, Berkeley Lab, US
– Jong Park, KAIST, Korea
– Peter N. Robinson, Charite Medical University Berlin, Germany
– Paul N. Schofield, University of Cambridge, UK
– Guergana Savova, Children’s Hospital Boston, MA, US
– Damian Smedley, European Bioinformatics Institute, UK
– Andreas Zankl, University of Sydney, Australia


July 12, 2014


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