[Corpora-List] Extended CFP: Phenotype Day at ISMB 2016

Nigel Collier nhc30 at cam.ac.uk
Fri Apr 1 10:52:24 CEST 2016

***************************************************************************** Call for Papers: Phenotype Day - joint initiative with BioOntologies SIG 8 July 2016 Orlando, Florida, US, co-located with ISMB 2016 ***************************************************************************** ******* EXTENDED DEADLINE: 10th of April ******* *****************************************************************************

- Confirmed invited speakers: -- Dr Zhiyong Lu (National Center for Biotechnology Information, US) -- Prof Wendy Chapman (University of Utah, US) -- A/Prof Melissa Haendel (Oregon Health and Science University, US)

- Special Issue of the Journal of Biomedical Semantics with selected accepted, extended publications. *****************************************************************************

Important Dates --------------------- - Paper Submission: *Apr 10, 2016* - Notifications: May 2, 2016 - Camera-Ready Versions: May 9, 2016

Description ---------------

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 an initiative developed jointly with the Bio-Ontologies Special Interest Group. 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. Selected accepted papers will be included in a Special Issue of the Journal of Biomedical Semantics.

Papers should be formatted using the following templates: * Full / Short paper template: http://phenoday2016.bio-lark.org/PhenoDay-Full.dot * Position / Poster template: http://phenoday2016.bio-lark.org/PhenoDay_Short-Poster-Position.dot

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://www.easychair.org/conferences/?conf=phenoday2016

Phenotype Day Co-Organizers ---------------------------- * Nigel Collier, University of Cambridge and European Bioinformatics Institute, UK * Anika Oellrich, King's College London, UK * Tudor Groza, Garvan Institute of Medical Research, Australia * Karin Verspoor, University of Melbourne, Australia * Nigam Shah, Stanford University, United States

Program Committee -------------------------- * Olivier Bodenreider, U.S. National Library of Medicine, US * Hong-Jie Dai, Taipei Medical University, Taiwan * Melissa Haendel, Oregon Health & Science University, US * Simon Jupp, European Bioinformatics Institute, UK * Jung-Jae Kim, Nanyang Technological University, Singapore * Jin-Dong Kim, Database Center for Life Science, Japan * Martin Krallinger, Spanish National Cancer Research Centre, Spain * Sebastian Koehler, Charite Medical University Berlin, Germany * Hilmar Lapp, Duke University, US * Suzanna E. Lewis, Lawrence Berkeley National Lab, US * Zhiyong Lu, National Institutes of Health, US * Chris Mungall, Berkeley Lab, US * Dietrich Rebholz-Schuhmann, National University of Ireland, Galway, Ireland * Peter N. Robinson, Charite Medical University Berlin, Germany * Paul N. Schofield, University of Cambridge, UK * Lynn Schriml, University of Maryland, US * Hagit Shatkay, University of Delaware, US * Damian Smedley, Queen Mary University London, UK * Nicole Washington, Helix, San Francisco, CA, US * Antonio Jimeno-Yepes, IBM, Australia * Andreas Zankl, University of Sydney, Australia

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