[Obo-anatomy] CfP - Phenotype Day @ BioLink/BioOntologies SIG, ISMB, 12 July 2014

[Melissa Haendel]

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Call for Papers: 

Phenotype Day - joint initiative of BioLink and BioOntologies SIG

12 July 2014

Boston, MA, co-located with  ISMB 2014

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 - Confirmed invited speakers: Dr. Peter Robinson (Charite Berlin) and Dr. Dietrich Rebholz-Schuhmann (University of Zurich) 

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

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Important Dates

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- Paper Submission: Apr 11, 2014

- Notifications: May 9, 2014

- Camera-Ready Versions: May 16, 2014

Description

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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

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* 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

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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:

* https://www.easychair.org/conferences/?conf=phenoday2014

Phenotype Day Co-Organizers

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* 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

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* 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 Servova, Children's Hospital Boston, MA, US

* Damian Smedley, European Bioinformatics Institute, UK

* Andreas Zankl, University of Sydney, Australia

Assistant Professor
Ontology Development Group, OHSU Library

www.ohsu.edu/library/ontology

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970