[Corpora-List] CFP: BioLINK SIG at ISMB 2014 "Supporting Bioscience Through Text Mining" + "Phenotype Day"

[Antonio Jimeno]

BioLINK 2014 will be held as a 2-day meeting at ISMB 2014 in Boston in
July, featuring a dynamic Day 1 addressing a range of biological
applications of text mining, and a special "Phenotype Day" on Day 2,
jointly organized with the BioOntologies SIG.

Title: Supporting Bioscience through Text Mining
Dates: Friday, July 11 & Saturday, July 12, 2014
URL: http://biolinksig.org/biolink-2014
Email: biolinksig2014 at biolinksig.org
Submission deadline: Friday, April 11, 2014

With the increasing availability of text data related to biology and
medicine in the scientific literature, database annotations, the
electronic health record, clinical trials data, and health information
online, exciting opportunities arise to provide access to pertinent
biomedical information and to advance biomedical knowledge. An
evolving research direction is the integration of information from
diverse data sources, including textual data, to support deeper
understanding of biological systems, the genomic basis of disease, and
genotype-phenotype relationships. We hope to attract research to this
SIG meeting that directly integrates text mining into computational
methods addressing biological problems. We therefore plan to dedicate
part of the workshop to the role of text mining for automated function
prediction and genetic variant interpretation, joining up with the
Automated Function Prediction SIG and the Vari SIG (formerly SNP SIG),
respectively, to have shared sessions. We s
 olicit submissions specifically for these shared sessions in addition
to the general sessions.

The second day of the SIG, July 12th, will be "Phenotype Day", a joint
session with the BioOntologies SIG and which will address the
systematic description of phenotypic variation. It will bring together
researchers across many disciplines to discuss phenotype-related
issues and resources, and to share their experience with defining,
representing, processing and using phenotype data. Please see
http://phenoday2014.bio-lark.org/ for more information. We strongly
encourage authors whose work is relevant to phenotypes to submit
directly to the special Phenotype Day event.

Suggested topics for paper submissions for Day 1 include (but are not
limited to) applications integrating text (in any form; medical or
clinical records or reports, clinical trials data, online health
information, the scientific literature) in the areas of:

Extraction and analysis of genotype-phenotype relationships
Translational medicine
Personalized/precision medicine
Pharmacovigilance
Phenotyping and disease modeling
Systems biology
Incorporation of text-mining derived data into larger biological and
bioinformatics workflows
New methods, measures and corpora for testing and evaluating text
mining in the biomedical domain

We plan to have a special session focused on text mining for Automated
Function Prediction. Papers targeting this session might address:
Automated Protein Function Prediction methods based on text mining
Hybrid/combination Automated Protein Function Prediction methods
integrating text mining
Literature- or Knowledge-based assessment of function prediction algorithms

We also plan to have a special session focused on text mining for
Genetic Variant Analysis. Papers targeting this session might address:
Pharmacogenomics
Literature extraction of mutation impacts and functional genomics
Analysis of genetic variants using text mining

Special Issue:
Selected authors from both Day 1 and Day 2 will be invited to submit
an extended version of their paper for a special issue of the Journal
of Biomedical Semantics, jointly with the BioOntologies SIG and
Phenotype Day. Papers will also be archived on-line and made publicly
available.

Key Dates:
April 11th, 2014 Submissions Due  (11:59pm in the time zone of your choice)
May 9th, 2014 Notifications
May 16th, 2014 Final Version Due

Submissions will be accepted in one of 3 categories:
Short Papers (4 pages)
Long Pages (8 pages)
Poster abstracts (1 page)

Submission Details:
Please see http://biolinksig.org/biolink-2014/submission/ for complete details.
Submissions for Day 1 should be made to the BioLINK SIG 2014 EasyChair
website at https://www.easychair.org/conferences/?conf=biolinksig2014
by April 11th, 2014 (11:59pm in the time zone of your choice)

Submissions for Day 2, Phenotype Day, will be handled separately.
Please see http://phenoday2014.bio-lark.org/#submission for more
information.
Parallel submissions to BioLINK SIG and Phenotype Day will be
accepted, however the organizers reserve the right to move papers
between the BioLINK SIG, BioOntologies SIG, and Phenotype Day for
reviewing and presentation.

Organizers:
Lynette Hirschman, MITRE Corporation, USA
Hagit Shatkay, Dept. of Computer and Information Sciences, Center for
Bioinformatics and Computational Biology, University of Delaware, USA
Karin Verspoor, National Information and Communication Technology
Australia (NICTA), Australia
biolinksig2014 at biolinksig.org

Program Committee:
(to date, others pending)

Anna Divoli, Pingar Research
Yana Bromberg, Rutgers University
Kevin Bretonnel Cohen, University of Colorado School of Medicine
Rezarta Islamaj Dogan, US National Library of Medicine
Antonio Jimeno, NICTA
Martin Krallinger, Spanish National Cancer Research Centre
Zhiyong Lu, US National Library of Medicine
Dietrich Rebholz-Schumann, University of Zurich
Luis M. Rocha, Indiana University
Jasmin Saric, Boehringer Ingelheim Pharma
Junichi Tsujii, Microsoft Research Asia
Alfonso Valencia, Spanish National Cancer Research Centre
W. John Wilbur, US National Library of Medicine

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