<4 weeks to submit! BioLINK SIG at ISMB 2014 "Supporting Bioscience Through Text Mining" + "Phenotype Day"

[Karin Verspoor]

Reminder: Just ONE MONTH until the submission deadline!

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.

We are also pleased to announce that William Hayes, Chief Technology Officer at Selventa, a company which aims to pioneer the analysis of Big Data to unravel the complexity of disease for precision medicine, will be our keynote speaker on Day 1.

Title: Supporting Bioscience through Text Mining
Dates: Friday, July 11 & Saturday, July 12, 2014
URL: http://biolinksig.org/biolink-2014
Email: biolink...@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 solicit 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, Department of Computing and Information Systems, The University of Melbourne, Australia
biolink...@biolinksig.org

Program Committee: 

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, The University of Melbourne
Martin Krallinger, Spanish National Cancer Research Centre
Zhiyong Lu, US National Library of Medicine

Mariana Neves, Hasso-Plattner-Institute, Germany
Dietrich Rebholz-Schumann, University of Zurich
Luis M. Rocha, Indiana University
Jasmin Saric, Boehringer Ingelheim Pharma

Michael Schroeder, TU Dresden
Junichi Tsujii, Microsoft Research Asia
Alfonso Valencia, Spanish National Cancer Research Centre
W. John Wilbur, US National Library of Medicine