LINGUIST List 22.977 Mon Feb 28 2011 Calls: Computational Ling/ Journal of Biomedical Informatics (Jrnl) Editor for this issue: Danniella Hornby <d-hornbyhotmail.com> LINGUIST is pleased to announce the launch of an exciting new feature: Easy Abstracts! Easy Abs is a free abstract submission and review facility designed to help conference organizers and reviewers accept and process abstracts online. Just go to: http://www.linguistlist.org/confcustom, and begin your conference customization process today! With Easy Abstracts, submission and review will be as easy as 1-2-3! Directory         1.     Kevin Bretonnel Cohen , Journal of Biomedical Informatics Message 1: Journal of Biomedical Informatics Date: 03-Feb-2011 From: Kevin Bretonnel Cohen <kevin.cohengmail.com> Subject: Journal of Biomedical Informatics E-mail this message to a friend Full Title: Journal of Biomedical Informatics Linguistic Field(s): Computational Linguistics Call Deadline: 15-Mar-2011 Journal of Biomedical Informatics Call for Papers: Mining the Pharmacogenomics Literature Guest editors: K. Bretonnel Cohen and Russ Altman Co-editors: Yael Garten, Udo Hahn, Nigam Shah We are inviting submissions for a special issue of the Journal of Biomedical Informatics on automatic or semi-automatic extraction of relationships between biomedical entities relevant to pharmacogenomics from the research literature. Accepted papers will focus on methods for the extraction of genotype-phenotype, genotype-drug, and phenotype-drug relationships and the novel use of these relationships for advancing pharmacogenomic research. Efforts aimed at creating benchmark corpora as well as comparative evaluation of existing relationship extraction methods are of special interest. The planned special issue aims to address the gap in coverage of text mining for pharmacogenomics, as an important initial application area of genomics in clinical medicine, and thus an important translational medicine activity. The issue is intended to focus particularly on genotype-phenotype-drug relationships. It will include broad categories of work that have been well-studied in the past, specifically text mining and reasoning, but will restrict submissions to applications of that work to the constrained area of pharmacogenomics, and particularly genotype-phenotype-drug relationships. Topics that are solicited include: - Relation extraction between genotypes, phenotypes, and drugs, and other semantic classes relevant to pharmacogenomics - Corpus development for pharmacogenomics text mining - Associating gene variants (mutations, alleles, rs/ss numbers) to the associated gene name - Using text mining to extract information about the association of drugs with clinical phenotpyes - Use of biological networks in combination with text mining to facilitate discovery - Work on the corpus of documents linked to by PharmGKB - Reasoning systems applied over the PharmGKB knowledge base -Creation of ontologies to help relate molecular action of drugs to their clinical effects. Work on gene taggers alone will not be considered. The key feature we seek is the use of language technologies to understand molecular basis of drug response, its variability, and its impact on phenotypes at the molecular, cellular, organ and whole organisms level. Approaches that combine text-mining and knowledge-based systems are of special interest. All submissions should follow the guidelines for authors available at the Journal of Biomedical Informatics web site (http://www.elsevier.com/locate/yjbin). JBI generally publishes at least one methodological review paper in each issue, and we would welcome a review of the state of the art in text mining for pharmacogenomics for this special issue. Authors may contact special issue lead editors (kevin.cohengmai.com or russ.altmanstanford.edu) with a proposed abstract before submission. Authors must submit their paper via the online Elsevier Editorial System (EES) at http://ees.elsevier.com/jbi. Authors can register and upload their text, tables, and figures, as well as subsequent revisions, through this website. Potential authors may contact the Publishing Services Coordinator in the journal's editorial office (jbielsevier.com) for questions regarding this process. When asked for the category of their submission, they should indicate that it is for the special issue on Mining the pharmacogenomics literature (which will appear as 'Pharmacogenomics' on the pull-down menu). Submission Deadline: March 15, 2011. Read more issues|LINGUIST home page|Top of issue Page Updated: 28-Feb-2011       About LINGUIST    |   Contact Us       While the LINGUIST List makes every effort to ensure the linguistic relevance of sites listed on its pages, it cannot vouch for their contents.