Text and knowledge mining for pharmacogenomics: Genotype-phenotype-drug relationships
A session of Pacific Symposium on Biocomputing 2012
Big Island of Hawaii, USA
January 3-7, 2012
E-mail: kevin punto cohen arroba gmail punto com
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Text and knowledge mining for pharmacogenomics: Genotype-phenotype-drug relationships

The technical area of this session is text and knowledge mining for pharmacogenomics, particularly focusing on genotype-phenotype-drug relationships. Broad categories of work that have been well-studied in the past are included, specifically text mining and reasoning, but submissions are restricted to applications of that work to the constrained area of pharmacogenomics, and particularly genotype-phenotype-drug relationships. For example, topics that are solicited include:

  • Work on the corpus of documents linked to by PharmGKB
  • Reasoning systems applied over the PharmGKB knowledge base
  • Relation extraction between genotypes, phenotypes, and drugs, and other semantic classes relevant to pharmacogenomics
  • Corpus development for pharmacogenomics text mining
Work on gene taggers would not be considered for inclusion. However, work on named entity taggers for other relevant semantic classes, such as drugs and phenotypes, would be considered responsive to the call for papers.

This is a full session, not a workshop, and all accepted papers will be published in the PSB proceedings and indexed in PubMed/MEDLINE. PSB has long been considered a high-prestige conference for publication of BioNLP papers, and some of the papers from PSB NLP sessions have gone on to be quite influential, such as Fukuda et al. (1998) on gene mentions and Schwartz and Hearst (2003) on abbreviation definitions.

This document last modified 05/07/11 15:05.