Special Workshop

 PSB 2010

GPD-Rxn Workshop: Genotype-Phenotype-Drug Relationship Extraction from Text

Co-chairs: Adrien Coulet, Nigam Shah, Larry Hunter, Chitta Baral and Russ B. Altman

The aim of this workshop is to bring together researchers working on the automatic or semi-automatic extraction of relationships between biomedical entities from research literature. The workshop will focus particularly on methods for the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships and the use of the relationships for advancing pharmacogenomic research.

Call For Participation

Advances in concept recognition have led to the development of various tools that enable the identification of biomedical entities and relationships between them in text. The aim of the GPD-Rxn workshop is to examine the current state of art and discuss the next steps for making the extraction of relationships between biomedical entities integral to the curation and knowledge management workflow in Pharmacogenomics. The workshop will focus particularly on the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships that are of interest to Pharmacogenomics.

Extracting and structuring such text-mined relationships is a key to support the evaluation and the validation of mulitple hypotheses that emerge form high throughput translational studies spaning multiple measurement modalities. In order to advance this agenda, it is essential that existing relationship extraction methods be compared to one another and that a community wide benchmark corpus emerges; against which future methods can be compared. The workshop aims to bring together researchers working on the automatic or semi-automatic extraction of relationships between biomedical entities from research literature in order to identify the key groups interested in creating such a benchmark.

Important topics relevant to this workshop include:

Approaches that combine text-mining and knowledge-based systems are of special interest.

Abstracts

We are soliciting both research and position abstracts (up to 500 words) related to the topics mentioned above. The GPD-Rxn workshop will combine invited talks, talks selected from abstract submissions to this call, and a panel discussion. Submitted abstracts that will be reviewed by the co-chairs for selecting submitted talks. In addition, other relevant submissions will have the possibility to be presented a poster-session at the end of the workshop. Workshop participants must register for PSB; abstracts may be submitted prior to registering. Authors of accepted abstracts must register for PSB as soon as they are notified of paper acceptance.

Abstracts should be emailed to Adrien Coulet (coulet at stanford dot edu).

Important Dates

Abstract deadline: September 30, 2009 extended deadline!
Speaker notification: October 15, 2009
Deadline for early registration: October 31, 2009
Workshop: January 7, 2009 2-5:30pm

For students (and anyone interested): click here for a suggested bibliography of the domain of the GPD-Rxn workshop

Click here for a PDF of the agenda, abstracts, and posters.

Contact: Adrien Coulet
Email: coulet at stanford dot edu

Back to the main PSB page Updated: December 31, 2009