Announcement of the PSB Workshop Genotype-Phenotype-Drug Relationship Extraction from Text

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         CALL FOR ABSTRACTS - PSB Workshop: GPD-Rxn Workshop
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 GPD-Rxn WORKSHOP: Genotype-Phenotype-Drug Relationship Extraction from Text

        Co-located with the Pacific Symposium on Biocomputing,
            January 4-8 2010, The Big Island of Hawaii

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 multiple hypotheses that emerge form
high throughput translational studies spanning 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
   * Natural Language Processing methods for the extraction of relationships
   * Machine learning methods for the characterization of biomedical
relationships
   * Use of prior knowledge to improve relationship extraction
   * Ontologies for relationships
   * Applications and uses of text-extracted relationships
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).

CO-CHAIRS
*Adrien Coulet
*Nigam Shah
*Larry Hunter
*Chitta Baral
*Russ B. Altman

IMPORTANT DATES
*Abstract deadline: September 15, 2009
*Speaker notification: October 15, 2009
*Deadline for early registration: October 31, 2009
*Workshop: Date to be announced; will be scheduled during the main
conference (January 5-8, 2010)

LINKS
PSB 2010: http://psb.stanford.edu/
GPD-Rxn Workshop: http://psb.stanford.edu/gdprxn-workshop.html

CONTACT
Adrien Coulet, coulet at stanford dot edu