<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.7226.0">
<TITLE>Call for papers: Workshop on language processing in the biomedical domain</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<P><FONT SIZE=2>Hi, CORPORA list people,<BR>
<BR>
The list of topics for this meeting includes a number of areas of<BR>
interest to corpus linguists, including:<BR>
<BR>
- corpus construction efforts<BR>
- evaluation and testing of systems<BR>
- test suites for biomedical language processing systems<BR>
<BR>
It's being held in Detroit, MI, the day before the ACL Tutorial Day.<BR>
<BR>
Workshop title: Linking Biological Literature, Ontologies and<BR>
Databases: Mining Biological Semantics<BR>
<BR>
Description<BR>
<BR>
This workshop will bring researchers in natural language processing in<BR>
the bioinformatics and biomedical domains together with scientists in<BR>
bioinformatics and biology. It follows successful workshops on the<BR>
topic at ACL 2002, 2003, and 2004, and NAACL 2004, as well as related<BR>
meetings at PSB (Pacific Symposium on Biocomputing) and ISMB<BR>
(Intelligent Systems in Molecular Biology). This will be a joint<BR>
workshop with the ISMB SIG on text mining for biology, and it will be<BR>
colocated with the ISCB annual meeting in Detroit, MI, on June 24,<BR>
2005.<BR>
<BR>
Recent years have seen an interesting confluence between the worlds of<BR>
bioinformatics and natural language processing. Molecular biologists,<BR>
confronted with new high-throughput sources of data, have recognized<BR>
that language processing can provide them with tools for handling a<BR>
flood of data that is unprecedented in the history of the life<BR>
sciences. The natural language processing community, in turn, has<BR>
become aware of the resources that the computational bioscience<BR>
community has made available, and there has been growing interest in<BR>
applying natural language processing techniques to mine the biological<BR>
literature to support complex applications in the biological domain,<BR>
ranging from identifying relevant literature (information retrieval)<BR>
to extraction of experimental finding to populate biological knowledge<BR>
bases to summarization, to present key facts to biologists in succinct<BR>
form.<BR>
<BR>
A number of successful conferences and workshops have resulted, with<BR>
significant progress in the areas of entity identification, concept<BR>
normalization, and system evaluation coming through competitions like<BR>
the KDD Cup, BioCreAtIvE and through shared resources like the Genia<BR>
corpus.<BR>
<BR>
This workshop will continue the interaction between these communities.<BR>
Papers on the role of ontologies in understanding biomedical texts<BR>
and on evaluation and testing of systems built for these domains are<BR>
especially invited, but submissions on all topics related to natural<BR>
language processing in the bioinformatics, biomedicine, and molecular<BR>
biology are welcome, including:<BR>
<BR>
- the role of ontologies and knowledge bases in understanding biomedical texts<BR>
- knowledge representation<BR>
- evaluation and testing of systems<BR>
- test suites for biomedical language processing systems<BR>
- entity identification and normalization<BR>
- information extraction<BR>
- information retrieval<BR>
- corpus construction efforts<BR>
- coreference and anaphora resolution<BR>
- visualization<BR>
<BR>
Target audience and expected number of participants<BR>
<BR>
The target audience is researchers in natural language processing in<BR>
the molecular biology, medical, and associated domains. We expect<BR>
these researchers to come from the fields of linguistics, computer<BR>
science, bioinformatics, medical informatics, and molecular biology.<BR>
<BR>
The expected number of participants is 70.<BR>
<BR>
Workshop length<BR>
<BR>
The workshop length will be one day.<BR>
<BR>
Organizing committee<BR>
<BR>
Kevin Bretonnel Cohen leads the Biomedical Text Mining Group at the<BR>
University of Colorado's Center for Computational Pharmacology. He is<BR>
the author of a number of papers and one book chapter on natural<BR>
language processing in the biomedical domain. Current projects in the<BR>
Center for Computational Pharmacology include an NIH R-01-funded<BR>
project to build a molecular biology knowledgebase using text data<BR>
mining; an information extraction project targeting assertions about<BR>
translocation of proteins; and ongoing research in software testing<BR>
techniques for natural language processing software.<BR>
<BR>
Lynette Hirschman is Chief Scientist for the Information Technology<BR>
Center at MITRE in Bedford, MA, where she leads MITRE's efforts in<BR>
bioinformatics and text mining for biology. Her group has been<BR>
responsible for the 2002 KDD Challenge Cup Evaluation Task 1:<BR>
Information Extraction for Biomedical Articles and the 2004<BR>
BioCreAtIvE challenge evaluation in biomedical entity extraction (in<BR>
conjunction with Alfonso Valencia and Christian Blaschke at the Centro<BR>
Nacional de Biotechnología). Recent research projects have included<BR>
the use of curated biological databases for noisy training data to<BR>
train statistical entity extraction systems, and tools to aid curators<BR>
for biological databases. She is the co-organizer of the ISMB Special<BR>
Interest Group on Text Mining for Biology (with Alfonso Valencia) and<BR>
is currently serving on the Gene Ontology Consortium Advisory<BR>
Committee.<BR>
<BR>
Christian Blaschke is the project leader for text mining and<BR>
information extraction systems at bioalma in Madrid. He was the first<BR>
author of the earliest paper on rule-based information extraction from<BR>
molecular biology literature. His recent projects have included being<BR>
an organizer of the first BioCreative (Critical Assessment of<BR>
Information Extraction Systems in Biology) competition on biological<BR>
text data mining. His current work involves leading the development<BR>
of text mining systems for pharmaceutical and biotechnology companies.<BR>
<BR>
Hagit Shatkay is an assistant professor in the School of Computing at<BR>
Queen's University in Kingston, Ontario. Her research is in the area<BR>
of machine learning as it applies to biomedical data mining. She is<BR>
an active member of the biomedical text-mining research community,<BR>
where her work focuses on biomedical information retrieval. She has<BR>
presented tutorials on biomedical literature mining at the Pacific<BR>
Symposium on Biocomputing, the Bioinformatics Summer School, and the<BR>
International Conference on Intelligent Systems for Molecular Biology,<BR>
and has recently established BLIMP, a web-based forum for Biomedical<BR>
Literature Mining Publications. Prior to joining Queen's University,<BR>
she was a researcher with the Informatics Research group at<BR>
Celera/Applied Biosystems, following a postdoctoral fellowship at the<BR>
National Center for Biotechnology Information. She holds a PhD in<BR>
computer science from Brown University, and an MSc and BSc in computer<BR>
science from the Hebrew University in Jerusalem.<BR>
<BR>
Program Committee<BR>
<BR>
We have assembled a strong set of people from academia, industry, and<BR>
government in the US, Europe, and Japan. The program committee<BR>
includes researchers with world-class reputations in this field.<BR>
<BR>
Sophia Ananiadou, University of Salford<BR>
Lan Aronson, NLM<BR>
Breck Baldwin, Alias-i Inc.<BR>
Olivier Bodenreider, NLM<BR>
Shannon Bradshaw, University of Iowa<BR>
Bob Carpenter, Alias-i Inc.<BR>
Jeff Chang, Duke Univeristy<BR>
Aaron Cohen, Oregon Health Sciences University<BR>
Nigel Collier, National Institute of Informatics, Japan<BR>
Lynne Fox, University of Colorado Health Sciences Center<BR>
Bob Futrelle, Northeastern University<BR>
Henk Harkema, University of Sheffield<BR>
Marti Hearst, University of California at Berkeley<BR>
Larry Hunter, University of Colorado School of Medicine<BR>
Steve Johnson, Columbia University<BR>
Marc Light, University of Iowa<BR>
Hongfang Liu, University of Maryland at Baltimore County<BR>
Alex Morgan, MITRE<BR>
James Pustejovsky, Brandeis University<BR>
Tom Rindflesch, NLM<BR>
Andrey Rzhetsky, Columbia University<BR>
Jasmin Saric, EML Research gGmbH<BR>
Lorrie Tanabe, NCBI, NLM<BR>
Jun-ichi Tsujii, University of Tokyo<BR>
Alfonso Valencia, Universidad Autonoma de Madrid<BR>
Karin Verspoor, Los Alamos National Labs<BR>
John Wilbur, NCBI, NLM<BR>
Hong Yu, Columbia University<BR>
<BR>
--<BR>
K. B. Cohen<BR>
Biomedical Text Mining Group Lead<BR>
Center for Computational Pharmacology<BR>
303-916-2417 (cell) 303-377-9194 (home)<BR>
<A HREF="http://compbio.uchsc.edu/Hunter_lab/Cohen">http://compbio.uchsc.edu/Hunter_lab/Cohen</A><BR>
<A HREF="http://www.ling.ohio-state.edu/~kcohen/">http://www.ling.ohio-state.edu/~kcohen/</A><BR>
</FONT>
</P>
</BODY>
</HTML>