LINGUIST List 16.580

Sat Feb 26 2005

Calls: Lang Acquisition/Syntax/Portugal; Comp Ling/USA

Editor for this issue: Amy Wronkowicz <>

As a matter of policy, LINGUIST discourages the use of abbreviations or acronyms in conference announcements unless they are explained in the text. To post to LINGUIST, use our convenient web form at


        1.    Joao Costa, Lisbon Workshop on Production vs Comprehension in the Acquisition of Syntax
        2.    Kevin Bretonnel Cohen, Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics

Message 1: Lisbon Workshop on Production vs Comprehension in the Acquisition of Syntax

Date: 25-Feb-2005
From: Joao Costa <>
Subject: Lisbon Workshop on Production vs Comprehension in the Acquisition of Syntax

Full Title: Lisbon Workshop on Production vs Comprehension in the Acquisition of

Date: 06-Jun-2005 - 06-Jul-2005
Location: Lisbon, Portugal
Contact Person: Joao Costa
Meeting Email:

Linguistic Field(s): Language Acquisition; Syntax

Call Deadline: 08-Apr-2005

Meeting Description:

Lisbon Workshop on Production vs Comprehension in the Acquisition of Syntax
Universidade Nova de Lisboa, June 6-7, 2005

Research on language acquisition has established that comprehension precedes
production. Many studies determine the acquisition of a certain property of the
grammar based on children's productions only or on comprehension data only.
Given the specificity of some syntactic constructions, in some cases, it is not
easy to access both production and comprehension data. Yet, it is widely
acknowledged that both sources of data are useful in order to deepen our
understanding on the development of grammar.

The aim of this workshop is to gather contributions, trying to answer questions
like the following:

a. Are there areas in syntax in which the usual comprehension-before-production
pattern is not found?
b. Developmental scales should be defined in terms of production, comprehension,
or both?
c. Since it is known that parameters are set at a very early stage, which
experimental methods can be used to test children's development in the
comprehension of syntax?
d. How can results from comprehension help us in explaining children's
production and vice-versa?

Papers are invited for 20 minute talks followed by discussion.
Please submit anonymous 2-page abstracts (font times new roman 12pt) in word or
PDF format to the following email address:
Deadline for submission: April 8, 2005
Notice of acceptance: April 30, 2005
Organizing Committee:
Workshop hosted by Centro de Linguística da Universidade Nova de Lisboa

Message 2: Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics

Date: 24-Feb-2005
From: Kevin Bretonnel Cohen <>
Subject: Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics

Full Title: Linking Biological Literature, Ontologies and Databases: Mining
Biological Semantics

Date: 24-Jun-2005 - 24-Jun-2005
Location: Detroit, MI, United States of America
Contact Person: Kevin Bretonnel Cohen
Meeting Email:
Web Site:

Linguistic Field(s): Computational Linguistics

Call Deadline: 11-Mar-2005

Meeting Description:

This workshop will bring researchers in natural language processing in the
bioinformatics and biomedical domains together with scientists in bioinformatics
and biology. It follows successful workshops on the topic at ACL 2002, 2003,
and 2004, and NAACL 2004, as well as related meetings at PSB (Pacific Symposium
on Biocomputing) and ISMB (Intelligent Systems in Molecular Biology). It is a
joint workshop with the ISMB SIG on text mining for biology, and it will be
colocated with the ISCB annual meeting in Detroit, MI, on June 24, 2005, the day
before the ACL Tutorial Day.

Recent years have seen an interesting confluence between the worlds of
bioinformatics and natural language processing. Molecular biologists,
confronted with new high-throughput sources of data, have recognized that
language processing can provide them with tools for handling a flood of data
that is unprecedented in the history of the life sciences. The natural language
processing community, in turn, has become aware of the resources that the
computational bioscience community has made available, and there has been
growing interest in applying natural language processing techniques to mine the
biological literature to support complex applications in the biological domain,
ranging from identifying relevant literature (information retrieval) to
extraction of experimental finding to populate biological knowledge bases to
summarization, to present key facts to biologists in succinct form.

A number of successful conferences and workshops have resulted, with significant
progress in the areas of entity identification, concept normalization, and
system evaluation coming through competitions like the KDD Cup, BioCreAtIvE and
through shared resources like the Genia corpus.

This workshop will continue the interaction between these communities. Papers
on the role of ontologies in understanding biomedical texts and on evaluation
and testing of systems built for these domains are especially invited, but
submissions on all topics related to natural language processing in the
bioinformatics, biomedicine, and molecular biology are welcome, including:

- the role of ontologies and knowledge bases in understanding biomedical texts
- knowledge representation
- evaluation and testing of systems
- test suites for biomedical language processing systems
- entity identification and normalization
- information extraction
- information retrieval
- corpus construction efforts
- coreference and anaphora resolution
- visualization

Target audience and expected number of participants

The target audience is researchers in natural language processing in the
molecular biology, medical, and associated domains. We expect these researchers
to come from the fields of linguistics, computer science, bioinformatics,
medical informatics, and molecular biology.

The expected number of participants is 70.

Workshop length

The workshop length will be one day.

Organizing committee

Kevin Bretonnel Cohen leads the Biomedical Text Mining Group at the University
of Colorado's Center for Computational Pharmacology. He is the author of a
number of papers and one book chapter on natural language processing in the
biomedical domain. Current projects in the Center for Computational
Pharmacology include an NIH R-01-funded project to build a molecular biology
knowledgebase using text data mining; an information extraction project
targeting assertions about translocation of proteins; and ongoing research in
software testing techniques for natural language processing software.

Lynette Hirschman is Chief Scientist for the Information Technology Center at
MITRE in Bedford, MA, where she leads MITRE's efforts in bioinformatics and text
mining for biology. Her group has been responsible for the 2002 KDD Challenge
Cup Evaluation Task 1: Information Extraction for Biomedical Articles and the
2004 BioCreAtIvE challenge evaluation in biomedical entity extraction (in
conjunction with Alfonso Valencia and Christian Blaschke at the Centro Nacional
de Biotechnología). Recent research projects have included the use of curated
biological databases for noisy training data to train statistical entity
extraction systems, and tools to aid curators for biological databases. She is
the co-organizer of the ISMB Special Interest Group on Text Mining for Biology
(with Alfonso Valencia) and is currently serving on the Gene Ontology Consortium
Advisory Committee.

Christian Blaschke is the project leader for text mining and information
extraction systems at bioalma in Madrid. He was the first author of the
earliest paper on rule-based information extraction from molecular biology
literature. His recent projects have included being an organizer of the first
BioCreative (Critical Assessment of Information Extraction Systems in Biology)
competition on biological text data mining. His current work involves leading
the development of text mining systems for pharmaceutical and biotechnology

Hagit Shatkay is an assistant professor in the School of Computing at Queen's
University in Kingston, Ontario. Her research is in the area of machine
learning as it applies to biomedical data mining. She is an active member of
the biomedical text-mining research community, where her work focuses on
biomedical information retrieval. She has presented tutorials on biomedical
literature mining at the Pacific Symposium on Biocomputing, the Bioinformatics
Summer School, and the International Conference on Intelligent Systems for
Molecular Biology, and has recently established BLIMP, a web-based forum for
Biomedical Literature Mining Publications. Prior to joining Queen's University,
she was a researcher with the Informatics Research group at Celera/Applied
Biosystems, following a postdoctoral fellowship at the National Center for
Biotechnology Information. She holds a PhD in computer science from Brown
University, and an MSc and BSc in computer science from the Hebrew University in

Program committee

We have assembled a strong set of people from academia, industry, and government
in the US, Europe, and Japan. The program committee includes researchers with
world-class reputations in this field.

Sophia Ananiadou, University of Salford
Lan Aronson, NLM
Breck Baldwin, Alias-i Inc.
Olivier Bodenreider, NLM
Shannon Bradshaw, University of Iowa
Bob Carpenter, Alias-i Inc.
Jeff Chang, Duke Univeristy
Aaron Cohen, Oregon Health Sciences University
Nigel Collier, National Institute of Informatics, Japan
Lynne Fox, University of Colorado Health Sciences Center
Bob Futrelle, Northeastern University
Henk Harkema, University of Sheffield
Marti Hearst, University of California at Berkeley
Larry Hunter, University of Colorado School of Medicine
Steve Johnson, Columbia University
Marc Light, University of Iowa
Hongfang Liu, University of Maryland at Baltimore County
Alex Morgan, MITRE
James Pustejovsky, Brandeis University
Tom Rindflesch, NLM
Andrey Rzhetsky, Columbia University
Jasmin Saric, EML Research gGmbH
Lorrie Tanabe, NCBI, NLM
Jun-ichi Tsujii, University of Tokyo
Alfonso Valencia, Universidad Autonoma de Madrid
Karin Verspoor, Los Alamos National Labs
John Wilbur, NCBI, NLM
Hong Yu, Columbia University

Respond to list|Read more issues|LINGUIST home page|Top of issue