[MOBY-l] CFP: The Joint BioLink and Bio-Ontologies Meeting, August 4-5, 2006

[Phillip Lord]

The Joint BioLINK and Bio-Ontologies SIG Meeting, August 4-5, 2006
In association with ISMB 2006, Fortaleza, Brazil, 2006


NEW THIS YEAR:

The two long-standing ISMB SIGS, Bio-ontologies and BioLINK, will hold
a single joint two-day workshop this year. The meeting will consist of
sessions that focus on the intersection of bio-ontologies and text
mining, as well as individual sessions on ontologies in the life
sciences (organized by the BioOntologies committee
(http://www.jbb06.org/ont-organisers.html), and on biomedical text
mining, linking text data to biology, (organized by the BioLINK
committee: http://www.jbb06.org/link-organisers.html)

Registration and participation will be for a single two-day workshop. 

Key Information
      
Program chairs: 

Bio-Ontologies Section: 
Robert Stevens (1), Phillip Lord (2), Robin McEntire (3),
James.A.Butler(3)

 1. School of Computer Science, University of Manchester, United Kingdom
 2. School of Computing Science, University of Newcastle, United Kingdom
 3. GlaxoSmithKline, USA

BioLINK Section: 

Hagit Shatkay (1), Lynette Hirschman (2), Christian Blaschke (3),
Alfonso Valencia (4)

 1. School of Computing, Queen's University, Canada
 2. MITRE, USA
 3. Bioalma, Spain
 4. Centro Nacional de Biotecnologia, Universidad Autonoma, Spain

Website:  http://www.jbb06.org

Main Conference: http://www.iscb.org/ismb2006


About the Workshop

Our goals in organizing the workshop are:
 1. To allow researchers in the two communities to participate in the
    activities of both SIGs;
 2. To encourage exchange of ideas and presentation cross-cutting
    research.

The joint sessions will encourage discussion on topics such as
ontology-based curation from the biomedical literature,
(semi-)automated creation of ontologies, use of ontologies to improve
text mining, and evaluation of ontologies, especially in terms of
ability to consistently capture biologically significant concepts from
the literature.

The ontology session will continue the important topics from previous
workshops.  Ontologies provide a mechanism for organising, sharing and
reconciling data. Within recent years, there has been a great deal of
interest in the use of ontologies within bioinformatics, particularly
in providing computationally accessible annotation, or standard data
models for complex data for microarray or pathway information. With
the increase in scope and use of ontologies within bioinformatics,
issues of scalability, expressiveness and best practices for modeling
are becoming more important. On the ontologies side, we are therefore
particularly interested in work involving multiple source ontologies,
and which cut across the different levels of granularity implicit
within biological systems.

The BioLink session will explore resources and tools for biomedical
text-mining. As biomedical literature and text in biology continue
their exponential growth, text-mining, information retrieval, and
natural language processing (NLP) are all becoming main-stream
practices in bioinformatics. This field is interdisciplinary in nature
and brings researchers applying NLP, text mining, information
extraction and retrieval in the biomedical domain, together with
scientists from bioinformatics and biology. We solicit submissions
from researchers working on all aspects of text mining as they apply
to bioinformatics and bio-medicine.

The workshop will offer an informal environment for presentation and
discussion of current research in biomedical ontologies and
text-mining.  The program will include presentations of short
papers, invited talks and posters. Papers and poster-abstracts will be
reviewed by the program committee. All accepted submissions will be
included in the SIG notes.

Submissions

We are inviting two types of submissions: 

 1. Short papers (up to 4 pages)
 2. Poster abstracts (up to 1/2 page). 

Authors should clearly indicate whether they would like their work to
be considered as related to Bio-Ontologies, Biomedical Text Mining
(BioLINK) or to the joint session.

Submissions details to be released soon. 

Listed below are suggested topics for each section. However, we
particularly encourage submissions that integrate aspects of both
text-mining and ontologies, for instance discussing the role of
ontologies and knowledge bases in text mining, use of ontologies to
improve biomedical text analysis, automated text categorization based
on ontology structure etc.

Suggested topics for Bio-Ontologies include but are not restricted to:

 - Biological Applications of Ontologies.
 - Reports on Newly Developed or Existing Bio-Ontologies.
 - Tools for Developing Ontologies.
 - Use of Semantic Web technologies in Bioinformatics
 - The implications of Bio-Ontologies or the Semantic Web for the drug
   discovery process
 - Current Research In Ontology Languages and its implication for
   Bio-Ontologies

Suggested topics for BioLINK include but are not restricted to:

 - Knowledge Representation
 - Testing and Evaluation 
 - Corpus Construction Efforts
 - Entity Identification and Normalization
 - Information Extraction
 - Information Retrieval
 - Text categorization.



May 1: Papers (up to 4 pages) and poster-abstracts (up to 1 page) due.
June 10: Notification to authors
June 20: Final version due