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[CFP] ECCB'05 Workshop on Biomedical Ontologies and Text Processing

Chris Wroe cwroe at
Fri Apr 15 06:57:21 PDT 2005

Apologies for those of you who get this more than once.


                  CALL FOR PAPERS

                ECCB'05 WORKSHOP ON

                28  September, 2005
                   Madrid, Spain

*********** Submission deadline 20 June, 2005 ******************

The workshop is part of the 4th European Conference on Computational
Biology (ECCB) (

Hosted by: Bioinformatics National Institute (INB)


Biomedical literature, bio-databases and bio-ontologies all play an
important role in supporting the work of biological researchers. Much
of the biological knowledge in our community is held in electronic
form as natural language text. However, not all experimental data is
appropriate to include in such research publications, and so is
instead stored in more structured bio-databases. Bio-ontologies
provide a common conceptual framework for structuring and annotating
this data to enable it to be pooled across databases. These three
resources contain overlapping information in different forms, and the
inter-dependencies between them are complex.

Text mining of biomedical literature is one way to ensure that the
large quantity of information in text is better reflected within
ontologies and databases. It can be used, for example, to add ontology
based annotation to bio-database entries. By exposing the vocabulary
and relationships within the literature, it can also assist in the
construction, refinement and validation of the ontologies themselves.
Even when used in isolation, the meaning of concepts within an
ontology must be interpreted by humans as well as computer systems.
Natural language, therefore, plays a vital role in ontology design.

Ontologies in turn can support text mining by for example: (i)
providing a framework for structuring terminologies and for clustering
synonyms; and (ii) defining the types of entities and relations that
text mining aims to discover during the process of analysing text.

Therefore text mining and ontologies have a lot in common and can be
mutually beneficial. However, bio-ontologies are frequently built
without explicitly taking into account the needs of the language
processing community. As a consequence language processing researchers
either ignore these valuable resources or are forced to adapt them
with difficulty. Furthermore, ontology builders are frequently
unaware of language processing tools, methodologies and applications
and how they might assist in the construction and evaluation of

The goal of this workshop is to bring together researchers from the
bio-ontology community with those from the biomedical text processing
community with a view to furthering their understanding each other's
needs and capabilities. Previous workshops in the area have tended
focus more either on bio-ontologies or on bio-text processing. While
some research has attempted to bridge this gap the aim of current
workshop is to focus explicitly on the relationship between
bio-ontologies and bio-text processing.

To that end we solicit papers that address any aspect of the
relationship between bio-ontologies and biomedical text processing.
Possible topics include, but are not limited to:

- Ontology-assisted information retrieval or extraction from biomedical text
- Language processing techniques and principles for
   building and maintaining bio-ontologies
- The relation between bio-ontologies and bio-lexicons and
   more generally the relation between ontologies and natural language
- The role of isa and part-whole relations in bio-ontologies and
   their relation to the lexical relations of hyponymy and meronymy
- The inclusion in biological databases of ontologically structured
   information automatically or semi-automatically extracted from the
   literature (aka curation)
- The evaluation of bio-ontologies through their use in language
   processing applications
- The use of bio-ontologies for the creation of annotated language
   resources (e.g. annotating texts with GO codes)
- The use of bio-ontologies to support co-reference resolution in
   biomedical texts

While the goal of the workshop is to focus on the relationship between
bio-ontologies and biomedical text processing, excellent papers that
address one or the other of these areas to the exclusion of the other
will be considered at the discretion of the programme committee.

The workshop will include paper presentations and discussion. The
papers should describe recent and previously unpublished work and may
be preliminary in nature. The programme committee will arrange the
presentations and discussion based on the quality of submissions and
may invite other presentations as well. See  for further details.

Abstracts of the workshop papers will be published in the main ECCB05
conference proceedings and the papers themselves will be published in
a separate workshop proceedings. Negotiations are underway for a
journal special issue in which the best papers from the workshop will
be published.


Paper submission:          June 20, 2005
Acceptance notification:   July 15, 2005
Final papers due:          July 22, 2005
Workshop:                  September 28, 2005


Position papers should be no more than 4000 words (5-8 pages). The
standard ACM conference style is recommended (see:

Papers must be submitted electronically in PDF or PostScript format. Please
consult the web site for further details


Chris Wroe (University of Manchester)   cwroe at
Rob Gaizauskas (University of Sheffield)   r.gaizauskas at
Christian Blaschke (Bioalma, Madrid)   blaschke at


Russ Altman (U. Stanford)
Sophia Ananiadou (NaCTeM)
A. Aronson (NLM)
Ted Briscoe (U. Cambridge)
Olivier Bodenrider (NLM)
Judith Blake (Jackson Laboratory)
Nigel Collier (Tokyo)
George Demetriou (U. Sheffield)
Carol Freidman (Columbia)
Ken Fukuda (Computational Biology Research Center, AIST, Tokyo)
Moustafa Ghanem (Imperial College)
Carole Goble (U. Manchester)
Lawrence Hunter (U. Colorado))
Udo Hahn (U. Jena)
Henk Harkema (U. Sheffield)
Lynette Hirschman (MITRE)
Ewan Klein (U. Edinburgh)
Phil Lord (U. Manchester)
Yves Lussier (Columbia University)
Adeline Nazarenko (Universite Paris-Nord, France)
Helen Parkinson (EBI)
Dietrich Rebholz-Schuhmann (EBI)
Patrick Ruch (University Hospital of Geneva)
Andrey Rzhetsky (Columbia University)
Stefan Schultz (U. Freiburg)
Robert Stevens (U. Manchester)
Jun'ichi Tsujii (U. of Tokoyo)
Alan Rector (U. Manchester)
Alfonso Valencia (Centro Nacional de Biotechnologia, Madrid)
Karin Verspoor (Los Alamos)
Bonnie Webber (U. Edinburgh)

Dr Chris Wroe
Clinical Research Fellow
Information Management Group
Dept of Computer Science
Manchester University

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