[Elsnet-list] BioNLP: special issue of the Journal of Biomedical Informatics

Kevin B. Cohen kevin.cohen at gmail.com
Fri Mar 28 17:05:35 CET 2008

Call for Papers

Special Issue on Biomedical Natural Language Processing: Journal of
Biomedical Informatics

Guest Editors:
Wendy W. Chapman, PhD
K. Bretonnel Cohen

Submission deadline: May 27, 2008

BioNLP is biomedical natural language processing, or the application
of natural language processing and text mining to the biomedical,
clinical, and genomic domains. The goal of this special issue of the
Journal of Biomedical Informatics (JBI) is to publish papers
describing novel work at the forefront of the new challenges and
possibilities that face the BioNLP community today.

The last decade saw rapid growth in the area of BioNLP. This body of
work has resulted in quantitative and qualitative differences in both
the types of tasks we can undertake and the levels of performance on
those tasks. There has been a recent resurgence of work in
foundational, lower-level linguistic analysis tasks such as
part-of-speech tagging, syntactic parsing, and semantic role labeling.
There has also been a new emphasis on higher-level
application-oriented work such as automated ICD9-CM code assignment,
use of NLP in clinical decision support, and management of the rapid
growth in the primary biomedical literature. These recent advances in
foundational technologies and in application types and domains have
created the possibility of a new era in biomedical text mining.  The
special issue is intended to help define and provide insights into
that future.

We solicit papers on new methodologies applied to text from
biomedical, clinical, or genomic domains. In addition to original
research papers, as is JBI's custom, we are soliciting one or more
methodological review papers on BioNLP methodologies. Possible topics
for this special issue include, but are not limited to, the following
subjects as applied to biomedical text:

*        Morphological processing
*        Part-of-speech tagging
*        Syntactic parsing
*        Tokenization
*        Coordination and conjunction processing
*        Negation and uncertainty identification
*        Word sense disambiguation
*        Reference resolution
*        Temporal modeling from text
*        Information retrieval
*        Information extraction and encoding
*        Text classification
*        Text summarization
*        Question-answering
*        Development and evaluation of annotation schemas
*        Corpus and test set generation and evaluation
*        Software testing and engineering for natural language
processing applications

In accordance with JBI's editorial policies, we are soliciting
full-length article submissions that present and evaluate new methods
rather than the application or evaluation of existing approaches (see
editorial guidelines at http://www.elsevier.com/locate/yjbin).

Any questions regarding the special issue may be sent to the guest
editors at jbi-nlp at list.pitt.edu. We welcome advance notice of your
intention to submit a paper. Inquiries about suitability should
include the subject line "suitability inquiry" and a short paragraph
describing the primary objective of the manuscript, emphasizing how
the objective matches the JBI editorial guidelines cited above.

Submissions: Manuscripts should be submitted to the JBI authors'
gateway (http://ees.elsevier.com/jbi/) no later than May 27, 2008.
Please be sure that your manuscript follows the JBI instructions for
authors available on that web site. You will be offered an opportunity
to specify the special issue ("Biomedical NLP") as the preferred venue
when you submit your manuscript to the gateway.

All appropriate submissions will be reviewed by at least two
evaluators in addition to the editors.  Papers returned for revisions
should generally be revised and resubmitted within four weeks.
Accepted manuscripts are immediately made available on the JBI web
site in Science Direct
(http://www.sciencedirect.com/science/journal/15320464) and indexed in
PubMed/MEDLINE.  Thus they will become widely accessible even before
the print version of the special issue is published.  Papers judged
inappropriate for the special issue may be referred to the JBI
editor-in-chief to be considered for publication in a regular issue of
the journal.

K. B. Cohen
Lead Artificial Intelligence Engineer, The MITRE Corporation, Human
Language Technology Division
Biomedical Text Mining Group Lead, Center for Computational Pharmacology
303-916-2417 (cell) 303-377-9194 (home)

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