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JBI: BNLP 2009 : Special Issue on Biomedical Natural Language Processing: Journal of Biomedical Informatics


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Submission Deadline May 27, 2008
Categories    NLP

Call For Papers

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

Any questions regarding the special issue may be sent to the guest editors at 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 ( 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 ( 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.

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