[Corpora-List] CfP: Special Issue on Literature-Mining Solutions for Life Science Research

[Jin-Dong Kim]

(Apologies for multiple copies)

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Call for Papers:
Special Issue of Advances in Bioinformatics on
"Literature mining solutions for life science research"
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Research and development in the area of biomedical literature analysis
aims at providing life scientists with effective means to access and
exploit knowledge contained in scientific publications. Virtually all
journal publications and many conference proceedings are nowadays
readily available in an electronic form --- for instance, as abstracts
through the MEDLINE citation index or as full-text article through
PubMed Central. but keeping up-to-date with and searching for recent
findings in a research domain remains a tedious task hampered by
inefficient and ineffective means for access and exploitation.
Biomedical text analysis aims to improve access to unstructured
knowledge by alleviating searches, providing auto-generated summaries
of documents and topics, linking and integrating publications with
structured resources, visualizing content for better understanding,
and guiding researchers to novel hypotheses and into knowledge
discovery.

Focused research over recent years has improved fundamental solutions
for biomedical text mining, such as document retrieval, named entity
recognition, normalization and grounding, and extraction of
relationships, with levels of accuracy that reach human annotators
when considering inter-annotator agreement. Consequently, more and
more integrative analysis tools were put forward by the text mining
community targeting a broad audience of end-users: generic and
task-specific search engines for life scientists; interfaces for
networks synthesis based on textual evidences; or more specialized
tools searching for transcription factors, or primer sequences.


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Aims and Scope
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This special issue of Advances in Bioinformatics aims at presenting
the richness of end-user-oriented biomedical text mining tools for
bioinformaticians, molecular biologists, biochemists, clinicians,
pharmacologists, and other researchers in life sciences. We solicit
publications that present and demonstrate applications that can be
used on a regular basis to support life science research, and are
focused on use cases and application approaches. Therefore, the
emphasis of this special issue is on round-up solutions that can
address real-life tasks in life science research, and not on
individual components for integration with literature mining
pipelines.

Potential topics include, but are not limited to:

 - search engines and literature navigation systems and their added
value --- content enrichment, summarization, cross-document analysis,
integration with other resources,
 - network and pathway synthesis and visualization, based on
literature evidence and integrated with knowledge bases,
 - plug-ins for data analysis pipelines and for visualization tools
such as Cytoscape and genome browsers (UCSC, Ensembl),
 - tools for assisting in literature-based knowledge discovery,
providing reasoning for hypothesis generation or contradiction
detection,
 - other solutions relying to a significant proportion on automated
literature analysis.

Submissions should discuss typical use cases to demonstrate the
ability to effectively access information and guide the researcher to
desired or unexpected findings. Readers and users should be able to
obtain a profound understanding of what can be achieved with each tool
and how much confidence can be put to the pieces of extracted
information (for instance, protein-protein interactions and filtered
documents). While the emphasis is on use cases, technical aspects
should be covered as well, in particular where methods have been
developed by the authors. The quality of core text mining components
presented in the papers should be demonstrated through an evaluation,
preferably on publicly available corpora.

Applications should be available as stand-alone or web-based
applications, or as plug-ins or web-services. For stand-alone
applications, we require the support of a common platform (Linux,
Windows Vista/XP/7, and Mac OS X). We will only consider solutions
that are free for academic and non-profit organizations, and for
non-academic users at least an open access trial version has to be
available.

We also solicit comprehensive, technical surveys and methodological
reviews focused on the assessment of existing literature mining tools
and natural language processing methods in the biomedical domain. We
expect to have two surveys within this special issue. Prospective
authors are encouraged to submit extended abstracts (two pages) to the
guest editors no later than June 30, 2011, to determine suitability
and avoid overlaps between these surveys.


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Important dates
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 - Pre-submission inquiries to determine suitability of surveys: June 30, 2011
 - Paper submission deadline: November 15, 2011
 - First round of reviews due:: February 15, 2011
 - Publication date: May 15, 2012


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Submission
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Papers have to be submitted through Advances in Bioinformatics'
Manuscript Tracking System at http://mts.hindawi.com/. Formatting
guidelines are available at
http://www.hindawi.com/journals/abi/guidelines/. Advances in
Bioinformatics is an online journal and there will be no page limit;
however, authors are encouraged to restrict their submissions to a
reasonable length.


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Contact
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Please feel free to contact the guest editors at any time during the
preparation of your manuscript:

 - Jörg Hakenberg
  Pharma Research and Early Development Informatics, Hoffmann-La
Roche Inc., Nutley, NJ, USA
  jorg.hakenberg (a) roche.com
 - Goran Nenadić
  School of Computer Science and Manchester Interdisciplinary
BioCenter, University of Manchester, UK
  g.nenadic (a) manchester.ac.uk
 - Dietrich Rebholz-Schuhmann
  European Bioinformatics Institute (EBI), Hinxton, Cambridgeshire, UK
  rebholz (a) ebi.ac.uk
 - Jin-Dong Kim
  Database Center for Life Science (DBCLS), Tokyo, Japan
  jdkim (a) dbcls.rois.ac.jp

For a PDF version of this CfP and updates, please visit
http://www2.informatik.hu-berlin.de/~hakenber/abi/ .

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