Call for Papers
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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. Nevertheless, 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.

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Potential topics include, but are not limited to:
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- 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 literature-based knowledge discovery, providing reasoning for hypothesis generation or contradiction detection,

- other solutions relying to a significant proportion on automated literature analysis.

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Submissions
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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
- Notification of acceptance: February 15, 2011
- Publication: May 15, 2012

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How to submit a paper
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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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About Advances in Bioinformatics
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Advances in Bioinformatics is a peer-reviewed, open access journal that publishes original research articles as well as review articles in all areas of bioinformatics. The journal has published special issues on "Genome Evolution" (2010) and on "Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data" (2009). Special issues currently open for submission are on "Computational Mass Spectrometry" and on "Biomedical Applications of Computational Methods: Results of the Successful Interplay between Bioinformatics and Experimental Work", both to appear in early 2012.

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

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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

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