Call for Papers

** EXTENDED DEADLINE: 19th February 2012 **

** NEW: The workshop will feature an invited talk by Prof. Jun'ichi Tsujii of Microsoft Research, Asia **

Over the past decade, biomedical text mining has received a large amount of interest. Faced with the rapidly increasing volume of biomedical literature, domain experts have an ever-increasing need for tools that can help them locate isolate relevant nuggets of information from this deluge of information in a timely and efficient manner. The response to such issues by the natural language processing community can be clearly evidenced in the biomedical natural language processing workshops that have been held over that past 10 years, in conjunction with ACL or NAACL meetings, to report the process in the field, as well as the founding of an ACL special interest group.

Biomedical text mining applications are reliant on high quality resources. These include databases and ontologies (e.g., Biothesaurus, UMLS Metathesaurus, MeSH and the Gene Ontology) and dictionaries/computational lexicons (e.g., the BioLexicon and the UMLS SPECIALIST lexicon). Recent years have also evidenced a large increase in the number of freely-available corpora (e.g., GENIA, GREC, AIMED, BioInfer, CRAFT, BioDRB) annotated with an expanding range of information types. These now include not only named entities and simple relations that hold between them, but also more complex event structures and coreference, as well as higher level information about how events are to be interpreted (e.g., facts, analyses, speculations, etc.) and discourse structure. Community shared tasks and challenges (e.g., JNLPBA, LL05, Biocreative I/II/III, BioNLP'09, BioNLP 2011, i2b2, etc.) also normally involve the production of annotated corpora (on which the participating systems are trained and evaluated) as well as helping to steer research efforts to focus on open research problems.

Following on from the success of two previous workshops, the workshop aims to bring together researchers who make use of biomedical text mining resources such as the above in their applications, or who are working on the development of new resources. The workshop will allow an assessment of the current state of the art of resources, and will provide a forum for the discussion of current problems, questions and open issues, which will be useful in guiding further research in this area. Such topics are very much relevant to META-NET (a Network of Excellence consisting of 54 research centres from 33 countries), which is dedicated to building the technological foundations of a multilingual European information society. META-NET aims to push forward research to allow a rapid expansion of language technologies; such efforts can only be acheived if appropriate resources are available. Since META-NET is concerned with enhancing information access for all European citizens, submissions concerning biomedical resources for languages other than English are particularly welcome. A further vital consideration to allow rapid building of new applications is that of interoperability and reuse. As a step towards this, several annotated corpora have been made UIMA-compliant, and are available in the U-Compare system, which allows easy construction of NLP workfows and evaluation against gold standard corpora.

Some specific questions that the workshop will aim to answer include the following:

  • Among the available resources, which are the most used? What makes a good resource? How can easily can resources be employed for different purposes? What efforts have been made to make resources reusable or interoperable? To what extent have these efforts been successful?
  • Which resources are underused and why? What could be done to improve or extend them to improve their utility?
  • Which types of resources are still lacking and what is needed urgently? Are any resources planned or in development to address such gaps? Are any resources available that cover languages other than English?
  • To what extent do the existing resources support processing of text in different biomedical subdomains? How easily can they be adapted to deal with different domains?

We invite papers reporting on resources that facilitate biomedical text mining, and the process of designing, building, updating, delivering, using and evaluating them. The workshop will focus both on the lexical and knowledge repositories themselves (e.g., terminologies, ontologies, controlled vocabularies, factual databases, annotated corpora, etc.) as well as on issues relating to their usability (e.g., design guidelines, standards for building resources, storage and exchange formats, interoperability issues, etc).

Topics of interest include but are not limited to:

  • Building biomedical resources: controlled vocabularies, terminologies, ontologies, corpora
  • Guidelines and annotation schemas, tools, challenges, interoperability
  • Reengineering existing biomedical or general language resources
  • Update, evolution, extension or enrichment of resources
  • Adapting resources to new sub-domains
  • Interoperability of resources and standards
  • Lightly annotated and noisy resources
  • Tools for exploration of resources
  • Data exchange formats
  • Evaluation, comparison and critical assessment of resources / evaluation metrics
  • Test suites