[Corpora-List] BioCreative IV Call for Participation

Kevin B. Cohen kevin.cohen at gmail.com
Wed Dec 12 21:50:20 CET 2012


BioCreative IV Challenge and Workshop

October 7-9, 2013, NCBI, Bethesda, Maryland, USA



BioCreative: Critical Assessment of Information Extraction in Biology (http://www.biocreative.org/) is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. Building on the success of the previous BioCreative Challenge Evaluations and Workshops (BioCreative I, II, II.5, III, and 2012 workshop) [1-5], the BioCreative Organizing Committee will host the BioCreative IV Challenge (http://www.biocreative.org/events/biocreative-iv/CFP/) at NCBI, National Institutes of Health, Bethesda, Maryland, on October 7-9, 2013. One key goal of BioCreative is the active involvement of the text mining user community in the design of the tracks, preparation of corpus and the testing of interactive systems. For BioCreative IV, the selection of the tracks has been driven in part by suggestions from the biocuration community during the BioCreative workshop 2012, and by our goal of addressing a major barrier on system usage/adoption: interoperability.

This time BioCreative IV will consist of five tracks:

Track 1: Interoperability (BioC) – Development of an interoperable BioNLP module that can be seamlessly coupled to BioC compliant modules (http://www.biocreative.org/events/biocreative-iv/CFP/#track1);

Track 2: Chemical and Drug Named Entity Recognition (CHEMDNER) – Detection of mentions of chemical compounds and drugs, in particular those chemical entity mentions that can subsequently be linked to a chemical structure (http://www.biocreative.org/events/biocreative-iv/CFP/#track2);

Track 3: Comparative Toxicogenomics Database (CTD) Curation – Provision of Web Services to identify gene, chemical, disease, and action term mentions supporting CTD curation in PubMed abstracts (http://www.biocreative.org/events/biocreative-iv/CFP/#track3);

Track 4: Gene Ontology (GO) curation – Development of modules to aid GO curators in identifying articles with curatable GO information (triage) and extracting gene function terms and the associated evidence sentences in full-length articles (http://www.biocreative.org/events/biocreative-iv/CFP/#track4);

Track 5: Interactive Curation (IAT) – Demonstration and evaluation of web-based systems addressing user-defined tasks, evaluated by curators on performance and usability.

An extended description of the tracks is offered at the end of this document (http://www.biocreative.org/events/biocreative-iv/CFP/#track5).


Teams can participate in one or more of these tracks. Team registration will start on November 19 and will continue until final commitment is requested by the individual tracks.

To register a team go to http://www.biocreative.org/news/biocreative-iv/team/


Registration starts November 19.

To check on upcoming deadlines please visit http://www.biocreative.org/events/biocreative-iv/CFP/#dates.


Cecilia Arighi, University of Delaware, USA Kevin Cohen, University of Colorado, USA Lynette Hirschman, MITRE Corporation, USA Martin Krallinger, Spanish National Cancer Centre, CNIO, Spain Zhiyong Lu, National Center for Biotechnology Information (NCBI), NIH, USA Carolyn Mattingly, North Carolina State University, USA Alfonso Valencia, Spanish National Cancer Centre, CNIO, Spain Thomas Wiegers, North Carolina State University, USA John Wilbur, National Center for Biotechnology Information (NCBI), NIH, USA Cathy Wu, University of Delaware and Georgetown University, USA


Chairs: Cecilia Arighi and Zhiyong Lu

Judith Blake, MGI, The Jackson Laboratory, USA Andrew Chatr-aryamontri, BioGrid, Canada Stan Laulederkind, Rat Genome Database, USA Donghui Li, TAIR, USA Sherri Matis, Astrazeneca, USA Fiona McCarthy, Agbase, USA Peter McQuilton, Flybase, UK Sandra Orchard, IntAct, UK Phoebe Roberts, Pfizer, USA Mary Schaeffer, MaizeGDB, USA Kimberly Van-Auken, Wormbase, USA

-- Kevin Bretonnel Cohen, PhD Biomedical Text Mining Group Lead, Computational Bioscience Program, U. Colorado School of Medicine 303-916-2417 (cell) 303-377-9194 (home) http://compbio.ucdenver.edu/Hunter_lab/Cohen

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