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LINGUIST List 23.5057

Tue Dec 04 2012

Confs: Computational Ling, Text/Corpus Ling/USA

Editor for this issue: Xiyan Wang <xiyanlinguistlist.org>

Date: 03-Dec-2012
From: Kevin Cohen <kevin.cohengmail.com>
Subject: BioCreative IV
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BioCreative IV
Short Title: BioCreative IV

Date: 07-Oct-2013 - 09-Oct-2013
Location: Bethesda, Maryland, USA
Contact: Cecilia Arighi
Contact Email: < click here to access email >
Meeting URL: http://www.biocreative.org/events/biocreative-iv/CFP/

Linguistic Field(s): Computational Linguistics; Text/Corpus Linguistics

Meeting Description:

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

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, please go to:



Registration starts November 19.

To check on upcoming deadlines please visit:



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

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