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Subject: [ E-Announce ] CHEMDNER CFP and training data release
From: <krallinger.martin_(on)_gmail.com>
Date received: 01 Aug 2013
Deadline: -
Start date: 07 Oct 2013

CALL FOR PARTICIPATION: CHEMDNER task: Chemical compound and drug
name recognition task (see

(1) The CHEMDNER task (part of The BioCreative IV competition) is
    a community challenge on named entity recognition of chemical
    compounds. The goal of this task is to promote the
    implementation of systems that are able to detect mentions in
    text of chemical compounds and drugs.

(2) The datasets relevant to the CHEMDNER tasks will all be
    listed under the following link:


The CHEMDER training set is now online, together with an updated
version of the annotation guidelines. They are available at:


 (3) Dates: Please notice the following CHEMDNER schedule, in
     particular the test set prediction due.

25th June: sample data collection, detailed task description,
annotation and evaluation script 31st July: training data
collection, annotations and updated guidelines 16th August :
development data annotations 3nd September: test set release 12th
September: test set prediction due 17th September: invite teams
for workshop presentation talks 19th September: CHEMDNER workshop
proceedings paper due (2-4 pages) 7th-9th October: BioCreative IV

(4) Frequently asked questions (FAQ). Considering the numerous
    questions we have got from various teams (many of them
    related to the CDI subtask ranking). We have placed online a
    FAQ document at:


(5) Evaluation workshop. The evaluation results will be presented
    at this workshop and in the corresponding workshop
    proceedings evaluation paper. This is in line with other
    community challenges such as Critical Assessment of protein
    Structure Prediction (CASP) experiments. There will be a
    session devoted to the CHEMDNER task during the workshop as
    well as a poster session and selected talks from
    participating teams. The link of the workshop as well as
    additional details and registration is online at:


(6) Workshop proceedings. The second volume of the BioCreative
    workshop proceedings will be devoted entirely to the CHEMDER
    task. The proceedings papers for the CHEMDER task should be
    2-4 pages long, describing your system and results obtained
    for the training or development set (or both). Please refer
    to the following URL for more information. For more details
    refer to:


(7) CHEMDER special issue publications

There will be a journal issue devoted to BioCreative IV and also
one for the CHEMDER task. This is in line with previous
BioCreative challenges were special issues were published in BMC
Bioinformatics, Genome Biology and the journal Database. We will
announce more details on the selection process and the target
journal after the workshop.


Martin Krallinger

Structural Computational Biology Group

Structural Biology and BioComputing Programme

Spanish National Cancer Research Centre (CNIO)


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