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CHEMDNER CFP and training data release


The CHEMDNER is a community challenge on named entity recognition of chemical compounds, to promote systems that can detect mentions in text of chemical compounds and drugs.



CHEMDNER taskCALL FOR PARTICIPATION: CHEMDNER task
Chemical compound and drug name recognition task

(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:

www.biocreative.org/resources/corpora/bc-iv-chemdner-corpus

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

www.biocreative.org/media/store/files/2013/CHEMDNER_TRAIN_V01.zip

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

  • 16 Aug : development data annotations
  • 3 Sep: test set release
  • 12 Sep: test set prediction due
  • 17 Sep: invite teams for workshop presentation talks
  • 19 Sep: CHEMDNER workshop proceedings paper due (2-4 pages)
  • 7-9 Oct: BioCreative IV workshop

(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:

www.biocreative.org/media/store/files/2013/chemdner_faq.pdf

(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:

www.biocreative.org/events/biocreative-iv/workshop

(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:

www.biocreative.org/events/biocreative-iv/workshop/#proceedings

(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.


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