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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

BioCreative V.5

BioCreative V.5 CFP [2016-11-14]

We are happy to announce the BioCreative V.5 Challenge (
Following the impact and success of previous BioCreative-related initiatives, text mining and language 
processing researchers world-wide are invited to used the BeCalm (Biomedical Annotation Metaserver) platform
 in order to implement text Annotation Servers and to provide their results for the following tasks:
  • TIPS (Technical interoperability and performance of annotation servers). (Technical interoperability of named entity recognition). This task will focus on the technical aspects of the evaluation of continuous text Annotation Servers (ASs) for named entity recognition. This is an open task, in the sense that it is not restricted to a particular named entity recognition task. Moreover, the Annotation Servers may be fully developed in-house or integrate third party recognition software as building block components. AS will consist of a "REST" (Representational State Transfer) API application that responds to the request by returning NER annotation results as structured data (represented in particular formats XML/BioC, JSON and TXT, see ).
  • CEMP (Chemical Entity Mention recognition). This tasks requires the recognition of chemical named entity mentions in text. This implies to return the start and end indices corresponding to all the chemical entity mentions.
  • GPRO (Gene and Protein Related Object recognition). For this task teams have to recognize mentions of gene and protein related objects (named as GPROs) in running text.
  • Participating teams do not need to send results for all of three sub-tasks. They can send results only for individual sub-tasks. In line with previous BioCreative challenges, the result of participating teams are presented at the BioCreative V.5. evaluation workshop that will take place in Madrid (Spain) in April 2017. See details of call for participation here here Task Organizers: Martin Krallinger, Spanish National Cancer Research Centre Anália Lourenço, University of Vigo Martin Pérez-Pérez, University of Vigo Gael Pérez-Rodríguez, University of Vigo Florentino Fdez-Riverola, University of Vigo Alfonso Valencia, Spanish National Cancer Research Centre