BioCreAtIvE (A critical assessment of text mining methods in
molecular biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...
) consists in a community-wide effort for evaluating
information extraction
Information extraction (IE) is the task of automatically extracting structured information from unstructured and/or semi-structured machine-readable documents and other electronically represented sources. In most of the cases this activity concer ...
and
text mining
Text mining, also referred to as ''text data mining'', similar to text analytics, is the process of deriving high-quality information from text. It involves "the discovery by computer of new, previously unknown information, by automatically extract ...
developments in the biological domain.
It was preceded by the Knowledge Discovery and Data Mining (KDD) Challenge Cup for detection of gene mentions.
Community Challenges
First edition (2004-2005)
Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task, the gene name normalization task, and the functional annotation of gene products task. The data sets produced by this contest serve as a Gold Standard training and test set to evaluate and train Bio-NER tools and annotation extraction tools.
Second edition (2006-2007)
The second BioCreAtIvE challenge (2006-2007) had also 3 tasks: detection of gene mentions, extraction of unique idenfiers for genes and extraction information related to physical protein-protein interactions.
It counted with participation of 44 teams from 13 countries.
Third edition (2011-2012)
The third edition of BioCreative included for the first time the InterActive Task (IAT), designed to evaluate the practical usability of
text mining
Text mining, also referred to as ''text data mining'', similar to text analytics, is the process of deriving high-quality information from text. It involves "the discovery by computer of new, previously unknown information, by automatically extract ...
tools in real-world
biocuration Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the ...
tasks.
Fifth edition (2016)
BioCreative V had 5 different tracks, including an interactive task (IAT) for usability of text mining systems and a track using the BioC format for curating information for
BioGRID.
See also
*
Biocuration Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the ...
References
External links
BioCreAtIve, 2007-2015BioCreAtIve 2, 2006-2007First BioCreAtIvE workshop, 2004BMC Bioinformatics special issue : BioCreAtIvE
Bioinformatics
Information science
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