BioCreAtIvE (A critical assessment of text mining methods in
molecular biology
Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...
) consists in a community-wide effort for evaluating
information extraction and
text mining
Text mining, text data mining (TDM) or 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 extracting information from differe ...
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, text data mining (TDM) or 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 extracting information from differe ...
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 th ...
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
The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally r ...
.
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 th ...
References
External links
BioCreAtIve, 2007-2015BioCreAtIve 2, 2006-2007First BioCreAtIvE workshop, 2004BMC Bioinformatics special issue : BioCreAtIvE
Bioinformatics
Information science
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