Document Detail


Collaborative biocuration--text-mining development task for document prioritization for curation.
MedLine Citation:
PMID:  23180769     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems for the biological domain. The 'BioCreative Workshop 2012' subcommittee identified three areas, or tracks, that comprised independent, but complementary aspects of data curation in which they sought community input: literature triage (Track I); curation workflow (Track II) and text mining/natural language processing (NLP) systems (Track III). Track I participants were invited to develop tools or systems that would effectively triage and prioritize articles for curation and present results in a prototype web interface. Training and test datasets were derived from the Comparative Toxicogenomics Database (CTD; http://ctdbase.org) and consisted of manuscripts from which chemical-gene-disease data were manually curated. A total of seven groups participated in Track I. For the triage component, the effectiveness of participant systems was measured by aggregate gene, disease and chemical 'named-entity recognition' (NER) across articles; the effectiveness of 'information retrieval' (IR) was also measured based on 'mean average precision' (MAP). Top recall scores for gene, disease and chemical NER were 49, 65 and 82%, respectively; the top MAP score was 80%. Each participating group also developed a prototype web interface; these interfaces were evaluated based on functionality and ease-of-use by CTD's biocuration project manager. In this article, we present a detailed description of the challenge and a summary of the results.
Authors:
Thomas C Wiegers; Allan Peter Davis; Carolyn J Mattingly
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-11-22
Journal Detail:
Title:  Database : the journal of biological databases and curation     Volume:  2012     ISSN:  1758-0463     ISO Abbreviation:  Database (Oxford)     Publication Date:  2012  
Date Detail:
Created Date:  2012-11-27     Completed Date:  2013-04-24     Revised Date:  2013-07-11    
Medline Journal Info:
Nlm Unique ID:  101517697     Medline TA:  Database (Oxford)     Country:  England    
Other Details:
Languages:  eng     Pagination:  bas037     Citation Subset:  IM    
Affiliation:
Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA. tcwieger@ncsu.edu
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MeSH Terms
Descriptor/Qualifier:
Cooperative Behavior*
Data Mining / methods*
Databases, Genetic*
Disease
Documentation / methods*
Genes
Humans
Internet
Toxicogenetics
User-Computer Interface
Grant Support
ID/Acronym/Agency:
ES014065/ES/NIEHS NIH HHS; R01 ES014065/ES/NIEHS NIH HHS
Comments/Corrections

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