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Title: BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics

Abstract

The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive tagging of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of themore » metagenomics community.« less

Authors:
 [1];  [2]
  1. Univ. of Delaware, Newark, DE (United States). Center for Bioinformatics and Computational Biology
  2. The MITRE Corporation, Bedford, MA (United States)
Publication Date:
Research Org.:
Univ. of Delaware, Newark, DE (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Contributing Org.:
The MITRE Corporation, Bedford, MA (United States)
OSTI Identifier:
1330427
Report Number(s):
DE-SC0010838
DOE Contract Number:  
SC0010838
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES; Annotation; BioCreative; Environmental Metadata; Metagenomics; Natural Language Processing; Text Mining

Citation Formats

Wu, Cathy H., and Hirschman, Lynette. BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics. United States: N. p., 2016. Web. doi:10.2172/1330427.
Wu, Cathy H., & Hirschman, Lynette. BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics. United States. doi:10.2172/1330427.
Wu, Cathy H., and Hirschman, Lynette. Sat . "BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics". United States. doi:10.2172/1330427. https://www.osti.gov/servlets/purl/1330427.
@article{osti_1330427,
title = {BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics},
author = {Wu, Cathy H. and Hirschman, Lynette},
abstractNote = {The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive tagging of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of the metagenomics community.},
doi = {10.2172/1330427},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2016},
month = {10}
}