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Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

MPG-Autoren
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Buttigieg,  Pier Luigi
HGF MPG Joint Research Group for Deep Sea Ecology & Technology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Pereira,  Emiliano
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Schnetzer,  Julia
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Zitation

Pafilis, E., Buttigieg, P. L., Ferrell, B., Pereira, E., Schnetzer, J., Arvanitidis, C., et al. (2015). Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.


Zitierlink: http://hdl.handle.net/21.11116/0000-0001-C3D6-1
Zusammenfassung
The microbial and molecular ecology communities have made substantial progress on developing standards for annotating samples with environment metadata. However, manually annotating samples is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool,EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of meta-genomic records and other samples. Behind its webbased user interface, the system combines published methods for named entity recognition of environments, organisms, tissues and diseases. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text miningassisted curation revealed that EXTRACT speeds up annotation by 15 - 25% and helps curators detect terms that would otherwise have been missed.