文章基本信息

标题：EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation
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作者：Evangelos Pafilis ; Pier Luigi Buttigieg ; Barbra Ferrell 等
期刊名称：Database
印刷版ISSN：1758-0463
电子版ISSN：1758-0463
出版年度：2016
卷号：2016
DOI：10.1093/database/baw005
语种：English
出版社：Oxford University Press
摘要：The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation 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 metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. 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-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.Database URL: https://extract.hcmr.gr/