EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation


Contact
pier.buttigieg [ at ] awi.de

Abstract

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.



Item Type
Article
Authors
Divisions
Primary Division
Programs
Primary Topic
Peer revision
Peer-reviewed
Publication Status
Published
Eprint ID
43662
DOI 10.1093/database/baw005

Cite as
Pafilis, E. , Buttigieg, P. L. , Ferrell, B. , Pereira, E. , Schnetzer, J. , Arvanitidis, C. and Jensen, L. J. (2016): EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation , Database, 2016 , baw005 . doi: 10.1093/database/baw005


Download
[img]
Preview
PDF
baw005.pdf

Download (819kB) | Preview
Cite this document as:

Share


Citation

Research Platforms
N/A

Campaigns

Funded by
info:eu-repo/grantAgreement/EC/FP7/287589


Actions
Edit Item Edit Item