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

Research output: Contribution to journalJournal articleResearchpeer-review

Standard

EXTRACT : interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. / Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl.

In: Database, Vol. 2016, baw005, 2016.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Pafilis, E, Buttigieg, PL, Ferrell, B, Pereira, E, Schnetzer, J, Arvanitidis, C & Jensen, LJ 2016, 'EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation', Database, vol. 2016, baw005. https://doi.org/10.1093/database/baw005

APA

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

Vancouver

Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C et al. EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database. 2016;2016. baw005. https://doi.org/10.1093/database/baw005

Author

Pafilis, Evangelos ; Buttigieg, Pier Luigi ; Ferrell, Barbra ; Pereira, Emiliano ; Schnetzer, Julia ; Arvanitidis, Christos ; Jensen, Lars Juhl. / EXTRACT : interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. In: Database. 2016 ; Vol. 2016.

Bibtex

@article{9b544ee4c6aa46e38d832895c51628c5,
title = "EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation",
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.Database URL: https://extract.hcmr.gr/.",
author = "Evangelos Pafilis and Buttigieg, {Pier Luigi} and Barbra Ferrell and Emiliano Pereira and Julia Schnetzer and Christos Arvanitidis and Jensen, {Lars Juhl}",
note = "{\circledC} The Author(s) 2016. Published by Oxford University Press.",
year = "2016",
doi = "10.1093/database/baw005",
language = "English",
volume = "2016",
journal = "Database",
issn = "1758-0463",
publisher = "Oxford University Press",

}

RIS

TY - JOUR

T1 - EXTRACT

T2 - interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

AU - Pafilis, Evangelos

AU - Buttigieg, Pier Luigi

AU - Ferrell, Barbra

AU - Pereira, Emiliano

AU - Schnetzer, Julia

AU - Arvanitidis, Christos

AU - Jensen, Lars Juhl

N1 - © The Author(s) 2016. Published by Oxford University Press.

PY - 2016

Y1 - 2016

N2 - 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/.

AB - 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/.

U2 - 10.1093/database/baw005

DO - 10.1093/database/baw005

M3 - Journal article

C2 - 26896844

VL - 2016

JO - Database

JF - Database

SN - 1758-0463

M1 - baw005

ER -

ID: 157550561