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

doi:10.1093/database/baw005

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

Journal Article · Fri Jan 01 00:00:00 EST 2016 · Database

DOI:https://doi.org/10.1093/database/baw005· OSTI ID:1253360

Pafilis, Evangelos ^[1]; Buttigieg, Pier Luigi ^[2]; Ferrell, Barbra ^[3]; Pereira, Emiliano ^[4]; Schnetzer, Julia ^[5]; Arvanitidis, Christos ^[1]; Jensen, Lars Juhl ^[6]

Hellenic Centre for Marine Research, Crete (Greece)
Helmholtz Centre for Polar and Marine Research, Bremerhaven (Germany)
Delaware Biotechnology Institute, Newark, DE (United States)
Max Planck Institute for Marine Microbiology, Bremen (Germany)
Max Planck Institute for Marine Microbiology, Bremen (Germany); Jacob Univ. gGmbH, Bremen (Germany)
Univ. of Copenhagen, Copenhagen (Denmark)

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. Here the 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.

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Research Organization:: Univ. of Delaware, Newark, DE (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0010838

OSTI ID:: 1253360

Journal Information:: Database, Vol. 2016; ISSN 1758-0463

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 21 works

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References (27)

The genomic standards consortium: bringing standards to life for microbial ecology Yilmaz, Pelin; Gilbert, Jack A.; Knight, Rob The ISME Journal, Vol. 5, Issue 10 https://doi.org/10.1038/ismej.2011.39	journal	April 2011
The environment ontology: contextualising biological and biomedical entities Buttigieg, Pier; Morrison, Norman; Smith, Barry Journal of Biomedical Semantics, Vol. 4, Issue 1 https://doi.org/10.1186/2041-1480-4-43	journal	January 2013
BRENDA in 2015: exciting developments in its 25th year of existence Chang, Antje; Schomburg, Ida; Placzek, Sandra Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1068	journal	November 2014
Uberon, an integrative multi-species anatomy ontology Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V. Genome Biology, Vol. 13, Issue 1 https://doi.org/10.1186/gb-2012-13-1-r5	journal	January 2012
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data Kibbe, Warren A.; Arze, Cesar; Felix, Victor Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1011	journal	October 2014
The mammalian phenotype ontology: enabling robust annotation and comparative analysis Smith, Cynthia L.; Eppig, Janan T. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 1, Issue 3 https://doi.org/10.1002/wsbm.44	journal	November 2009
LINNAEUS: A species name identification system for biomedical literature Gerner, Martin; Nenadic, Goran; Bergman, Casey M. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-85	journal	January 2010
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text Pafilis, Evangelos; Frankild, Sune P.; Fanini, Lucia PLoS ONE, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pone.0065390	journal	June 2013
Anatomical Entity Recognition with a Hierarchical Framework Augmented by External Resources Xu, Yan; Hua, Ji; Ni, Zhaoheng PLoS ONE, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pone.0108396	journal	October 2014
Comprehensive comparison of large-scale tissue expression datasets Santos, Alberto; Tsafou, Kalliopi; Stolte, Christian PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1054	journal	January 2015
An overview of MetaMap: historical perspective and recent advances Aronson, Alan R.; Lang, François-Michel Journal of the American Medical Informatics Association, Vol. 17, Issue 3 https://doi.org/10.1136/jamia.2009.002733	journal	May 2010
Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications Savova, Guergana K.; Masanz, James J.; Ogren, Philip V. Journal of the American Medical Informatics Association, Vol. 17, Issue 5 https://doi.org/10.1136/jamia.2009.001560	journal	September 2010
DNorm: disease name normalization with pairwise learning to rank Leaman, R.; Islamaj Dogan, R.; Lu, Z. Bioinformatics, Vol. 29, Issue 22 https://doi.org/10.1093/bioinformatics/btt474	journal	August 2013
DISEASES: Text mining and data integration of disease–gene associations Pletscher-Frankild, Sune; Pallejà, Albert; Tsafou, Kalliopi Methods, Vol. 74 https://doi.org/10.1016/j.ymeth.2014.11.020	journal	March 2015
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life Pafilis, Evangelos; Frankild, Sune P.; Schnetzer, Julia Bioinformatics, Vol. 31, Issue 11 https://doi.org/10.1093/bioinformatics/btv045	journal	January 2015
Reflect: augmented browsing for the life scientist Pafilis, Evangelos; O'Donoghue, Seán I.; Jensen, Lars J. Nature Biotechnology, Vol. 27, Issue 6 https://doi.org/10.1038/nbt0609-508	journal	June 2009
The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth Parr, Cynthia S.; Wilson, Nathan; Leary, Patrick Biodiversity Data Journal, Vol. 2 https://doi.org/10.3897/BDJ.2.e1079	journal	April 2014
The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology Hurwitz, Bonnie L.; Sullivan, Matthew B. PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0057355	journal	February 2013
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts Wei, C. -H.; Harris, B. R.; Li, D. Database, Vol. 2012, Issue 0 https://doi.org/10.1093/database/bas041	journal	January 2012
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles Cejuela, J. M.; McQuilton, P.; Ponting, L. Database, Vol. 2014, Issue 0 https://doi.org/10.1093/database/bau033	journal	January 2014
Egas: a collaborative and interactive document curation platform Campos, D.; Lourenco, J.; Matos, S. Database, Vol. 2014, Issue 0 https://doi.org/10.1093/database/bau048	journal	January 2014
Text-mining-assisted biocuration workflows in Argo Rak, Rafal; Batista-Navarro, Riza Theresa; Rowley, Andrew Database, Vol. 2014 https://doi.org/10.1093/database/bau070	journal	January 2014
VIROME: a standard operating procedure for analysis of viral metagenome sequences Wommack, K. Eric; Bhavsar, Jaysheel; Polson, Shawn W. Standards in Genomic Sciences, Vol. 6, Issue 3 https://doi.org/10.4056/sigs.2945050	journal	July 2012
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
DISEASES: Text mining and data integration of disease???gene associations Pletscher-Frankild, Sune; Palleja, Albert; Tsafou, Kalliopi https://doi.org/10.1101/008425	preprint	August 2014
The gene normalization task in BioCreative III Lu, Zhiyong; Kao, Hung-Yu; Wei, Chih-Hsuan BMC Bioinformatics, Vol. 12, Issue S8 https://doi.org/10.1186/1471-2105-12-s8-s2	journal	October 2011
Comprehensive comparison of large-scale tissue expression datasets Santos, Alberto; Tsafou, Kalliopi; Stolte, Christian PeerJ PrePrints https://doi.org/10.7287/peerj.preprints.1072v1	posted_content	May 2015

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ezTag: tagging biomedical concepts via interactive learning Kwon, Dongseop; Kim, Sun; Wei, Chih-Hsuan Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky428	journal	May 2018
Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts Tsueng, Ginger; Nanis, Max; Fouquier, Jennifer T. Bioinformatics https://doi.org/10.1101/564187	journal	February 2019
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SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data Venkatesan, Aravind; Kim, Jee-Hyub; Talo, Francesco Wellcome Open Research, Vol. 1 https://doi.org/10.12688/wellcomeopenres.10210.1	journal	January 2016
MER: a Shell Script and Annotation Server for Minimal Named Entity Recognition and Linking Couto, Francisco M.; Lamurias, Andre Unpublished https://doi.org/10.13140/rg.2.2.29900.46727	text	January 2018
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data Venkatesan, Aravind; Kim, Jee-Hyub; Talo, Francesco Wellcome Open Research, Vol. 1 https://doi.org/10.12688/wellcomeopenres.10210.2	journal	January 2016
Crowdsourcing and curation: perspectives from biology and natural language processing Hirschman, Lynette; Fort, Karën; Boué, Stéphanie Database, Vol. 2016 https://doi.org/10.1093/database/baw115	journal	January 2016
Overview of the interactive task in BioCreative V Wang, Qinghua; S. Abdul, Shabbir; Almeida, Lara Database, Vol. 2016 https://doi.org/10.1093/database/baw119	journal	January 2016
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges Singhal, Ayush; Leaman, Robert; Catlett, Natalie Database, Vol. 2016 https://doi.org/10.1093/database/baw161	journal	January 2016
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw992	journal	October 2016
EXTRACT 2.0: text-mining-assisted interactive annotation of biomedical named entities and ontology terms Pafilis, Evangelos; Bērziņš, Rūdolfs; Jensen, Lars Juhl https://doi.org/10.1101/111088	preprint	February 2017

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