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/.
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece, pafilis@hcmr.gr.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Pafilis
authors.affiliation: Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany.
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Buttigieg
authors.affiliation: Delaware Biotechnology Institute, Newark, DE 19711, Delaware, USA.
authors.forename: Barbra
authors.initials: B
authors.lastname: Ferrell
authors.affiliation: Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany.
authors.forename: Emiliano
authors.initials: E
authors.lastname: Pereira
authors.affiliation: Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Campus Ring 1, 28759, Bremen, Germany, and.
authors.forename: Julia
authors.initials: J
authors.lastname: Schnetzer
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
authors.forename: Christos
authors.initials: C
authors.lastname: Arvanitidis
authors.affiliation: Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark pafilis@hcmr.gr.
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D004463:Ecology / Q000379:methods*; D023281:Genomics; D006801:Humans; D020407:Internet; D056186:Metagenomics; D010641:Phenotype; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface