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

Research output: Contribution to journalJournal articleResearchpeer-review

  • Evangelos Pafilis
  • Pier Luigi Buttigieg
  • Barbra Ferrell
  • Emiliano Pereira
  • Julia Schnetzer
  • Christos Arvanitidis
  • Jensen, Lars Juhl

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/.

Original languageEnglish
Article numberbaw005
JournalDatabase: The Journal of Biological Databases and Curation
Number of pages7
Publication statusPublished - 2016

ID: 157550561