Building gold standard corpora for medical natural language processing tasks.

Journal Article (Journal Article)

We present the construction of three annotated corpora to serve as gold standards for medical natural language processing (NLP) tasks. Clinical notes from the medical record, clinical trial announcements, and FDA drug labels are annotated. We report high inter-annotator agreements (overall F-measures between 0.8467 and 0.9176) for the annotation of Personal Health Information (PHI) elements for a de-identification task and of medications, diseases/disorders, and signs/symptoms for information extraction (IE) task. The annotated corpora of clinical trials and FDA labels will be publicly released and to facilitate translational NLP tasks that require cross-corpora interoperability (e.g. clinical trial eligibility screening) their annotation schemas are aligned with a large scale, NIH-funded clinical text annotation project.

Full Text

Duke Authors

Cited Authors

  • Deleger, L; Li, Q; Lingren, T; Kaiser, M; Molnar, K; Stoutenborough, L; Kouril, M; Marsolo, K; Solti, I

Published Date

  • 2012

Published In

Volume / Issue

  • 2012 /

Start / End Page

  • 144 - 153

PubMed ID

  • 23304283

Pubmed Central ID

  • PMC3540456

Electronic International Standard Serial Number (EISSN)

  • 1942-597X


  • eng

Conference Location

  • United States