Gold-standard ontology-based annotation of concepts in biomedical text in the CRAFT corpus: Updates and extensions

Michael Bada, Lawrence Hunter, Nicole Vasilevsky, Melissa Haendel

Research output: Contribution to journalConference articlepeer-review


Ontologies are increasingly used for semantic integration across disparate curated biomedical resources, while gold-standard annotated corpora are needed for accurate training and evaluation of text-mining tools. Bringing together the respective power of these, we created the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of full-length, open-access biomedical journal articles that have been manually annotated both syntactically and semantically with select Open Biomedical Ontologies (OBOs), the first release of which includes ∼100,000 annotations of concepts mentioned in the text of 67 articles and mapped to the classes of eight prominent OBOs. Here we present our continuing work on the corpus, including updated versions of these annotations with newer versions of the ontologies, new annotations made with two additional OBOs, annotations made with newly created extension classes defined in terms of existing classes of the ontologies, and new annotations of roots of prefixed and suffixed words.

Original languageEnglish (US)
JournalCEUR Workshop Proceedings
StatePublished - 2016
Event2016 Joint International Conference on Biological Ontology and BioCreative - Food, Nutrition, Health and Environment for the 9 Billion, ICBO-BioCreative 2016 - Corvallis, United States
Duration: Aug 1 2016Aug 4 2016


  • Annotation
  • Corpus
  • Markup
  • Ontology

ASJC Scopus subject areas

  • General Computer Science


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