title: Concept annotation in the CRAFT corpus.
abstract: BACKGROUND
  Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.
  
  
  RESULTS
  This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement.
  
  
  CONCLUSIONS
  As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.
authors: Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. mike.bada@ucdenver.edu
authors: Michael
authors: M
authors: Bada
authors: Miriam
authors: M
authors: Eckert
authors: Donald
authors: D
authors: Evans
authors: Kristin
authors: K
authors: Garcia
authors: Krista
authors: K
authors: Shipley
authors: Dmitry
authors: D
authors: Sitnikov
authors: William A
authors: WA
authors: Baumgartner
authors: K Bretonnel
authors: KB
authors: Cohen
authors: Karin
authors: K
authors: Verspoor
authors: Judith A
authors: JA
authors: Blake
authors: Lawrence E
authors: LE
authors: Hunter
mesh_terms: D019295:Computational Biology / Q000379:methods; D057225:Data Mining; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods; D009323:Natural Language Processing; D012660:Semantics; D018875:Vocabulary, Controlled