ArticleBMC bioinformatics2012
Concept annotation in the CRAFT corpus.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers, 2 of them syntheses that pooled it.
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Who cites it
92 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Cancer-Alterome: a literature-mined resource for regulatory events caused by genetic alterations in cancer.Scientific data · 2024Article
- Use of Natural Language Processing to Identify Sexual and Reproductive Health Information in Clinical Text.Methods of information in medicine · 2023Article
- Europe PMC annotated full-text corpus for gene/proteins, diseases and organisms.Scientific data · 2023Article
- Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII.Database : the journal of biological databases and curation · 2023Article
- Features of lexical complexity: insights from L1 and L2 speakers.Frontiers in artificial intelligence · 2023Article
32 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
backgroundManually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.
resultsThis 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.
conclusionsAs 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.