Background: The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene name may refer to different genes (often from different organisms). For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes. We provided 281 expert-annotated abstracts containing 684 gene identifiers for training, and a blind test set of 262 documents containing 785 identifiers, with a gold standard created by expert annotators. Inter-annotator agreement was measured at over 90%.

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.

Exponential growth of the peer-reviewed literature and the breakdown of disciplinary boundaries heralded by genome-scale instruments have made it harder than ever for scientists to find and assimilate all the publications relevant to their research. The widespread adoption of title/abstract word search, primarily through the National Library of Medicine's PubMed system (http://www.ncbi.nlm.nih.gov/pubmed), was the first major change in the way bioscientists found relevant publications since the origin of Index Medicus in 1879. (Although it remains useful for locating pre-1966 literature (Hersh, 2003), Index Medicus ceased publication in 2004.) However, PubMed is only the beginning of a revolution in how scientists use the biomedical literature. Computational tools that classify documents, extract factual information, generate summaries, and generally process human language are providing powerful new tools for staying on top of the torrent of publications. The biomedical literature is growing at a double-exponential pace; over the last 20 years, the total size of MEDLINE (the database searched by PubMed) has grown at a ~4.2% compounded annual growth rate, and the number of new entries in MEDLINE each year has grown at a compounded annual growth rate of ~3.1% (see Figure 1). There are now more than 16,000,000 publications in MEDLINE; more than three million of those were published in the last 5 years alone. The number of MEDLINE entries with a 2005 publication date was 666,029-more than 1800 per day. Large as MEDLINE is, it captures only bibliographic information and abstracts. Electronic access to the full texts, including graphics and figures, is also on the rise, and sophisticated linkages between publications and data repositories or other supplementary materials increase the amount of information available still further. Although online full-text materials are increasingly prevalent, dramatic increases in subscription prices and decreases in library budgets have paradoxically decreased access for some researchers. Toll-free linking, where copyright owners allow free search but charge per view, is one approach to ameliorating this problem. An alternative strategy toward this goal is the recent establishment of a movement toward a new "Open Access" model of scientific publishing. On April 11, 2003, a group of individuals interested in promoting open access to the scientific literature drafted a statement of principles that is

Motivation: Knowledge base construction has been an area of intense activity and great importance in the growth of computational biology.