Evaluating the automatic mapping of human gene and protein mentions to unique identifiers.
We have developed a challenge task for the second BioCreAtIvE (Critical Assessment of Information Extraction in Biology) that requires participating systems to provide lists of the EntrezGene (formerly LocusLink) identifiers for all human genes and proteins mentioned in a MEDLINE abstract. We are distributing 281 annotated abstracts and another 5,000 noisily annotated abstracts along with a gene name lexicon to participants. We have performed a series of baseline experiments to better characterize this dataset and form a foundation for participant exploration.
Morgan
Alexander A
AA
MITRE Corporation, 202 Burlington Road Bedford, MA 01730, USA. alexmo@stanford.edu
Wellner
Benjamin
B
Colombe
Jeffrey B
JB
Arens
Robert
R
Colosimo
Marc E
ME
Hirschman
Lynette
L
D019295:Computational Biology; D030541:Databases, Genetic; D030562:Databases, Protein; D015894:Genome, Human; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D016239:MEDLINE; D040901:Proteomics / Q000706:statistics & numerical data