title: CharProtDB: a database of experimentally characterized protein annotations.
abstract: CharProtDB (http://www.jcvi.org/charprotdb/) is a curated database of biochemically characterized proteins. It provides a source of direct rather than transitive assignments of function, designed to support automated annotation pipelines. The initial data set in CharProtDB was collected through manual literature curation over the years by analysts at the J. Craig Venter Institute (JCVI) [formerly The Institute of Genomic Research (TIGR)] as part of their prokaryotic genome sequencing projects. The CharProtDB has been expanded by import of selected records from publicly available protein collections whose biocuration indicated direct rather than homology-based assignment of function. Annotations in CharProtDB include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. Each annotation is referenced with the source; ideally a journal reference, or, if imported and lacking one, the original database source.
authors.affiliation: J Craig Venter institute, 9704 Medical Center Drive Rockville, MD 20850, USA. rmadupu@jcvi.org
authors.forename: Ramana
authors.initials: R
authors.lastname: Madupu
authors.forename: Alexander
authors.initials: A
authors.lastname: Richter
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Dodson
authors.forename: Lauren
authors.initials: L
authors.lastname: Brinkac
authors.forename: Derek
authors.initials: D
authors.lastname: Harkins
authors.forename: Scott
authors.initials: S
authors.lastname: Durkin
authors.forename: Susmita
authors.initials: S
authors.lastname: Shrivastava
authors.forename: Granger
authors.initials: G
authors.lastname: Sutton
authors.forename: Daniel
authors.initials: D
authors.lastname: Haft
mesh_terms: D030562:Databases, Protein; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology
chemical_list: D011506:Proteins