title: Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.
abstract: The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Arighi
authors.affiliation: Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, New York, United States of America.
authors.forename: Veronica
authors.initials: V
authors.lastname: Shamovsky
authors.affiliation: Department of Immunology, Duke University, Durham, North Carolina, United States of America.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Masci
authors.affiliation: School of Dental Medicine, State University of New York at Buffalo, Buffalo, New York, United States of America.
authors.forename: Alan
authors.initials: A
authors.lastname: Ruttenberg
authors.affiliation: Department of Philosophy and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America.
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.affiliation: Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D. C., United States of America.
authors.forename: Darren A
authors.initials: DA
authors.lastname: Natale
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America; Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D. C., United States of America.
authors.forename: Cathy
authors.initials: C
authors.lastname: Wu
authors.affiliation: Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, New York, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: D'Eustachio
mesh_terms: D000818:Animals; D064229:Biological Ontologies; D002645:Chickens; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D021381:Protein Transport; D015398:Signal Transduction; D051193:Toll-Like Receptors / Q000378:metabolism*
chemical_list: D051193:Toll-Like Receptors