title: Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data.
abstract: The broadly defined mission of the Biomedical Informatics Research Network (BIRN, www.nbirn.net) is to better understand the causes human disease and the specific ways in which animal models inform that understanding. To construct the community-wide infrastructure for gathering, organizing and managing this knowledge, BIRN is developing a federated architecture for linking multiple databases across sites contributing data and knowledge. Navigating across these distributed data sources requires a shared semantic scheme and supporting software framework to actively link the disparate repositories. At the core of this knowledge organization is BIRNLex, a formally-represented ontology facilitating data exchange. Source curators enable database interoperability by mapping their schema and data to BIRNLex semantic classes thereby providing a means to cast BIRNLex-based queries against specific data sources in the federation. We will illustrate use of the source registration, term mapping, and query tools.
authors.affiliation: UC San Diego, La Jolla, CA, USA.
authors.forename: William
authors.initials: W
authors.lastname: Bug
authors.forename: Vadim
authors.initials: V
authors.lastname: Astahkov
authors.forename: Jyl
authors.initials: J
authors.lastname: Boline
authors.forename: Christine
authors.initials: C
authors.lastname: Fennema-Notestine
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Grethe
authors.forename: Amarnath
authors.initials: A
authors.lastname: Gupta
authors.forename: David N
authors.initials: DN
authors.lastname: Kennedy
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Rubin
authors.forename: Brian
authors.initials: B
authors.lastname: Sanders
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Turner
authors.forename: Maryann E
authors.initials: ME
authors.lastname: Martone
mesh_terms: D001927:Brain Diseases / Q000175:diagnosis* / Q000628:therapy*; D003628:Database Management Systems; D016208:Databases, Factual; D004282:Documentation / Q000379:methods; D033181:Information Dissemination / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D008490:Medical Informatics / Q000379:methods*; D009323:Natural Language Processing; D012107:Research Design; D057386:Search Engine; D012660:Semantics; D014481:United States