KaBOB (Knowledge Base Of Biomedicine)
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kabob-build
kabob-core
kabob-dev
kabob-query
kabob-view
local-repository
scripts
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README.md
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README.md

KaBOB

KaBOB (Knowledge Base Of Biomedicine)

This library is associated with the publication:

KaBOB: Ontology-Based Semantic Integration of Biomedical Databases
Kevin M Livingston, Michael Bada, William A Baumgartner, Lawrence E Hunter
BMC Bioinformatics (2015, to appear)

Please cite when using.

KaBOB is built on top of the KR library, and numerous biomedical ontologies and data sources, which are parsed using the datasources library. KaBOB is primarily written in Clojure and is driven by Maven as well as a collection of Bash shell scripts.

The KaBOB code builds and manages a collection of RDF triples that allow querying of data using a common biomedical model based on the Open Biomedical Ontologies (OBOs). It iteratively loads triples into a triplestore and runs queries agains those triples to generate new triples, which are then loaded. (repeat)

Subdirectories:

  • scripts the primary scripts for running KaBOB
    to get a feel for a full load see build-kabob-ag.sh
    you can change your specific settings in ENV.sh
  • kabob-core primary KaBOB library and common code
  • kabob-build code specific for building KaBOB
    the rule files are also located here
  • kabob-dev primary developer entry point, useful for establishing a REPL

Other components (which maybe should be in indepnedent projects, although they are built sepeartely by Maven into independent jars):

  • kabob-query example queries and tools for common interactions
  • kabob-view incomplete, experimental web viewer for KaBOB data
  • local-repository a Maven setupo for plugging in Virtuoso

Acknowledgements

open sourced by:
CCP Lab
University of Colorado Denver
primary contact: Kevin Livingston
contributers: Bill Baumgartner, Mike Bada