RegenBase: A Searchable Database to Organize Regeneration Knowledge via Ontologies

Vance Lemmon, University of Miami School of Medicine

The RegenBase Project is to develop a novel information system to seamlessly
integrate diverse data that are produced by neuroscientists and cell biologists
studying nerve regeneration in the context of spinal cord injury system injury
with other resources, such as the Neuroscience Information Framework and the
BioAssay Ontology.

Tremendous progress has been made during the last decade developing semantic
web technologies with the goals of formalizing knowledge, linking information
across different domains, and integrating large heterogeneous data sets from
diverse sources.  To develop RegenBase on a fast-track with limited resources,
we will leverage technologies and tools from the National Center for Biological
Onotology and the recently launched BioAssay Ontology.  The long-term goal of
the RegenBase system is seamless “on-the fly” data integration and analysis
via a semantic “Linked Data" approach that is scalable with respect to
information volume and complexity.  RegenBase will incorporate biomedical
domain-level ontologies, including our recently developed BioAssay Ontology
(BAO), to semantically associate related data types and to provide a knowledge
context of the underlying experiments and screening outcomes.

The overarching goal of this proposed RegenBase system is to allow bench
scientists to link data and results from studies on nervous system injury and
disease to data and knowledge from other domains with an emphasis on molecular
targets, biological pathways and the small molecules that perturb their
function to speed the development of novel therapeutics.