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The "omics" revolution has generated reams of data increasingly isolated
from the broader biological context in which it exists. Systems biology,
through combined application of system sciences, life sciences and
informatics, aims to create a more holistic understanding of biological
systems to better enable discovery of biologically-driven diagnostics
and therapeutics. We will describe our efforts to deliver the promise of
systems biology through large-scale, high-fidelity acquisition,
structured modeling, and computational management of scientific
knowledge and biomedical ontologies.
Ingenuity Pathway Analysis (IPA) is a software application that enables
biologists and bioinformaticians to model complex biological systems by
identifying and exploring biological mechanisms, pathways and functions
relevant to their experimental datasets and drug discovery research
questions. IPAs algorithmic analytics integrate functional and physical
relationships such gene regulations, protein-protein interactions,
post-translational modifications, and drug-target interactions at the
gene, protein, cellular and tissue levels. The results provide
semantically-consistent representations of biochemical pathways and
biological functions implicated by empirical data sets, and help
scientists to compile panels of biomarkers for follow-on screening
assays. This technology has been successfully deployed to 10,000s of
life sciences researchers at all major pharmaceutical and research
organizations worldwide, with applications throughout the drug discovery
process, from early stage target ID and validation, to later stage
activities such as toxicology, pharmacogenomics, biomarker
identification, and alternative indications of approved drugs.
IPA is built on the Ingenuity Knowledge Platform (IKP), a semantic
knowledge representation platform that contains a large-scale,
manually-curated, ontologically-structured database of experimental
findings describing millions of relationships between proteins, genes,
complexes, cells, tissues, drugs, and diseases. We will describe the
core capabilities of IPA and its research applications, and as well as
provide an "under the hood" view of the IKP technology. IPA is available
for evaluation at http://www.ingenuity.com/.
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