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AIC Seminar Series

Ingenuity Pathways Analysis: Research Applications of Systems

Ramon FelcianoIngenuity Systems[Home Page]

Notice:  hosted by Vinay Chaudhri

Date:  Thursday, June 19th 2008 at 4:00pm

Location:  EJ228 (SRI E building)  (Directions)


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. IPA’s 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

   Bio for Ramon Felciano

Dr. Felciano co-founded Ingenuity in 1998 and leads the company’s science and technology R&D efforts, holding the positions of Chief Technology Officer and Vice President, Research. Previous to founding Ingenuity, Dr. Felciano co-founded SUMMIT, the Stanford University Medical Media and Information Technologies lab, where he held the position of Associate Director. Dr. Ramon Felciano holds a Ph.D. and M.S. in Biomedical Informatics, a B.S. in Computer Science and a B.A. in English and French Literature from Stanford University. While at Stanford, Dr. Felciano performed research on interaction design, scientific information visualization, and distributed knowledge-based biomedical information systems. His doctoral research with Dr. Russ Altman focused on the automatic generation of knowledge-driven scientific information visualization. Dr. Felciano is a founding member of RiboWeb, one of the first to successful applications of semantic technologies to support to collaborative molecular biology over the Internet. Dr. Felciano’s other research efforts include Lamprey, a patented user tracking technology for the World Wide Web; and the study of Human Error in Medicine and its impact on the design of medical information systems. Dr. Felciano has authored several patents, articles and papers in Nature, Gene, ISMB, Briefings in Bioinformatics, AMIA, CHI, and STQE.

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