Systems Reconstruction (SR) technology for knowledge management and OMICS data analysis

At GeneGo, we believe that pathway analysis of inherently complex high-throughput biological and chemistry data must be based on a fundamental understanding of human and mammalian biology. That requires technology and expertise. Over the last 9 years, we have developed a unique approach of systems reconstruction™ for extracting invaluable knowledge from experimental articles and patents, structuring it in computer-readable form and storing in a semantically consistent database. The “knowledge” - derived data, represented as ontologies, protein interactions and gene-disease associations, signaling and metabolic pathways, normal and pathology process models, can then be used for functional analysis of OMICs datasets by series of bioinformatics and cheminformatics software tools such as network generation algorithms, ontology enrichment, interactome calculations, pathway modeling, QSAR models etc.

To accommodate the complex aspects of mammalian functionality - such as coordinated expression of multiple genes to bring about a prescribed function, gene alleles in form of SNPs and mutations, RNA splice variants, protein isoforms, complexes, and families - GeneGo has developed a database of novel architecture. The key aspect of its data schema is semantic consistency between the entities from as different fields of study as human genetics, medicinal chemistry, toxicity, systems biology and translational medicine. This consistency, based on combining standard and proprietary ontologies, unique controlled vocabulary and a comprehensive ID system, enables application of sophisticated analytical and search tools, not available in public domain or from other vendors.