BioXM™ Knowledge Management Environment

The BioXM™ Knowledge Management Environment is a fully customizable knowledge management (KM) solution for better integrated and knowledge-based drug discovery and development. This project-centered, distributed software platform provides a central inventory of information and knowledge. Users create, manage and visualize scientific models as an extendible network of interrelated concepts. The BioXM platform facilitates communication and collaboration within research environments, allowing you to focus on science.

One of the areas in which the BioXM platform has been used for knowledge management includes a project for the US National Cancer Institute (NCI) with Sophic Systems Alliance to create an up-to-date index of all human cancer-related genes, which includes compound and disease relationships.

Benefits for research

• Supports data-driven and hypothesis-driven research
• Supports decision making
• Connects and visualizes data, information and knowledge
• Facilitates new insights and new working hypothesis
• Enables full data integration for discovering novel relationships and patterns in biological networks
• Builds new data connections and networks on-the-fly
• Enhances existing data integration platforms (SRS, BioRS, etc.), for example, by adding a semantic layer describing data connectivity
• Enables mapping of proprietary knowledge on top of public ontologies

Benefits for corporations

• Provides a powerful KM solution for drug discovery development
• Supports decision makers
• Shares data and knowledge between individual user groups
• Enables full data integration, fast retrieval and complete visualization of both scientific and business data
• Captures relationships between any information: pharmacogenomics, epidemiology, patent data, translational medicine, etc.
• Provides maximum flexibility without additional programming
• Ensures fast return on investment

References

Maier D, Kalus W, Wolff M, Kalko S G, Turan N, Falciani F and Losko S (2008) The BioXM™ Knowledge Management Environment: a general and visually driven framework applied to the integration of large biological datasets. Bioinformatics Submitted
More information about the BioBridge Project

Sameith K, et al (2008) Functional Modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. Bioinformatics Advance Access, published online on September 17, 2008 Abstract

Gómez-Garrido A, et al (2008) Integration of transcriptomics data into systems biology modeling in the BioBridge portal. CCIS Series. Abstract

Ilgenfritz H, Kalus W, Heumann K and Losko S (2007) Modeling and exploration of biological networks using the BioXM Knowledge Management Environment. Presented at International Symposium on Networks in Biology. Amsterdam, The Netherlands PDF, 3 MB

Losko S, Wenger K, Kalus W, Ramge A, Wiehler J and Heumann K (2006) Knowledge Networks of Biological and Medical Data: An Exhaustive and Flexible Solution to Model Life Science Domains. Lecture Notes in Computer Science 4075: 232-239 Abstract

Ramge A, Losko S and Heumann K (2006) Integration of biological data using BioXM Knowledge Management Environment. Presented at Bioinformatics Munich: from Genomes to Systems Biology Workshop. Munich, Germany PDF, 1.2 MB

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Content partners

The BioXM software was developed in collaboration with RingRows GmbH, Martinsried.