BioXM Knowledge Management Environment

Category Cross-Omics>Biomarker Discovery/Tools

Abstract The BioXM™ Knowledge Management Environment is a fully customizable knowledge management solution for systems biology, evidence-based drug discovery, nutrigenomics and other areas such as translational medicine. This project-centered, distributed software platform facilitates communication and collaboration in a research environment.

Users create, manage and visualize scientific models as an extendible network of interrelated concepts describing a particular area of research.

Both public and proprietary information sources, such as public databases, experimental results, text-mining analyses or patient records can be integrated into one unified scientific model. The resulting model representing the accumulated knowledge of the specific domain can then be browsed and mined interactively.

Scientists conveniently stay in touch with recent additions or changes in knowledge that should be available to the entire organization while focusing specifically on generating knowledge in a particular field.

Note: Life science knowledge management -- The vast quantities of information generated by academic and industrial research groups are reflected in a rapidly growing body of scientific literature and exponentially expanding resources of formalized data, including experimental data from "-omics" platforms, phenotype information and clinical data.

Processes in biological systems are interrelated on many levels and their regulation presents a complexity that needs to be understood in detail to successfully manage risks in the development of products for the life science market.

Product features/capabilities include:

Data integration using semantic technologies -- The BioXM Knowledge Management Environment is designed for the aggregation and semantic modeling of scientific processes. Nearly every aspect of the BioXM system can be configured without the need to write new software or to know anything about relational database schemas. All configurations are done using the graphical user interface the BioXM client application provides.

1) The semantic of a scientific area of interest (e.g., clinical research) is captured by creating a network model of related, scientifically relevant elements.

2) The user can easily configure different element and relationship types, e.g., elements of type "gene" or "protein" can be linked together using a relation of type "gene regulation" or "protein-protein interaction".

3) A context (a region within the larger knowledge network) allows modeling and organization of pathways. Relationships between contexts and other semantic objects can be established.

4) Experimental data (e.g., expression data tables) can be integrated as specialized BioXM objects.

Research collaboration, information publishing and project management -- The BioXM Knowledge Management Environment provides both a central inventory of information and knowledge and a project-based, personalized work environment. This combination allows a scientist to design working models and annotate preliminary information that may be published later to a broader audience.

1) All semantic objects (e.g., relations or contexts) can be annotated.

2) Related information can be organized using configurable forms. The BioXM system supports many different attribute types, such as Text, Numeric, Date, Files, List of Values or Ontologies. Text files are indexed and automatically become searchable.

3) Hierarchical organization of these annotation forms enables complex data models [e.g., Minimum Information About a Microarray Experiment (MIAME) or The Physiotherapy Evidence Database (Pedro)].

4) Entire areas of interest can be organized through the use of ontologies. A variety of ontology formats are supported and the user can import multiple ontologies to create large semantic networks.

5) Versatile importers support a wide range of file formats, which make it easy to import networks and annotation.

Enterprise technology - a modular, scalable architecture -- The BioXM platform is a Java-based, client-server enterprise system. The primary user interface provides a comfortable, visual and highly interactive user experience.

The BioXM server has modular, open architecture, thus ensuring expandability and maintainability. Multiple hardware platforms and operating systems are supported.

The functionality of the BioXM system can be extended by adding optional modules. These are the virtual integration of public and proprietary scientific databases using the BioRS™ Integration and Retrieval System (see G6G Abstract Number 20180) and text-mining capabilities provided by the BioLT™ Literature Mining Tool (see G6G Abstractt Number 20093).

The BioLT tool combines biological and medical term dictionaries with advanced free-text querying capabilities, which allow building of special- interest knowledge bases.

To further ensure interoperability, applications can be built on top of the BioXM server using a Web Services Application Programming Interface (API). An external query mechanism allows users to extend the BioXM search engine with external tools, which provides, for example, connectivity with statistic tools or other analysis software.

System Requirements

Technical requirements of the minor release version 3.0 (199) of the BioXM™ Knowledge Management Environment.


Manufacturer Web Site BioXM Knowledge Management Environment

Price Contact manufacturer.

G6G Abstract Number 20179

G6G Manufacturer Number 100421