BioXM™ Knowledge Management EnvironmentData integration using semantic technologies The BioXM...
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Agile solution building for life science enterprises BioXM™ Knowledge Management Environment Semantic data integration made easy The BioXM™ platform is a fully customizable knowledge management solution for life science research. It provides a central inventory of information and knowledge integrated in a unified scientific model. Users create, manage and visualize their model as an extendible network of interrelated concepts describing a particular area of research. > Integrate public information and proprietary data — from ontologies to high-throughput experimental results to business information > Keep repositories of scientific objects, e.g., a gene index, a patient registrer, a phenotype catalog, a compound and drug database > Connect clinical data, study information and statistical analysis results with molecular data from early drug discovery > Use the BioXM graphical front end to integrate statistical methods such as R and BioConductor Focus on science The resulting model represents the accumulated knowledge of a scientific domain. The model can be browsed and mined interactively. Researchers can focus on science and make connections that were not previously apparent. > Find novel links between related biological processes based on your experimental results > Identify biomarker candidates based on automated literature analysis and compare the results with your data > Generate connectivity networks based on a selection of relationship types from multiple sources in a single step > Visualize relationships between information sets: nutrigenomics, epidemiology, patient data, translational medicine, etc. > Inspire new insights and ground-breaking working hypotheses Connect, communicate and collaborate This project-centered, distributed software platform facilitates communication and collaboration within research environments. Scientists easily stay in touch with recent additions or changes in knowledge made available to the entire organization. > Share data and knowledge between user groups > Keep track of ongoing projects with one-click smart folders generating reports and overviews of your project's key objects > Organize, review, compare, annotate and modify biological pathways originating from different sources > Define rule sets how scientific objects interact with each other and associate evidences from public sources and your experiments > Flexibly adapt to new advances in research, without programming effort Integrate Connect Create Product Profile BioXM visualization of relations between patients, compounds, diseases and genes BioXM Web App reporting compound data
Transcript of BioXM™ Knowledge Management EnvironmentData integration using semantic technologies The BioXM...
Agile solution building for life science enterprises
BioXM™ Knowledge Management Environment
Semantic data integration made easyThe BioXM™ platform is a fully customizable knowledge management solution for life science research. It provides a central inventory of information and knowledge integrated in a unified scientific model. Users create, manage and visualize their model as an extendible network of interrelated concepts describing a particular area of research.
> Integrate public information and proprietary data — from ontologies to high-throughput experimental results to business information > Keep repositories of scientific objects, e.g., a gene index, a patient registrer, a phenotype catalog, a compound and drug database > Connect clinical data, study information and statistical analysis results with molecular data from early drug discovery > Use the BioXM graphical front end to integrate statistical methods such as R and BioConductor
Focus on scienceThe resulting model represents the accumulated knowledge of a scientific domain. The model can be browsed and mined interactively. Researchers can focus on science and make connections that were not previously apparent.
> Find novel links between related biological processes based on your experimental results > Identify biomarker candidates based on automated literature analysis and compare the results with your data > Generate connectivity networks based on a selection of relationship types from multiple sources in a single step > Visualize relationships between information sets: nutrigenomics, epidemiology, patient data, translational medicine, etc. > Inspire new insights and ground-breaking working hypotheses
Connect, communicate and collaborateThis project-centered, distributed software platform facilitates communication and collaboration within research environments. Scientists easily stay in touch with recent additions or changes in knowledge made available to the entire organization.
> Share data and knowledge between user groups > Keep track of ongoing projects with one-click smart folders generating reports and overviews of your project's key objects > Organize, review, compare, annotate and modify biological pathways originating from different sources > Define rule sets how scientific objects interact with each other and associate evidences from public sources and your experiments > Flexibly adapt to new advances in research, without programming effort
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BioXM visualization of relations between patients, compounds, diseases and genes BioXM Web App reporting compound data
Biomax and BioXM are registered trademarks of Biomax Informatics AG in Germany and other countries. Java is a trademark of Oracle Corporation and its affiliates.Registered names, trademarks, etc., used in this document, even when not specifically marked as such, are not to be considered unprotected by law.
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Data integration using semantic technologiesThe 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 configuration is done using the graphical user interface the BioXM client application provides.
> The semantic of a scientific area of interest (e.g., clinical research) is captured by creating a network model of related, scientifically relevant elements.
> 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".
> A context (a region within the larger knowledge network) allows modeling and organiza- tion of pathways. Relationships between contexts and other semantic objects can be established.
> Experimental data (e.g., expression data tables) can be integrated as specialized BioXM objects.
Research collaboration, information publishing and project managementThe 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.
> All semantic objects (e.g., relations or contexts) can be annotated. > 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.
> Hierarchical organization of these annotation forms enables complex data models. > 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.
> Versatile importers support a wide range of file formats, which make it easy to import networks and annotation.
A modular, scalable architectureThe BioXM platform is a Java™-based, client–server enterprise system. The BioXM server has modular, open architecture, thus ensuring expandability and sustainability. Multiple hardware platforms and operating systems are supported. The primary client application provides a comfortable, visual and highly interactive experience for advanced users and administrators right on their workstation desktops. In addtion, the BioXM system provides an alternative, web browser-based client for quick deployment of preconfigured solutions.
The BioXM system allows publishing browser-based Web Apps that dynamically access the semantic network maintained by the BioXM enterprise server, thus providing an easy-to-use frontend for untrained users. The BioXM Web Apps automatically adapt to the device and web browser used. The BioXM responsive design web publishing framework allows administrators to easily publish BioXM smart folders, reports and graphs, and enables users to interactively browse, annotate, add and modify content in the knowledge environment.
Patient Disease
TissueSample
ExpressionExperiment
Gene
Drug
NCI Thesaurus
GO
EC
PDQ
“Diagnosis”
“Disease Association”
“Drug Association”
“Medication”
“Sampling”
“Expression Profiling”
“Study Participation”“Trial Subject”
“Treatment”
Data model sketch
Graphical model in the BioXM system
BioXM™ Knowledge Management Environment
BioXM Web Apps adapt to the device used
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