BioXM™ Knowledge Management Environment

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What's new in BioXM version 3.0?

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The BioXM Knowledge Management Environment, version 3.x.

Here, a graphical representation of a dynamically generated connectivity network is shown. The selection in the opened "Information Layer Chooser" changes the default graph style definitions to dynamically visualize the strength of the available evidence supporting the relations found. In addition, the genes shown in the graph are automatically colored according to their overall connectivity with any cancer disease, based on evidence obtained by a literature analysis

Dynamic visualization

BioXM version 3.3 introduces the possibility to select a background graphic specific for an information layer. The selected background can be saved together with the information layer settings as a graph state. This allows the creation of highly informative presentations of, for example, standard signaling or metabolic pathways similar to typical presentations in textbooks or other scientific publications.

The information layer chooser allows selection of any user-imported background graphic. Clicking "Manage Images..." allows the deletion or import of new background graphics. Only SVG files are supported as background graphics files.

A graphical representation of the "catabolism of hexose derivatives". This particular graph presents only the main metabolites and enzymes of this biochemical pathway; co-factors are hidden using the information layer filtering options.

In this graph, the same biochemical pathway as in the figure above is shown with the dynamic visualization of the information layer functionality used to overlay the results of an experiment series. The information about fold changes of the genes expressing the enzymes participating in this pathway are visualized by changing the color of the enzyme representation with measurements in the experiment series of interest.

A standard signaling pathway (here: type II diabetes mellitus pathway) with its components mapped to actual human genes. In this example, this standard pathway is used below to visualize the results of a series of gene expression experiments.

Using information layers, the graph shown in the standard signalling pathway (see figure above) is dynamically changed to visualize a genes participation in a specific cluster by changing the gene objects background color. In addition, the generated heat map is directly shown for the shown genes.

This screenshot shows a data matrix that was generated as the result of a series of gene expression experiments. In this example, cluster analysis scripts using R and BioConductor are integrated into the BioXM system using its analysis API, providing on the-fly reporting of cluster numbers and heat maps.

Association queries

This simple example shows how to use association queries for visualization of virtual relations in the BioXM graph viewer. The graph shows the drug albuterol as an instance of an entry from the NCI Thesaurus ontology. The "Display Associated Objects..." context-menu item allows the execution of the "Substance class members" association query for the selected "Anti-asthmatic Agent" ontology entry.

This screenshot shows the definition of the association query used in the previous figure. This simple query searches for all compounds classified by the NCI Thesaurus, including all compounds that are inferred from sub-classes of the selected ontology entry. The query builder allows fast and flexible creation of queries answering even very complex scientific questions.

This result view of the executed association query shows all inferred instances of the NCI Thesaurus "Anti-asthmatic Agent" entry as virtual relations. The visualization style of virtual relations (a dashed line is used in this example) can easily be configured.

This example shows the application of association queries without visualization of virtual relations. Here, three genes of interest are selected. Their "Display Associated Options" context-menu option allows the execution of an association query, user-configured specifically for objects of type "gene". This example, "Connecting Network" searches for an optimized network connecting the three genes of interest based on all known relationships of the global BioXM knowledge network using shortest path algorithms.

The association query "Connecting Network" searches for an optimized network connecting the three genes of interest. The network is created based on all known relationships of the global BioXM knowledge network using shortest path algorithms. This screenshot shows the result of executing the association query, displaying, for example, associated disease phenotypes based on literature-derived relations and other relations, such as functional classification using Gene Ontology (GO).

Data model viewer and graphical domain modeling

View of a user-configured data model. This simple example shows a data model specific for managing proteins and peptides and their relationships. The graph shows a selection of the "building blocks" a BioXM user can use to create and extend a scientific data model. Here, the semantic object types "Elements" and "Ontologies" are used. "MEDLINE" is integrated as external database using the BioRS Integration and Retrieval middleware.

BioXM version 2.0

BioXM main application window

The BioXM platform provides a user-defined project tree with full drag-and-drop functionality. Repositories provide easy access to all information for which a user has permission. A graphics panel provides the visualization for both browsing and drag-and-drop modeling.

BioXM query builder

The BioXM query builder allows the construction of complex queries to find information within the large network of knowledge. The query builder ensures the creation of correctly formulated queries by providing access to all valid search criteria. A query can be saved as template in which search parameters are defined as variables. Query templates provide easy answers to the most common questions without the need to construct complex queries repeatedly.

This query identifies all genes or proteins associated with lung cancer and returns all compounds or drugs inhibiting these genes.

This query searches for all patients diagnosed with adenocarcinoma, where a tissue sample was taken that has been a sample for an Affymetrix experiment.

This query searches for all genes associated with adenocarcinoma or any subtype of adenocarcinoma as defined by the NCI Thesaurus ontology.

BioXM graph visualization

A graphical overview displays the network of information managed within the BioXM platform. Selective expansion of information and easy navigation and browsing allow the exploration and use of knowledge derived from different scientific areas.

BioXM search result table

Query search results are displayed in a table, which can be configured to display relevant information. The user can switch between views with the drop-down menu at the top of every table view. Tables can be sorted and exported in different file formats. Subsets of the search results can be selected, annotated and put into a user-defined project folder.

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