BiblioSphere PathwayEdition Release Notes

2011: BiblioSphere has been discontinued and will not be updated anymore

BiblioSphere has been replaced by the Genomatix Pathway System GePS. All licensed users will be able to continue to use the software until the end of their license term. We encourage you to switch to GePS, however, as it offers the full functionality of BiblioSphere plus additional unique features. To make the transition as smooth as possible for you, we have compiled a "BiblioSphere to GePS" transition guide that will help you get started with the Genomatix Pathway System.

December 2010: BiblioSphere Release 7.24

Data update

Gene annotation based on ElDorado 12-2010

February 2010: BiblioSphere Release 7.23

Data update

Gene annotation based on ElDorado 02-2010

July 2009: BiblioSphere Release 7.22

Data update

Gene annotation based on ElDorado 07-2009

New Organisms

Arabidopsis thaliana
Drosophila melanogaster (beta version)
Saccharomyces cerevisiae
Schizosaccharomyces pombe

November 2007: BiblioSphere Release 7.1

New Filter

Signal Transduction Pathway Association Filter:
The new filter restricts the BiblioSphere to sentences that define a relation to an annotated signaling pathway gene and contain at least one signaling keyword.

New External Links

Signal transduction pathways now contain links to external pathway maps from BioCarta, KEGG, and STKE for many pathway components.

June 2007: BiblioSphere Release 7.0

New Data Sources

NetPro database
The new version integrates Molecular Connection's NetPro™ database of expert curated protein interactions into BiblioSphere networks.

New Filters

Expert Curated:
The new level filters for connections between genes that have been approved by experts from Genomatix or MolecularConnections (NetPro™).

Features of previous releases:

Data Sources

Pathways from Science's Signal Transduction Knowledge Environment
Genomatix has integrated the Connections Maps of Science's Signal Transduction Knowledge Environment stke into BiblioSphere Pathway Edition. This enables the user to map the genes in his network to known signal transduction pathways, and retrieve detailed information about their function.
Genomatix Expert Curated Gene-Gene Relations
Genomatix has integrated its proprietary knowledge-base of expert curated data on gene regulation into BiblioSphere Pathway Edition. This unique data source adds the semantics of gene-gene relationships to the dynamically generated BiblioSphere gene networks, providing information like "Gene A activates transcription of gene B" or "Gene A physically interacts with gene B".
Signal Transduction Pathways
Portions of Gene Ontology relevant to signal transduction as well as data compiled from literature have been combined to enable the identification of canonical pathways linked to the focused network.
Metabolic Pathway Associations
Metabolic pathway associations from BioCyc have been integrated to allow the identification of metabolic events relevant to your set of genes.
Homonym distinction
Distinction between homonyms (by context analysis).

Views

Pathway View with stke pathway associations:
Find genes associated with stke signal transduction pathway, and launch the new Canonical Pathway View to map them onto an interactive pathway diagram.
Canonical Pathway View
Based on Science's Connections maps expert curated pathways that are connected to your BiblioSphere network can be displayed. Genes that belong to your BiblioSphere network can be identified by their label. Clicking on a gene or a connection line launches the Browser to display detailed background information at the stke website.
Pathway View with expert curated gene-gene relationships
Gene groups are compiled into easily comprehensible dynamic network graphs combining hand curated gene-gene relationships with data derived from automated knowledge extraction. Networks can be customized by filters and focused in a gene centered way to perform shortest path analysis.
Cellular Localization View
Based on GO Annotations genes are assigned to their subcellular location and visualized as a diagrammed cell layout, allowing you to identify subcellular regions and compartments relevant to your gene set.
View of expression ratios
Expression ratios of micro array experiments can be read from Excel files allowing user-adjustable color coding for superimposition with gene-gene and pathway associations.
Gene-Gene Connections
The spreadsheet view of cocitations contained in a BiblioSphere contains links to the Cocitation Browser and supplies the functionality to export data for further analysis with external applications.
TF Analysis
The TF Analysis component displays the results of MatInspector analysis for transcription factor binding sites in the promoters of cocited genes and links to promoter analysis with GEMS Launcher.
Filter Statistics
For each hierarchical filter added to a BiblioSphere a spreadsheet with statistical analysis of overrepresented annotations is displayed.
Documents
This view component directly links to each PubMed abstract in your BiblioSphere.
BiblioSphere 3D
The 3D-view of the BiblioSphere now contains a "Gene Radar" for easier navigation.

Filters

Hierarchical Filters
Hierarchical filters (GOFilter, MeSHFilter, TissueFilter) now support multiple selection. Each hierarchical filter displays overrepresented annotations and has a corresponding statistical view component.
GOFilter
The GOFilter was divided into the three subcategories "molecular function", "biological process" and "cellular component".
MeSHFilter
The MeSHFilter filters the documents actually contained in your BiblioSphere. Documents that meet the filter criteria can be retrieved via the integrated Documents view component.
FreeTextFilter
The new FreeTextFilter supports boolean queries and offers field sensitive fulltext search of the documents contained in your BiblioSphere.
User data filter for expression values
You can set a range of expression values to be excluded from an uploaded data file. (E.g. if you want to have very high and very low expression values only.) For multi-class data files, this filter can be applied separately for each column.

Other features

Search Functions
BiblioSpheres can be built from fulltext pubmed queries, MeSH term queries or lists of pubmed ids.
Integration of user defined gene annotation
The new Version allows integrating user defined gene annotation (e.g. gene to pathway assignments) which can be displayed as additional information in gene relation networks.
Project Management
Manage your analyses by organizing them into project folders. Quickly access previous results with a few mouse clicks or add new searches to existing projects.
Multi-column data upload
Upload of multi-class data files containing more than one column of data is possible.