Edinburgh Pathway Editor (EPE)

Category Cross-Omics>Pathway Analysis/Tools

Abstract EPE is a visual editor designed for the annotation, visualization and presentation of a wide variety of biological networks, including metabolic, genetic and signal transduction pathways.

It is based on a metadata driven architecture, which makes it very flexible in drawing, storing, presenting and exporting information related to the network of interest.

EPE allows visual representation to field standards Systems Biology Graphical Notation (SBGN), storage and retrieval of annotation data such as kinetic and other numerical data in relational databases (local and remote for enterprise development) and it links graphical objects to external databases and web resources to show all available information on demand.

1) EPE uses a small number of 'basic objects' to represent the main concepts of the 'biological network'.

"Shape" represents the ‘biological object’ or subsystem, treated as "a black box" with a number of Ports interfacing with it.

'Process' visualizes sequences of events e.g. a biochemical reaction or protein interaction.

'Link' is used to represent any pair-wise relation between objects including "identity" or "act on" relations.

'Label' is a visual object that is used to represent textual information and to allow links to other maps and resources.

The EPE concept of "Context" (see below...) separates metadata and visual standards from pathway maps and pathway data.

It allows one to tune the "drawing palette" for a selected type of map. With the context that one could create a new object with special customized properties.

The context is a collection of objects their properties and their default values. The context allows the user to create new objects on the basis of objects that exist.

The context property editor provides a great flexibility in the description of storage standards and the visual presentation.

Edinburgh Pathway Editor: Context --

One of the main advantages of the EPE is its ability to represent information using any visual notation. The key object to facilitate this ability is the Context of the map.

The Context is the main repository for the storage of the map metadata.

It defines a list of objects that will be used for drawing a map, visual and data properties of these objects, links to the external databases and default values.

In the future, the manufacturer will compare several contexts and maps created using different contexts.

2) There is a further type of info that is usually Not shown in visual representations of the pathway map.

It captures ‘toe provenance’ of the relations including literature annotation and links to databases corroborating the relationships depicted in the map.

This information is normally stored in the database or as annotation comments to the map.

EPE allows the user to customize the list of object properties, to store this data within an object, and to visualize it via linked pages or pop-up windows.

3) External database and ontology references are closely related to the annotation information.

4) EPE stores information about maps in a relational format [Relational Database Management Systems (RDBMS) format].

Apache Derby (Apache Derby is an open source relational database implemented entirely in Java) and Oracle are now supported by EPE as internal persistent storage.

Apache Derby is treated as local storage and Oracle could be used for enterprise sharing of information within a development team and for publishing.

Any other type of persistent storage could be implemented as a plug-in.

5) EPE supports data sharing and distribution through Open Database Connectivity (ODBC) and also through an open Extensible Markup Language (XML) export format.

The XML files can be used for archiving and backup.

Diagrams created with EPE, can be exported to common image formats including JPEG (JPEG is a commonly used method of compression for photographic images), Portable Network Graphic (PNG), WMF (Windows Meta Files) and Scalable Vector Graph (SVG) or saved as a fully functional and hyperlinked HyperText Markup Language (HTML) tree or as a model in the Systems Biology Markup Language (SBML) format.

6) EPE was created as an Eclipse stand-alone application, with the Eclipse open framework architecture. This enables the development of extensions to enhance its existing capabilities.

Specific plug-ins, to perform scientific computing and other tasks can be easily incorporated. For example, connection to external ontologies has been implemented using the plug-in architecture.

The default solution just opens reference URLs in a new browser window.

However, the Application Programming Interface (API) for external ontologies connections also allows users to create fully functional plug- ins with complex searching and visualization of external database content.

7) EPE allows users to create hyperlinks between maps, which makes it possible to organize information as a hierarchy of maps.

It makes the process of analysis and verification easier, by allowing you to focus on a small subset of data, covered by the whole model.

8) A Java-based architecture makes it possible to run EPE on different platforms from Mac to UNIX workstations.

XML-based export allows the easier exchange of diagrams and support for the Oracle-based RDBMS storage system allows team development of large scale models.

System Requirements

Contact manufacturer.


Manufacturer Web Site Edinburgh Pathway Editor

Price Contact manufacturer.

G6G Abstract Number 20464

G6G Manufacturer Number 104091