Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract PathwayAccess is an extensible suite of CellDesigner plug-ins which connect CellDesigner - (see G6G Abstract Number 20159), directly to pathway databases using respective Java application programming interfaces (API’s).

The process is streamlined for creating new PathwayAccess plug-ins for specific pathway databases.

Three PathwayAccess plug-ins, MetNetAccess, BioCycAccess, and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc - (see G6G Abstract Number 20230), and Reactome - (see G6G Abstract Number 20267).

PathwayAccess plug-ins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases, and visually integrate pathway data from different databases using standard Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN).

PathwayAccess Functionality --

PathwayAccess plug-ins directly interacts with pathway databases so that the user can download one or more pathways to a CellDesigner model and upload (or commit) a CellDesigner model to a database.

The PathwayAccess plug-in framework confers three (3) major benefits, depending on whether individual database API’s support data retrieval and modification.

1) Firstly, the plug-ins makes pathways stored in remote databases available to the advanced modeling and simulation functionality already provided by CellDesigner.

2) Secondly, SBGN implemented by CellDesigner provides a standard representation for biologists to curate pathway databases; the user can create a pathway model and commit it to the database of their choice.

A user can also download a pathway model from a database, edit it, and commit it back to the database, either replacing the original pathway or creating a different version.

3) Thirdly, CellDesigner can be effective in visually comparing and integrating pathway data from one or many different databases; metabolic networks can be downloaded directly into CellDesigner and integrated into custom super-pathways.

CellDesigner can export pathways into files for loading into other software such as Cytoscape - (see G6G Abstract Number 20092), where SBGN is an ancillary feature to network analysis functions.

Note: Since CellDesigner and most data-sources' user interfaces provide good automatic layouts, layouts are left to the data-sources and CellDesigner independently.

PathwayAccess Pathway Integration across Databases --

When PathwayAccess plug-ins downloads pathways, they are integrated with the growing model in memory.

CellDesigner is suited to support integration because it uses the XML-based SBML data model Not only for file storage, but also for objects in memory - ideal for representing annotations integrated from different sources.

Among other annotations, PathwayAccess stores synonyms this way, enabling it to match integrated objects in the same subcellular compartment that may be named differently across databases.

To prevent duplicate reactions in integrated pathways, a ‘reaction hashing’ algorithm calculates a unique integer for every combination of reaction substrates, products, and catalysts.

Each PathwayAccess plug-in has a unique, but editable highlight color, which can be used to color the model objects, downloaded using that plug-in. Objects from multiple databases are colored by mixing the colors of the plug-ins that downloaded them.

PathwayAccess Creating New PathwayAccess Plug-ins --

The PathwayAccess framework includes a core library plus one or more independent plug-ins. A ‘plug-in developer’ can easily create a new CellDesigner plug-in which communicates with any pathway database providing a Java API.

Simply create a new CellDesigner plug-in object using the PathwayAccess library and define a set of simple database query operations, depending on whether the plug-in will support download and/or saving a model to the database.

To create a PathwayAccess plug-in which downloads a pathway, define 18 simple functions such as get the synonyms of an object (pathway, metabolite, gene, etc).

To design a commit feature, define nine (9) simple functions such as add substrates to a reaction in the database.

With these simple operations defined for communicating with a database, PathwayAccess handles all interaction both with CellDesigner and the database, similarly to Cytoscape’s Data Integration Request for Comments, and provides a way to enrich objects beyond the annotation used for integration.

PathwayAccess Impact --

The PathwayAccess suite of CellDesigner plug-ins is an advanced tool for researchers who work with ‘metabolic pathway’ data and wish to take advantage of graphical and computational CellDesigner features.

By directly accessing and publishing to pathway databases, decentralized pathway integration and comparison is made possible by simply saving and loading SBML files.

While three (3) PathwayAccess plug-ins have been released, the practical scope of the PathwayAccess library is as wide as the number of databases to which CellDesigner can connect because communication only requires a Java API.

MetNetAccess, BioCycAccess, ReactomeAccess and future PathwayAccess plug-ins enable CellDesigner users to expose pathway data to analytical CellDesigner functions as well as visually integrate and curate pathway data from different databases using standard SBGN - something which has been previously prevented by disparate in-silico representations of biological objects.

System Requirements

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Manufacturer Web Site PathwayAccess

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G6G Abstract Number 20643

G6G Manufacturer Number 104241