Pathway Commons

Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract Pathway Commons is a collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.

Access is via a web portal for browsing, query and download.

Database providers can share their pathway data via a common repository and avoid duplication and reduce software development costs.

Bioinformatics software developers can increase efficiency by sharing software components.

Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.

Pathway Commons does Not compete with or duplicate efforts of pathway databases or software tool providers. Pathway Commons will add value to these existing efforts by providing a shared resource for publishing, distributing and querying pathway information.

Existing database groups will provide pathway curation; Pathway Commons will provide a mechanism and the technology for sharing.

A vital aspect of Pathway Commons is clear author attribution. Curation teams at existing databases must be supported as much as possible by researchers to ensure they can keep performing their valuable work.

Pathway standard exchange format and others --

BioPAX, or Biological Pathway Exchange, is a standard exchange format for biological pathways. Pathway databases that make their data available in this format can be imported into Pathway Commons.

BioPAX is developed through a collaborative effort by many pathway databases.

Other pathway related standard exchange formats exist, each geared towards a unique type of pathway information.

Pathway Commons also currently supports the Proteomics Standards Initiative Molecular Interaction (PSI-MI) format, which stores molecular interactions, such as protein-protein interactions.

The Systems Biology Markup Language (SBML) and the Cell Markup Language (Cell-ML - see G6G Abstract Number 20293 and G6G Abstract Number 20294), which represent mathematical models of pathways, will be supported through a conversion to BioPAX format by the BioModels database group (see G6G Abstract Number 20295).

What biologists can be do with the Pathway Commons information --

You can browse available pathway information and answer questions such as:

How the pathways were collected --

Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction.

Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset.

The type of information that is part of each pathway --

Pathways from different databases are defined by different levels of detail.

Details that may be included are proteins, small molecules, DNA, RNA, complexes and their cellular locations, different types of physical interactions, such as molecular interaction, biochemical reaction, catalysis, complex assembly and transport, post-translational protein modifications, original citations, experimental evidence and links to other databases e.g. of protein sequence annotation.

Note: Some information is only available in the downloaded BioPAX files.

The quality of Pathway Commons --

The quality of ‘Pathway Commons’ pathways are dependent on the quality of the pathways from source databases.

Pathway Commons allows users to filter data by various criteria, including data source, which should allow viewing a restricted subset of high quality data.

In the future, Pathway Commons will implement published algorithms to automatically assess data quality and allow this as an additional filter.

Neighborhood Maps --

Pathway Commons displays ‘neighborhood maps’ for proteins. Each map displays the direct interactors of the protein.

The central circle (node) is the selected protein and neighbors are connected by lines colored according to Pathway Commons Simple Interaction Format (SIF) rules.

If the neighborhood map is greater than 200 nodes, Pathway Commons tries to reduce the size of the map by removing all nodes and edges whose interaction type is "INTERACTS_WITH".

Alternatively, you may define search filters to limit the results, which can also reduce the map size.

Pathway Commons Database Stats --

Number of Pathways: 1,493; Number of Interactions: 690,730; Number of Physical Entities: 110,210; Number of Organisms: 516.

Pathway Commons cPath --

cPath (see G6G Abstract Number 20098) is open source database software that runs the Pathway Commons website.

Future plans for Pathway Commons --

The Pathway Commons work group will provide software systems to collect, store and integrate pathway data from database groups, with clear author attribution; store, validate, index and maintain the information to enable efficient, maximum quality access; distribute pathway information to the scientific public; and, provide a basic set of end user software for browsing and analysis.

Pathway Commons will be adding more databases over time. Pathway Commons will also support additional types of pathway data, such as gene regulation, molecular states and genetic interactions as these features are added to BioPAX.

System Requirements



Manufacturer Web Site Pathway Commons

Price Contact manufacturer.

G6G Abstract Number 20366

G6G Manufacturer Number 104015