What is Pathway Commons?
Pathway Commons aims to collect and disseminate biological pathway and interaction data. Data is collected from partner databases and is represented in the BioPAX standard. By representing data in BioPAX, Pathway Commons is able to provide a detailed representation of a variety of biological concepts including: Biochemical reactions; gene regulatory networks; and genetic interactions; transport and catalysis events; and physical interactions involving proteins, DNA, RNA and small molecules and complexes.
Is it free to use?
Yes. All of the data provided by Pathway Commons is free! In particular, Pathway Commons distributes pathway information with the intellectual property restrictions of the source database; Only databases that are freely available for academics are included. All of the software that we provide is open-source.
What can I do with this information?
How can I access the data?
Does Pathway Commons compete with other pathway databases?
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, querying, and analyzing pathway information. Existing database groups will provide pathway curation, Pathway Commons will provide a mechanism and the technology for sharing. A key aspect of Pathway Commons is clear author attribution. Curation teams at existing databases must be supported by researchers to ensure they can keep performing their valuable work. Pathway Commons enables database providers to share their data in an efficient manner by avoiding duplication of effort and reducing software development overhead.
How is the data in Pathway Commons represented?
Pathway Commons uses the Biological Pathway Exchange (BioPAX) standard to represent data. 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.
What kind of biological concepts are represented?
Pathway Commons leverages the richness and versatility of BioPAX to store data. Details that can be included are biochemical reactions; gene regulatory networks; genetic interactions; proteins, small molecules, DNA, RNA, complexes and their cellular locations; complex assembly and transport; post-translational protein modifications; citations; experimental evidence; and links to other databases e.g. protein sequence annotation. Some information is only available in the downloaded BioPAX files.
How were the pathway data integrated?
Pathway data are downloaded directly from source databases. Each source has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Warehouse data (canonical molecules, ontologies) are converted to BioPAX utility classes and saved as the initial BioPAX model, which forms the foundation for integrating data and for id-mapping. Pathway and binary interaction data (interactions, participants) are normalized next and merged into the database. Original reference molecules are replaced with the corresponding BioPAX warehouse objects.
What happened to the old Pathway Commons site?
The legacy site has not been updated since 2011 and is not actively maintained.
We are a data provider. Why should we export our data to BioPAX?
Benefits of exporting your data to BioPAX and distributing it via Pathway Commons include: