Frequently Asked Questions (FAQs)
- General Questions
- Questions targeted at Biologists
- Questions targeted at Computational Biologists and Software Developers
What is Pathway Commons?
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.
Is Pathway Commons free?
Yes, it's free! Pathway Commons distributes pathway content with the intellectual property restrictions of the source database. However, only databases that are freely available or free to academics are included.
Does Pathway Commons compete with other pathway databases?
No. 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.
What are the 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. We 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.
What is BioPAX?
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. More information is available at http://biopax.org.
What other standard pathway exchange formats are there?
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), which represent mathematical models of pathways, will be supported through a conversion to BioPAX format by the BioModels database group.
What will Pathway Commons not do?
Pathway Commons will not duplicate advanced features of source databases that are often optimized for the type of data and users specific to a source database. Examples include pathway visualization, certain advanced queries and all types of analysis tools. Users are encouraged to explore these features by following hyperlinks from Pathway Commons.
What pathway databases exist?
We have compiled a comprehensive list of pathway databases at Pathguide.
Will Pathway Commons support the Systems Biology Graphical Notation?
We believe a standard visual representation is crucial for the future of systems biology. We are actively involved in SBGN development and most BioPAX level 3 concepts can already be represented in SBGN Process Diagrams. We will start providing neighborhood maps in SBGN once we update our software and resolve remaining mapping issues.
How do I link to Pathway Commons?
Pathway Commons supports stable identifiers provided through source databases for Proteins (BioPax Level2 Protein PhysicalEntities). Stable links to Pathway Commons are provided through integrated external annotations (BioPax Level 2 UnificationXrefs) using the unique identifiers from databases Uniprot, Entrez Gene and RefSeq. To link to Pathway Commons using these identifiers, use the following URL http://www.pathwaycommons.org/pc/stable.do?db=X&id=Y where X can be one of: UNIPROT, ENTREZ_GENE or REFSEQ and Y is the identifiers defined within that resource.
For example, the URL below returns the Pathway Commons data for the protein P48754: http://www.pathwaycommons.org/pc/stable.do?db=UNIPROT&id=P48754. An example Entrez Gene ID URL would look like: http://www.pathwaycommons.org/pc/stable.do?db=ENTREZ_GENE&id=672. An example link RefSeq Acession number URL would look like: http://www.pathwaycommons.org/pc/stable.do?db=REFSEQ&id=NP_000312
Currently, stable identifiers to interactions and pathways are not available. The pathway commons database, cPath, uses internally generated identifiers (cPath IDs) for pathways, reactions, complexes and small molecules. These identifiers are unique within the cPath database, however, they are not stable between releases. We therefore, do not recommend linking to pathway commons with URLs that use cPath IDs.
Can I curate pathways with my own data in Pathway Commons?
Currently, pathway curation is not supported. Pathway commons retrieves data directly from established and well maintained pathway data sources. Pathway commons is reliant on data updates from these sources and the curation and maintenance protocols of the individual data providers. Curation is a non trivial task for which specific tools have been developed, a few of these are listed below.
What can I do with this information?
You can browse available pathway information and answer questions such as:
- What proteins interact with my favorite protein?
- What pathways involve my favorite protein?
- Is my favorite protein involved in transport events or biochemical reactions?
- What enzymes use my favorite metabolite as a substrate?
- And many more...
How were the pathways 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.
What kind of information 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. Some information is only available in the downloaded BioPAX files.
How good is the quality of Pathway Commons?
The quality of Pathway Commons pathways is 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.
How are Neighborhood Maps generated?
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. See the full description of Simple Interaction Format (SIF) for more information regarding the interaction type "INTERACTS_WITH" and other interaction types.
What can I do with this information?You can download the pathways in BioPAX Level 2 format for global analysis. Details about the BioPAX format
How many pathways are part of Pathway Commons?
Please see the statistics page for up to the minute information.
What is cPath?
cPath is open source database software that runs Pathway Commons website. You can download it for your own use from the cPath developer site.
Main features include:
- Import pipeline capable of aggregating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2, Reactome and others available in PSI-MI or BioPAX format.
- Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats.
- Data visualization and analysis via Cytoscape.
- Simple HTTP URL based XML web service.
- Complete software is freely available for local install. Easy to install and administer.
- Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG), and aims to meet "silver-level" requirements for software interoperability and data exchange.
Can I access Pathway Commons data via a web service?
Yes! A web service is available to answer specific queries with computer readable responses. This is designed to enable third party software and scripts to easily access the information.