Virtual Journal discontinued 2015
In June 2015, the Virtual Journal was discontinued as part of Science Signaling. With the availability of many articles either through open access or without a fee 6-12 months after publication, the value of this feature was diminished. For more details please see the Virtual Journal help page.
Database of Cell Signaling archived 2015
In June 2015, Science Signaling archived the graphical interface into the Database of Cell Signaling. Although the Database is useful for novices interested in exploring canonical pathways, the scope of the networks and complexity of the regulatory events involved in cellular signaling pathways has outstripped the architecture of the Database. AAAS decided to focus efforts in other areas of scientific communication and is not redeveloping or updating the data in the Database or the data entry software. However, for those readers interested in the data that was available as of the most recent update, the XML files of the data in the Database are now available without any special licensing restrictions for academic users. Academic users are individuals at academic or public or governmental research institutions performing non-commercial research and development. These files are available in Systems Biology Markup Language (SMBL) Level 2 version 1.
Note there was an error in the pathways XML files (an attribute was empty that should not have been present in the XML). An updated version of the files has been made available as of 13 November 2015:
- Description of the XML Files and Schema for the Data in SBML
- XML Files from the most recent update 8 February 2012
Questions, including those pertaining to non-academic use of the database, may be directed to firstname.lastname@example.org.
Overview of the Database Structure
The data are organized into "Canonical Pathways," idealized or generalized pathways that represent common properties of a particular signaling module or pathway, and "Specific Pathways," instances in which components are known to act together in a particular organism, tissue, or cell type. Pathway Authorities entered canonical and specific components into the Database and then incorporated these components into pathways. Each component has a minimum set of information that is independent of any pathway in which it appears. This is the "pathway-independent" component information and is found in the “components” XML file. Once components are placed in a pathway, they acquire additional "pathway-dependent" component information, which is part of the information found in the “pathways” XML files. Each pathway has a unique identifier and its own XML file. Only specific components can participate in specific pathways and only canonical components can participate in canonical pathways. Each specific component has a canonical component "parent". Various elements in the data are derived from controlled vocabularies and are each item in a controlled vocabulary has a unique identifier that is used in the component XML and pathway XML files. The information about the controlled vocabularies is in the “vocabularies” XML file. The “users” XML file is a list of the contributors and editors and developers who have updated data in the Database and these are referenced in the components and pathways XML files.