Science Signaling Database of Cell Signaling

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

Abstract The Database of Cell Signaling provides information on the components of 'cellular signaling pathways' and their relations to one another, which are organized into pathways called 'Connections Maps', which also serve as the graphical interface into the database.

Scientists with expertise in a given field, designated as 'Pathway Authorities', provide the information. With canonical or general data about 'cell signaling', as well as specific data about particular signaling processes in specific organisms and cells, there is information for both novices to cell signaling and experts.

Connections Maps -- The Connections Maps are dynamically generated graphical interfaces to a database of information on the components of cellular signaling pathways and their relations to one another.

Database Structure -- The Connections Maps provide information on "Canonical Pathways" -- idealized or generalized pathways that represent common properties of a particular signaling module or pathway.

Also recorded are "Specific Pathways" -- instances in which components are known to act together in a particular organism, tissue, or cell type.

Pathway Authorities enter canonical and specific components into the database and then incorporate 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 of information.

Once components are placed in a pathway, they acquire additional "pathway-dependent" component information. It is this information that is accessed by clicking on any of the component symbols in a pathway diagram.

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".

Links at the top of the pathway-dependent component information pages can take you to the pathway-independent component information. As you navigate from a pathway, you will first arrive at a pathway-dependent component record.

From that page, you can use the links to the pathway-independent information, which provides general information about the component including links to canonical component parent information.

Pathway Display -- Two (2) display options are available for the dynamically generated pathway diagrams - a Graphics Interchange Format (GIF) display and a Scalable Vector Graphics (SVG) display.

The SVG display is available for Windows users at the present time and provides some additional navigational cues that are Not available with the GIF display.

However, the SVG display requires a free plug-in from Adobe and is limited in its compatibility with browsers and operating systems.

Note: The plug-in does Not work with Mac running Safari or IE, nor with Netscape 6.0 on Windows. Mac users should use IE without downloading the SVG plug-in to load the GIF display of the pathway.

Windows users with the 'Adobe SVG plug-in' installed can view the pathways with an interactive set of tools that allow users to:

1) Zoom in;

2) Zoom out;

3) Move around (pan) in the map of the pathway;

4) Return to the map's original orientation;

5) View text descriptions of the components and relations by mousing over the map;

6) Click on the components and relations to view more detailed information about the components and relations;

7) See colored relations when navigating through components shared in more than one pathway (inter-pathway connections).

Without the SVG plug-in, you will continue to be able to click on the component and relation symbols to access the detailed information and navigate among pathways through inter-pathway connections.

Component Symbols Inter-path links (diamond-shaped components) are special relationships that are defined by the Pathway Authorities who identify signaling components and cascades that are shared by more than one pathway.

Clicking on a diamond-shaped component will take you to the other pathway through an Authority-defined inter-path relation. Rectangle-shaped components are a placeholder used by Authorities to define a collection of related signaling components that participate in a pathway.

Other components are oval shaped and can be either single-subunit protein components, components with multiple subunits that act as a complex, or non-protein components, such as lipids, ions, or chemical mediators.

Pathway Walking -- As components in the database are incorporated into multiple independent pathways, all the other components with which a given component interacts and all of the pathways in which these interactions occur are displayed in tables in the pathway- dependent component records.

One can also see the pathways in which a component participates in a table in the pathway-independent component records. Pathway Walking thus begins to uncover the signaling "hubs" and the network properties of the cellular signaling world.

Relations -- Authorities can provide an opinion on the strength of the evidence that a particular Relation is biologically meaningful. They choose between four (4) degrees of certainty: Speculative, Implied, Strongly Implied, or Demonstrated.

Citations -- Links to full text of papers (when available within the Science Signaling) cited on data pages or links to the Medline database of abstracts for the pathways, pathway-dependent and pathway- independent component information, and relations are available when chosen by the Pathway Authority.

Also, links to nucleotide or protein sequence data in the Entrez database or links to other external databases are available when selected by the Pathway Authority.

Access to the Connections Maps database through the Science Signaling website is available free with registration.

The Connections Maps data in SBML-compatible XML and XML schema documentation is available.

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