Terms, Software Tips & Data Attributes
The Connections Maps provide a graphical interface to a database of information on components of cellular signaling pathways and their relations. Pathway Authorities recruited by the editorial staff of Science Signaling provide the information in the database.
- Canonical -- idealized or generalized information that represent common properties of a particular signaling component or pathway
- Specific -- examples of components and pathways from a particular organism, tissue, and cell type
- Component -- the basic element in the database, containing information about the molecules that participate in cellular signaling
- Relation -- a description of the interaction between components, the symbols in the pathway maps represent effects on signaling activity: stimulatory (+), inhibitory (-), undefined effect (?), or neutral (without effect on the biochemical activity of the target component) (0)
- Pathway -- the organization of components into a cascade with information about the interactions between the components
- Pathway-independent information -- general information about a component that is not limited to a particular pathway
- Pathway-dependent information -- information that is relevant to the function of that component in the context of the particular pathway
The Pathways are displayed in two possible formats: SVG and GIF. The SVG display is available for Windows PC 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 SVG and is limited in its compatibility with browsers and operating systems. 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.
If you are using Windows with an Adobe SVG-compatible browser (IE), you can view the pathways with an interactive set of tools that allow you to
- Zoom in
- Zoom out
- Move around in the map of the pathway
- Return to the map's original orientation
- View text descriptions of the components and relations by mousing over the map
- Click on the components and relations to view more detailed information about the components and relations
Without the SVG plug in, a GIF image will display and you will continue to be able to click on the component and relation symbols to access the detailed information.
If are experiencing problems viewing the SVG versions of the pathways on a Windows computer using IE. Please try the following steps:
- Go to Add/Remove programs in the Control Panel
- Remove Adobe SVG viewer
- Restart your computer
- Open a brower and download the viewer again from the Adobe SVG site
- Close all browser windows
- Open IE and navigate to a Connections Maps pathway
Attributes of the Data Records
- Pathway Boundaries-- Boundaries are arbitrary and reflect the Authorities' preferences for beginning and ending points.
- Relation Certainty-- Authorities can provide an opinion on the strength of the evidence that a particular Relation is biologically meaningful. They choose from four degrees of certainty: Speculative, Implied, Strongly Implied, or Demonstrated.
- Literature Citations-- The literature citations represent a subset of the literature selected by the Authorities to represent key papers and references useful for understanding the pathways, components, or relations. Links to full text of papers (when available within Science Signaling) or links to the Medline database of abstracts are provided for literature cited in Pathway, Component, or Relation records.
- Database Citations-- Links to nucleotide or protein sequence data in the Entrez database are available for many components, as well as links to certain other organismal databases.
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The data in the Database of Cell Signaling in SBML-compatible XML and XML schema documentation are now available. Please refer to the terms for use and use the Request for Data form to obtain the proper license for academic or commercial users.