Announcing a new interactive pathway viewer at WikiPathways

[Kristina Hanspers]

We are pleased to introduce a new interactive pathway viewer at
WikiPathways as part of the latest release (milestone 30).

This viewer is now incorporated in each pathway page and allows you to
drag the pathway or zoom to interesting parts. You can also search and
highlight elements in the pathway and get link-outs to other databases
in the backpage. All features of the viewer are described in detail
below.

== Basic functionality ==
- You can drag the pathway to pan, scroll to zoom and click on a gene
box to see the backpage.
- Use the search box to find elements in the pathway. Search hits are
highlighted in yellow while typing and clicking enter will focus the
view on the relevant element and highlight it.
- The search box can be hidden by clicking the magnifier icon next to
it.

== Highlighting ==
- You can specify elements that should be highlighted in a url, for
example:

http://test.wikipathways.org/index.php?title=Pathway:WP4&label=CRH&xref=8525,Entrez%20Gene

- Highlights are organized into a box on the left with an entry for
each highlight. Clicking one of the highlights focuses the viewer on
the corresponding element on the pathway.
- The url parameters for highlighting can be "label" (to match by text
label) or "xref" (to match by xref, format: id,datasource).

- You can specify multiple parameters to highlight multiple items. You
can also specify an array of highlight colors using the color
parameter:

http://test.wikipathways.org/index.php?title=Pathway:WP4&label=CRH&xref=8525,Entrez%20Gene&label=invalid&label=DAG&colors=red,orange,green

- Labels or xrefs that can't be located on the pathway are shown in
gray ("label=invalid" in the example above). Id mapping is not
performed for xrefs, only exact matches are highlighted.

== Backpage ==
- Selecting an element in the pathway displays its backpage in the
left side panel.
- The back page is organized into sections for each system and
contains link-outs to all cross-references for the xref
- To find other pathways with the selected element, click the "Find
pathways with..." link at the top of the back page. This initializes a
search at WikiPathways for the element.

== Pathway widget ==
You can also directly access a full-page version of the viewer on via
a specific url:

http://test.wikipathways.org/wpi/PathwayWidget.php?id=WP4

This is convenient for full-screen viewing, or for including the
viewer in any web page through an iframe. Details are available here:
http://test.wikipathways.org/index.php/PathwayWidget


Regards,

WikiPathways team