PathwayMap - Revision history

Admin: 3 revisions

2011-10-26T06:18:44Z

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← Older revision	Revision as of 08:18, 26 October 2011
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imported>HeikoNeuweger at 20:17, 9 March 2009

2009-03-09T20:17:37Z

← Older revision		Revision as of 22:17, 9 March 2009
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	__NOTOC__		__NOTOC__
	[[ProMeTra]] [[PathwayMaps]]		== [[ProMeTra]] [[PathwayMaps]] ==

	A [[PathwayMap]] in [[ProMeTra]] is a SVG image designed using e.g. Inkscape which additionally contains		A [[PathwayMap]] in ProMeTra is a SVG image designed using e.g. Inkscape which additionally contains
	some labeled rectangles. The labeling defines which experimental data associated to		some labeled rectangles. The labeling defines which experimental data associated to
	entities from functional genomics (transcripts, proteins, metabolites) can be represented		entities from functional genomics (transcripts, proteins, metabolites) can be represented
	inside the image.		inside the image. Users can add other graphical elements such as lines, shapes, and text to SVG [[PathwayMaps]], only the specially labeled elements will be modified by ProMeTra.

	[[Image:PathwayMap$pathway.png]]		[[Image:PathwayMap$pathway.png]]

			=== Annotate SVG elements using Inkscape ===

	To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.		To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.
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	[[Image:PathwayMap$xmleditor.png]]		[[Image:PathwayMap$xmleditor.png]]

	* Add the 'Metabolite' attribute and set the value to e.g. C00037		* Add the ''Metabolite'' attribute and set the value to e.g. C00037

	~~[[Image:PathwayMap$attribute.png]]~~

	[[~~Media~~:PathwayMap$~~sample~~.~~svg~~]]		[[Image:PathwayMap$xml.png]]

	~~[[Image:PathwayMap$xml.png]]~~		=== Annotate SVG elements using a text Editor ===

	You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite''		You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite''
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	[[Image:PathwayMap$editor.png]]		[[Image:PathwayMap$editor.png]]

			=== Data connection ===

			ProMeTra will be able to identify the attributes ''Protein'', ''Metabolite''
			or ''Transcript'' in your rectangular SVG elements and use the associated identifiers (e.g. C00037) to connect to
			experimental datasets that users upload or obtain from MeltDB, ProSE or Emma2 via WebServices.

imported>HeikoNeuweger at 20:05, 9 March 2009

2009-03-09T20:05:02Z

← Older revision		Revision as of 22:05, 9 March 2009
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	To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.		To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.

			* Open a SVG Pathway image in Inkscape

			[[Image:PathwayMap$inkscape.png]]

			* Select a rectangular image element (e.g. the Glycine rectangle as in the example)

			[[Image:PathwayMap$glycine.png]]

			* Select XML Editor from the Edit Menu ...

			[[Image:PathwayMap$xmleditor.png]]

			* Add the 'Metabolite' attribute and set the value to e.g. C00037

			[[Image:PathwayMap$attribute.png]]

			[[Media:PathwayMap$sample.svg]]

	[[Image:PathwayMap$xml.png]]		[[Image:PathwayMap$xml.png]]

			You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite''
			or ''Transcript'' identifiers to the rectangle elements manually. In the following example the ''Transcript'' element for the ''C.glutamicum'' gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a ''Metabolite'' (KEGG Compound C00441).

			[[Image:PathwayMap$editor.png]]

imported>HeikoNeuweger at 19:47, 9 March 2009

2009-03-09T19:47:46Z

New page

__NOTOC__
[[ProMeTra]] [[PathwayMaps]]

A [[PathwayMap]] in [[ProMeTra]] is a SVG image designed using e.g. Inkscape which additionally contains
some labeled rectangles. The labeling defines which experimental data associated to
entities from functional genomics (transcripts, proteins, metabolites) can be represented
inside the image.

[[Image:PathwayMap$pathway.png]]

To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.

[[Image:PathwayMap$xml.png]]