ProMeTraWiki/PathwayMap - Revision history

Alu: /* Annotate SVG elements using Inkscape */

2012-03-21T09:19:50Z

Annotate SVG elements using Inkscape

← Older revision		Revision as of 11:19, 21 March 2012
Line 15:		Line 15:
	* Open a SVG Pathway image in Inkscape		* Open a SVG Pathway image in Inkscape

	[[File:~~ProMeTra_PathwayMap_inkscape~~.png]]		[[File:Prometra Inkscape inkscape.png]]

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

Alu at 09:16, 21 March 2012

2012-03-21T09:16:34Z

← Older revision		Revision as of 11:16, 21 March 2012
Line 7:		Line 7:
	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.		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~~:~~ProMeTraWiki$$PathwayMap$pathway~~.png]]		[[File:ProMeTra_PathwayMap_pathway.png]]

	=== Annotate SVG elements using Inkscape ===		=== Annotate SVG elements using Inkscape ===
Line 15:		Line 15:
	* Open a SVG Pathway image in Inkscape		* Open a SVG Pathway image in Inkscape

	[[~~Image~~:~~ProMeTraWiki$$PathwayMap$inkscape~~.png]]		[[File:ProMeTra_PathwayMap_inkscape.png]]

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

	[[~~Image~~:~~ProMeTraWiki$$PathwayMap$glycine~~.png]]		[[File:ProMeTra_PathwayMap_glycine.png]]

	* Select XML Editor from the Edit Menu ...		* Select XML Editor from the Edit Menu ...

	[[~~Image~~:~~ProMeTraWiki$$PathwayMap$xmleditor~~.png]]		[[File:ProMeTra_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~~:~~ProMeTraWiki$$PathwayMap$xml~~.png]]		[[File:ProMeTra_PathwayMap_xml.png]]

	=== Annotate SVG elements using a text Editor ===		=== Annotate SVG elements using a text Editor ===
Line 34:		Line 34:
	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).		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~~:~~ProMeTraWiki$$PathwayMap$editor~~.png]]		[[File:ProMeTra_PathwayMap_editor.png]]

	=== Data connection ===		=== Data connection ===

Alu at 15:26, 20 March 2012

2012-03-20T15:26:28Z

Admin: 2 revisions

2011-10-26T06:14:55Z

2 revisions

← Older revision	Revision as of 08:14, 26 October 2011
(No difference)

imported>HeikoNeuweger at 15:25, 13 March 2009

2009-03-13T15:25:57Z

← Older revision		Revision as of 17:25, 13 March 2009
Line 5:		Line 5:
	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. 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.		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:ProMeTraWiki$$PathwayMap$pathway.png]]		[[Image:ProMeTraWiki$$PathwayMap$pathway.png]]

imported>HeikoNeuweger at 21:40, 9 March 2009

2009-03-09T21:40:52Z

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. 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:ProMeTraWiki$$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.

* Open a SVG Pathway image in Inkscape

[[Image:ProMeTraWiki$$PathwayMap$inkscape.png]]

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

[[Image:ProMeTraWiki$$PathwayMap$glycine.png]]

* Select XML Editor from the Edit Menu ...

[[Image:ProMeTraWiki$$PathwayMap$xmleditor.png]]

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

[[Image:ProMeTraWiki$$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''
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:ProMeTraWiki$$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.

← Older revision		Revision as of 17:26, 20 March 2012
Line 1:		Line 1:
	__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. 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.		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:ProMeTraWiki$$PathwayMap$pathway.png]]		[[Image:ProMeTraWiki$$PathwayMap$pathway.png]]

	=== Annotate SVG elements using Inkscape ===		=== Annotate SVG elements using Inkscape ===
Line 15:		Line 15:
	* Open a SVG Pathway image in Inkscape		* Open a SVG Pathway image in Inkscape

	[[Image:ProMeTraWiki$$PathwayMap$inkscape.png]]		[[Image:ProMeTraWiki$$PathwayMap$inkscape.png]]

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

	[[Image:ProMeTraWiki$$PathwayMap$glycine.png]]		[[Image:ProMeTraWiki$$PathwayMap$glycine.png]]

	* Select XML Editor from the Edit Menu ...		* Select XML Editor from the Edit Menu ...

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

	=== Annotate SVG elements using a text Editor ===		=== 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''
	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).		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:ProMeTraWiki$$PathwayMap$editor.png]]		[[Image:ProMeTraWiki$$PathwayMap$editor.png]]

	=== Data connection ===		=== Data connection ===

	ProMeTra will be able to identify the attributes ''Protein'', ''Metabolite''		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		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.		experimental datasets that users upload or obtain from MeltDB, ProSE or Emma2 via WebServices.