ProMeTraWiki/PathwayMap: Difference between revisions
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== | == ProMeTra PathwayMaps == | ||
A | 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$$PathwayMap$pathway.png]] | |||
=== Annotate SVG elements using Inkscape === | === Annotate SVG elements using Inkscape === | ||
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* Open a SVG Pathway image in Inkscape | * Open a SVG Pathway image in Inkscape | ||
[[Image:ProMeTraWiki$$PathwayMap$inkscape.png]] | |||
* Select a rectangular image element (e.g. the Glycine rectangle as in the example) | * Select a rectangular image element (e.g. the Glycine rectangle as in the example) | ||
[[Image:ProMeTraWiki$$PathwayMap$glycine.png]] | |||
* Select XML Editor from the Edit Menu ... | * Select XML Editor from the Edit Menu ... | ||
[[Image:ProMeTraWiki$$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$$PathwayMap$xml.png]] | |||
=== Annotate SVG elements using a text Editor === | === Annotate SVG elements using a text Editor === | ||
You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite'' | You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite'' | ||
or ''Transcript'' identifiers to the rectangle elements manually. In the following example the ''Transcript'' element for the ''C.glutamicum'' gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a ''Metabolite'' (KEGG Compound C00441). | or ''Transcript'' identifiers to the rectangle elements manually. In the following example the ''Transcript'' element for the ''C.glutamicum'' gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a ''Metabolite'' (KEGG Compound C00441). | ||
[[Image:ProMeTraWiki$$PathwayMap$editor.png]] | |||
=== 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. | ||
Revision as of 16:26, 20 March 2012
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.
File:ProMeTraWiki$$PathwayMap$pathway.png
Annotate SVG elements using Inkscape
To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.
- Open a SVG Pathway image in Inkscape
File:ProMeTraWiki$$PathwayMap$inkscape.png
- Select a rectangular image element (e.g. the Glycine rectangle as in the example)
File:ProMeTraWiki$$PathwayMap$glycine.png
- Select XML Editor from the Edit Menu ...
File:ProMeTraWiki$$PathwayMap$xmleditor.png
- Add the Metabolite attribute and set the value to e.g. C00037
File:ProMeTraWiki$$PathwayMap$xml.png
Annotate SVG elements using a text Editor
You may also edit the SVG file (XML Format) with any text editor and add the Protein, Metabolite or Transcript identifiers to the rectangle elements manually. In the following example the Transcript element for the C.glutamicum gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a Metabolite (KEGG Compound C00441).
File:ProMeTraWiki$$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.