SEED Viewer Manual/OrganismPage - Revision history

TobiasPaczian: /* Browse, Compare and Download */

2008-11-18T14:48:46Z

Browse, Compare and Download

TobiasPaczian: /* Menu and General Information */

2008-11-18T14:39:02Z

Menu and General Information

TobiasPaczian: /* Menu and General Information */

2008-11-18T14:38:02Z

Menu and General Information

TobiasPaczian: /* Menu and General Information */

2008-11-18T14:35:25Z

Menu and General Information

DanielaBartels: /* Subsystem Information */

2008-11-18T14:28:38Z

Subsystem Information

DanielaBartels at 14:23, 18 November 2008

2008-11-18T14:23:55Z

DanielaBartels: /* Subsystem Information */

2008-11-18T14:13:47Z

Subsystem Information

DanielaBartels: /* Organism Page */

2008-11-18T14:03:33Z

Organism Page

DanielaBartels: /* Browse, Compare and Download */

2008-11-18T14:00:09Z

Browse, Compare and Download

DanielaBartels: /* Browse, Compare and Download */

2008-11-18T13:56:57Z

Browse, Compare and Download

@@ Line 30: / Line 30: @@
 '''Download'''
-This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page.
+This tab provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page.
 [[Image:OrgsDownload.png]]

@@ Line 5: / Line 5: @@
 Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].
-The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page).
+The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there is an existing Wikipedia page).
 If you click on '''click for full list''', you will find more specific information about the organism.

@@ Line 3: / Line 3: @@
 === Menu and General Information ===
-Two categories are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].
+Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].
 The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page).

@@ Line 3: / Line 3: @@
 === Menu and General Information ===
-Two menus are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].
+Two categories are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].
 The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page).

@@ Line 36: / Line 36: @@
 === Subsystem Information ===
-This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table|Table]].
+This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]].
 '''(1) Subsystem Statistics'''
-The leftmost bar chart (Subsystem Coverage) depicts the percentage of proteins from the selected organism that are in subsystems.
+The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems.
 In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category.
@@ Line 51: / Line 51: @@
 Click on the second tab of the tab view to get the tabular view of the Features in Subsystems.
-The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the gene name of all features in subsystems in the organism.
+The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism.

← Older revision		Revision as of 14:13, 18 November 2008
Line 37:		Line 37:

	This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table\|Table]].		This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table\|Table]].
		+
		+	'''(1) Graphical overview'''
		+
		+	The leftmost bar chart (Subsystem Coverage) depicts the percentage of proteins from the selected organism that are in subsystems.
		+
		+	In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category.
		+
		+	[[Image:OrgsSubsystems.png]]

← Older revision		Revision as of 14:03, 18 November 2008
Line 33:		Line 33:

	[[Image:OrgsDownload.png]]		[[Image:OrgsDownload.png]]
		+
		+	== Subsystem Information ==
		+
		+	This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all proteins in subsystems in a [[WebComponents/Table\|Table]].

@@ Line 17: / Line 17: @@
 '''Browse'''
-Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser] for the selected organism.
+Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.
 It lets you browse the features of your organism.
@@ Line 24: / Line 24: @@
 '''Compare'''
-Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page.
+Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link.
 [[Image:OrgsCompare.png]]
 '''Download'''
 [[Image:OrgsDownload.png]]