KaPPA-View 4
The Kazusa Plant Pathway Viewer, Version 4.0

Manual on User Map Creationver. 1.0

Kazusa DNA Research InstituteContents

Contents

1. INTRODUCTION ............................................................................................... 1
1-1. Outline .......................................................................................................................... 1
1-2. Installing Inkscape ....................................................................................................... 1
1-3. Recommended Settings .............................................................................................. 5

2.CREATING AND SAVING FILES ....................................................................... 8
2-1. Creating a File .............................................................................................................. 8
2-1-1. Set the image size to 800 x 600 pixels .............................................................................. 8

2-2. Saving a File ................................................................................................................ 9
2-2-1. Save a file in the "Plain SVG" format ................................................................................. 9

3. CREATING OBJECTS AND ASSIGNMENT OF IDS ...................................... 11
3-1. Creating an Object ..................................................................................................... 11
3-1-1. Setting of Stroke and Fill .................................................................................................. 12

3-2. Setting ID ................................................................................................................... 14
3-2-1. Attention .......................................................................................................................... 15

4. CREATING MAP OBJECTS ........................................................................... 17
4-1. Gene .......................................................................................................................... 17
4-1-1. Creating an Object ........................................................................................................... 17
4-1-2. Adding IDs ....................................................................................................................... 18

4-2. Gene Box ................................................................................................................... 19
4-2-1. Creating an Object ........................................................................................................... 20
4-2-2. The Orientation of a Gene Box and the Order of a Gene Symbol ................................... 23
4-2-3. Adding IDs ....................................................................................................................... 24

4-3. Compound ................................................................................................................. 24
4-3-1. Creating an Object ........................................................................................................... 24
4-3-2. Adding IDs ....................................................................................................................... 26

4-4. Enzymatic Reaction ................................................................................................... 27
4-4-1. Creating an Object ........................................................................................................... 27
4-4-2. Adding IDs ....................................................................................................................... 32

4-5. Link to Another Map ................................................................................................... 32ii

KaPPA-View4 Manual on User Map Creation

4-5-1. Creating Objects .............................................................................................................. 32
4-5-2. About conversion of a text to outlines .............................................................................. 36
4-5-3. Adding IDs ....................................................................................................................... 37

5. OTHER OBJECTS .......................................................................................... 39
5-1. Grouped Object .......................................................................................................... 39
5-1-1. Grouping Objects Together ............................................................................................. 39
5-1-2. Coloring Rule of Grouped Objects ................................................................................... 40

5-2. Font ............................................................................................................................ 41
5-2-1. Standard Font: Arial ......................................................................................................... 41
5-2-2. Using Other Fonts............................................................................................................ 41
5-2-3. Conversion of a text to outlines ....................................................................................... 41

5-3. Text Object ................................................................................................................. 42
5-4. Image ......................................................................................................................... 42
5-5. Creating Line and circle Objects with Inkscape ......................................................... 43
5-5-1. Creating Line Objects ...................................................................................................... 44
5-5-2. Creating Circle Objects .................................................................................................... 47
5-5-3. Loading Templates .......................................................................................................... 49

6. USING USER MAPS ON KAPPA-VIEW4 ....................................................... 50
6-1. Checking behavior of User Map ................................................................................ 50
6-1-1. Accessing to KaPPA-View4 ............................................................................................. 50
6-1-2. Uploading User Map for checking .................................................................................... 51
6-1-3. Browsing User Maps on KaPPA-View4 ........................................................................... 53
6-1-4. Registering User Maps on KaPPA-View4 (for Power Users) ........................................... 54

6-2. Sending User Maps to KaPPA-View4 Administrators (for Power Users） ................. 54
6-2-1. Sending a User Map ........................................................................................................ 55
6-2-2. Note ................................................................................................................................. 56

7. OTHERS.......................................................................................................... 58
7-1. About Us .................................................................................................................... 58
Team KaPPA-View .................................................................................................................... 58

7-2. Acknowledgements .................................................................................................... 58
7-3. References ................................................................................................................. 58
7-4. Manual Version .......................................................................................................... 58

APPENDICES ..................................................................................................... 59iii

Contents

Appendix A. List of Recommended Settings of Objects ................................................... 59
Appendix B. List of ID formats of Objects ......................................................................... 62

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KaPPA-View4 Manual on User Map Creation

1. Introduction
KaPPA-View4 Classic (http://kpv.kazusa.or.jp/kpv4/) is a metabolic
pathway database for representation and analysis of correlation networks ofgene co-expression and metabolite co-accumulation and omics data (Sakurai etal., 2011 Nucleic Acids Research 39: D677-684). In addition to the pathway maps
available as default, users can utilize their own map data for their analyses. Thisfunction extends the possibility of KaPPA-View4, for analyzing metabolic
pathways not provided as default, for analyzing with carefully curated metabolic
maps, for investigating about genes and metabolites not drawn on the default
maps, and for making attractive data representations.
This manual describes procedures to create the map data that can be loaded
onto KaPPA-View4. Refer to "Advanced Manual" or "Beginners' manual" formore details on KaPPA-View4 functions and operations.

1-1. Outline
The pathway maps of KaPPA-View4 were prepared as files in Scalable Vector
Graphics (SVG) format. The SVG data are exchanged to Flash objects when they
displayed on the Internet browsers. To realize the color painting of the gene,metabolite and reaction symbols according to the omics data analyzing, eachsymbol on the SVG maps has to be distinguished by the system, and therefore,
each symbol must have an identifier that described in a defined rule.
Inkscape (http://www.inkscape.org/) is one of free software suitable forcreating SVG data that enables editing of the IDs. It works on multiple platforms,
has various drawing functions, and used by many users. In this manual, we
describe the procedures for map data creation using Inkscape ver.0.46 forWindows. Please refer to the online manual of the Inkscape for the usage of thetool itself.

1-2. Installing Inkscape11. Introduction

Inkscape is a free open-source drawing software. This manual introduces
Inkscape ver. 0.46.
Go to the following URL.
http://www.inkscape.org/

Click “Download” in the menu on the left.

Select the installer for Windows.

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KaPPA-View4 Manual on User Map Creation

A page in Source forge opens, and then download automatically starts.
Click “direct link” if download doesn’t start.

Save the installer (Inkscape-0.46.win32.exe) on your local disk.

Double click the installer to start installing.

Click on "Install".

3

1. Introduction

Click “Next” to accept the license agreement.

Click “Next.”
Users can customize the component of the program by altering the settings suchas selecting languages in "translation".

Choose install directory and click “Install.”Installation proceeds.

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KaPPA-View4 Manual on User Map Creation

Click "Finish"

Click "Finish" again then Inkscape starts.

The initial page is shown below.

1-3. Recommended Settings
Following setting will allow users even more efficient map creation.
Click “File” and select "Inkscape Preferences..."5

1. Introduction

Click "Transform" and set the values as follows.
Item

Operation

Description

Scale stroke width

Uncheck

The line width stays constant
while the object size is modified.

Scale rounded corners

Checkin rectangles

The radius of the round angles
proportionally resized with
object size change.

Transform gradientsCheck

The gradients (color gradations)
are moved along with theobjects, facilitates users torecognize the direction of thegene boxes when they arerotated.

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KaPPA-View4 Manual on User Map Creation

Click “Close.”This setting can be changed also from the menu on the main window.

72. Creating and Saving Files

2.Creating and Saving Files
This section introduces basic conventions of the SVG files to be displayed
properly on KaPPA-View4. Please refer to the following sections for creating
individual objects.

2-1. Creating a File

2-1-1. Set the image size to 800 x 600 pixels
KaPPA-View4 uses the image size of 800(width) by 600(height) pixels as default.
We strongly recommend choosing this image size, because various functions suchas Multiple Map View and printing maps are optimally processed with the image
size.
Start Inkscape. Click “File” and select “Document Properties...”Type 800 into "Width", 600 into "Height", and select “px” for the unit. Then click“Close.”8

KaPPA-View4 Manual on User Map Creation

2-2. Saving a File

2-2-1. Save a file in the "Plain SVG" format
Click “File” and select “Save As...” to save the SVG map created.

Choose “Plain SVG” for the format of the file. Don't choose other formats.
Give a file name and click "Save" button.

92. Creating and Saving Files

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KaPPA-View4 Manual on User Map Creation

3. Creating Objects and Assignment of IDs
By adding appropriate IDs to the figures drawn on Inkscape (objects),
KaPPA-View4 system paints the objects in proper colors according to theexperimental values such as changes of gene expressions and metabolite
accumulations. In this section we introduce the basic operation of Inkscape tocreate objects and assignment of the IDs to them.

3-1. Creating an Object
An "object" is a drawing created on the Inkscape canvas. Create an object byclicking the toolbox on the left of the window and then doing appropriate mouse
operations on the canvas.

The tools commonly used for creation of User Maps of KaPPA-View4 are as
follows.
"Create rectangles and squares" tool
"Draw Bezier curves and straight lines" tool
"Create and edit text objects" tool11

3. Creating Objects and Assignment of IDs

A square object created with "Create rectangles and squares" tool will look likebelow.

The color of the stroke and fill may vary depending on the environment of yourPC.

3-1-1. Setting of Stroke and Fill
An Inkscape object consists of a closed area and the line surrounding it. They arecalled fill and stroke respectively.

•Color Setting
Set the color of stroke and fill by clicking “Object” in the menu and selecting “Filland Stroke...” Clicking the button shown below works as well.

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KaPPA-View4 Manual on User Map Creation

Color setting must be done in order to realize dynamic color painting by the
KaPPA-View4 system according to the experiment data.

By selecting No paint button () of "Fill and Stroke" window users can choose

not to color the object. Please note that the color won’t be shown according to thedata under this setting. For instance, select white or any other preferred color
and avoid no paint for the fill when drawing a square that represents a gene.
When drawing a curved arrow that shows enzymatic reaction, select no paint for
the fill so that the color of inner area of the arc doesn’t change.

•Stroke Style and Stroke Tip Shape
Inkscape provides functions to change the stroke style and tip shape, but the line
style and, start, middle, and end point markers aren’t shown appropriately in
KaPPA-View4. When creating an arrow for such as enzymatic reactions create
the arrowhead and the line of an arrow as two separate objects and group them
together (see 4-4. Enzymatic Reaction and 5-1. Grouped Objects). Dotted lines
can be created with a line drawn as a line object. (see 5-5. Creating Line andcircle Objects with Inkscape).

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3. Creating Objects and Assignment of IDs

disabled for
KaPPA-View
maps

3-2. Setting ID
In order to allow the KaPPA-View4 system to color the objects according to theexperiment data. ID acceptable to the system must be attached to each object.
Assignment of IDs to the objects is done with XML Editor.
Click “Edit“ of the menu and select “XML Editor...” or simply click the button
shown below to open an XML Editor window.

The XML editor and the canvas interlock with each other. Any item selected on
the XML editor will be selected on the canvas as well and vice versa.

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KaPPA-View4 Manual on User Map Creation

The selected item will be highlighted on the left side of the XML editor, and theattributes of the selected object will be line up on the right side of the editor.
When “id” from the Attribute list is selected, present value of the id will be
displayed in the lower right window. Type a proper value into the area circled redin the figure below, and click "Set" to assign the value as the ID of the object.

3-2-1. Attention
The following care must be taken when attaching an ID to an object.

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3. Creating Objects and Assignment of IDs

1) One SVG file cannot contain more than one objects of the same ID attribute.
When identical ID is added to a different object, the ID of the object thatoriginally had the now shared ID will be automatically changed to the default ID.
It is often the case that the users want to draw one compound on several places ofa map. In such cases, group the objects together and assign an ID to the grouped
objects. The procedure is covered in 5-1. Grouped Objects.
2) The ID input area allows newline characters (returns), but KaPPA-View4
cannot properly process the inserted newline characters. Carefully set IDs not toinsert any spaces or newline characters before or after the ID.
3) Please be sure to press "Set" to confirm the change after typing the ID. If the"Set" button isn’t clicked the value won’t be reflected. Check the upper-right areaof the XML editor window to see if the ID value is properly changed.
4) Only use proper ID format KaPPA-View4 can recognize that will be covered
the following chapters. Otherwise colors and other aspects won’t be displayed
properly.

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KaPPA-View4 Manual on User Map Creation

4. Creating Map Objects
This chapter describes about the rules on drawing and attaching IDs for eachtype of object, in order to color the objects for genes, compounds, and enzymatic
reactions on the created User Map properly in KaPPA-View4.
KaPPA-View4 converts parts of SVG data into Flash in the process of displaying.
Since not all of the SVG expressions can be properly displayed on Flash, it ispossible that Inkscape created map won’t be displayed on KaPPA-View4 properly.
Make sure the rules covered in this chapter are followed for proper displaying.

4-1. GeneBy assigning a gene ID used in KaPPA-View4 into rectangular objects, users cancolor each individual gene according to the gene expression. To display all thegenes assigned to a particular enzymatic reaction, a gene box object can be used(see 4-2. Gene Box).

4-1-1. Creating an Object
Use "Create rectangles and squares" tool () to create a square symbol torepresent a gene. Make sure to set the color of the fill for data-according coloring.
The color of the stroke won’t be affected.
Typical attributes of KaPPA-View4 gene rectangular objects are as follows.
KaPPA-View element
SVG Object
Attribute

A square representing each generect （required）
Description

Value

width

Width

10

heightHeight1017

4. Creating Map Objectsrx

Roundness0

toward X-axisryRoundness0

toward Y-axis
style

fill

Color of the fill

#FFFFFF White（except
for no paint）

strokeColor of the stroke#000000 Black

stroke-width

Stroke width

1.5 pxUser can change the roundness of the corner of objects that are created withtool and drag the white dots appeared on the selected rectangulartool. Clickobjects, by which the values for "rx" and "ry" attributes would be altered.

4-1-2. Adding IDs
Use the following format to ID for rectangular objects that represent genes.
ID format of gene objects
text

text+(integer number)_g

Gene IDs used in KaPPA-View4 system or user-defined ID
starting with "TMG"
Gene objects with a user-defined ID will be colored when the ID
and the corresponding experiment data are described in the
uploaded or POST transferred data file.

Integer number

Use different integer numbers to draw one gene on more than
one place of the same map.

example）

At1g12340(1)_g
TMG001(1)_g

The gene IDs used in the system can be downloaded from the Download page ofthe KaPPA-View4 site. Please refer to “KaPPA-View4 Users’ Manual.”

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KaPPA-View4 Manual on User Map Creation

4-2. Gene Box
A gene box is usually placed near enzymatic reaction arrow to represent several
genes that correspond to the reaction. In KaPPA-View4 system, a gene box IDs
and the corresponding gene IDs are interlocked, therefore all the genes areautomatically displayed based on the gene box without creating rectangles foreach gene.
A gene box is also utilized as an inset area for displaying various data on it
according to the display mode of KaPPA-View4, such as the Universal Map Modefor data comparison between the species and a mode for data comparison
between the experiments in a species. User Maps created by users cannot beutilized for these extra representations (see the table below), however, thedisplaying mechanism of gene box facilitates users to efficiently show all thegenes assigned to the gene box on the User Maps.
A Gene Box drawn with Inkscape
A gene box is indicated with the pale blue
gradation

KaPPA-View4 display
A representation in normal mode where genes forone of selected species are displayed in the areaof the gene box.
A data comparison mode where two experiment
data obtained from a species are compared on thegene box.
Not available for User Maps
A representation in the Universal Map Mode where
genes from multiple species are arrayed in thegene box with their selected experiment data.
Not available for User Maps

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4. Creating Map Objects

An example of a representation in the Universal
Map Mode when the gene box didn't have enoughspace to display all the genes. By clickingof the gene box, genes of each species
can be viewed in a pop-up window.
Not available for User Maps

Users cannot edit the enzymatic reaction to genes relationship that saved in thesystem. Administrator may update or curate the data without announcement.
To display certain genes individually on a map, draw them according to 4-1.
Genes.

4-2-1. Creating an Object
KaPPA-View4 processes gene boxes considering its direction (rotation) to
properly order the genes along with the enzymatic reaction arrow. Follow theprocedure below to create an object efficiently checking the direction of the genebox.
1) Create a rectangle object with "Create rectangles and squares" tool (Set the fill color any desirable color. If the corner is round, make it pointreferring 4-1. Genes

2) Set the gradation
Select the rectangle object and set the fill to "Linear gradient".

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KaPPA-View4 Manual on User Map Creation

The square object will reflect the gradation.

3) Select the object withtool, and gradation controller will appear.

Move the controller so the color is the darkest on the upper line.
Move the left controller to the upper line.

Place the right controller at the center of the square.

5) Edit the width and the height of the object and place it on a desired position
using

tool.

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4. Creating Map Objects

To rotate the rectangle object, use the "Rotate" or "Flip" tools on the tool bar).

(

Caution:In Inkscape, the resize controllers appear around an object by clicking the object
withtool. When the object is clicked again, the rotate and skew controllers
appear, and users can arbitrarily rotate objects by dragging the rotate controllers.
But never arbitrarily rotate the objects like that because KaPPA-View4 is only
capable of processing the objects precisely rotated by 90 degrees.

First Click

Second Click

Rotate arbitrarily

Below is the value setting of the attributes required for a gene box object. Users
can draw rectangles matching the requirements if they follow the orders
mentioned above.

22

KaPPA-View element

A square representing a gene box

SVGObject

rect （Required）

Attribute

Description

Value

KaPPA-View4 Manual on User Map Creationrx

Roundness

not defined （Required）

toward X-axisryRoundness

not defined （Required）

toward Y-axis
transform

Rotating the object

One of the below (Required）

etc.

・not defined (default)・scale(-1,-1)
・scale(1,-1)
・scale(-1,1)・matrix(0,1,1,0,0,0)・matrix(0,-1,1,0,0,0)・matrix(0,1,-1,0,0,0)・matrix(0,-1,-1,0,0,0)Gene boxes aren’t visible on KaPPA-View4, so the fills and the strokes can becolored arbitrarily.

4-2-2. The Orientation of a Gene Box and the Order of a Gene Symbol
Genes in a gene box are drawn from left to right, top to bottom like shown below.

Place gene boxes using this property so that the genes are ordered along the
enzymatic reaction arrow.

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4. Creating Map Objects

Caution:The small squares of genes in the above picture are how they will be displayed on
KaPPA-View4. They don’t need to be actually drawn when users create a genebox.

4-2-3. Adding IDs
Add IDs to gene boxes following the format below.
ID format of a gene box object
numberB+numberCorresponding to the numeric part of enzymatic reaction ID
starting with "R"

example）

B00001The latest information on the gene box ID and the corresponding genes can be
downloaded from Download page of the KaPPA-View4 web site.

4-3. Compound
Compounds are represented by circular symbol on KaPPA-View4 maps. By
embedding a compound ID into an object, changes of the compound
accumulations can be represented on the maps according to the experiment data.

4-3-1. Creating an Object
A circular symbol to represent a compound is created with "Create rectangles
and squares" tool (and arcs" tool () as a "rectangle" object. Note that "Create circles, ellipses,) that create "path" object isn’t used.

The default maps installed in KaPPA-View4 may create a compound as a "circle"
object. The proper color can be expressed, but with Inkscape a circle object cannot

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KaPPA-View4 Manual on User Map Creation

be created with simple steps. If it is inevitable follow the procedure introduced in
5-5. Creating Line and circle Objects with Inkscape.
1) Create a rectangular object withthe canvas to draw a square.

tool. Press and hold Ctrl key and dragtool and click the object to show the corner roundness
2) Select thecontroller. Drag the controller to make the rectangular circle.

Set the fill color so that the color will be expressed according to the data. The
color of the stroke won’t be affected.
Typical attributes of a circular symbol for compound of KaPPA-View4 are as
follows
KaPPA-View element

A circle representing a compound

SVG Object

rect （recommended）

Attribute

Description

Value

width

Width

20

heightHeight20

rx

Roundness

10

toward X-axisryRoundness

10

toward Y-axis
style

fill

Color of the fill

#FFFFFF White（except
for no paint）

strokeColor of the stroke#000000 Black25

4. Creating Map Objects

stroke-width

Stroke width

2.0 pxcircle （Not recommended. Only used in

SVG Object

KaPPA-View default map）
Attribute

Description

Value

r

Radius9

Color of the fill

#FFFFFF White（except

style

fill

for no paint）
strokeColor of the stroke#000000 Black

stroke-width

Stroke width

2.0 px4-3-2. Adding IDs
IDs for compound objects follow the format below.
ID format of a compound object

KPC+number,C+number,G+number,D+number, OR
TMC+number

Description

KPC+number is compound ID format used in KaPPA-View4
Classic system.
C, G or D+number are compound ID format used in KaPPA-View4
KEGG.
TMC+number is a user-defined ID. If the IDs and corresponding
experiment values are described in the uploaded or POST
transferred file, the color will be displayed according to the data.

example）

KPC00005
TMC00001

To look up the compound ID used in the system, download Compound
Information File from the Download page or use the Search function of
KaPPA-View4.

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KaPPA-View4 Manual on User Map Creation

4-4. Enzymatic Reaction
Enzymatic reactions that connect compounds represented as arrows on
KaPPA-View4. When expressing an experiment data, an arrow is colored basedon the average value of genes assigned to the reaction.

4-4-1. Creating an Object
An enzymatic reaction object is created with "Create Bezier curves and straight). Arrowheads are also created with the tool (lines" tool (stroke and an arrowhead to express an arrow.

). Combine a

Users must take some cares when creating an enzymatic reaction object.
Arrowheads and dashed lines, which can be stylized by Inkscape functions,cannot be properly viewed on KaPPA-View4. Dashed lines can only be chosen forstraight lines created with a "line" object which cannot be created with the Bezier) (see 5-5. Creating Line and circle Objects with Inkscape). A curved line
tool (
should not be assigned fill color.
1) Draw a straight line with the Bezier tool ().

Define the start point by left clicking on the canvas. Move the cursor to the end
point. By doing this action with pressing Ctrl key, slope of the line will be fixed tosome defined degrees, facilitates to draw exactly horizontal and vertical lines.

Right click at the end point to finish drawing.

27

4. Creating Map Objects

Line segments are created as a "path" object. Select "No paint" for the fill color.

Make sure to select "No paint" for the fill color of a line because when drawing a
curved line shown below with fill color, inner side of the curve will be colored on
KaPPA-View4.
2) Create an arrowhead also using the Bezier tool ().

Grid line assists users to draw a symmetry arrowhead. Select "View" from themenu and click "Grid".

The canvas will be gridded.

Draw a symmetrical arrowhead with the Bezier tool ().

Left click at each point. When the end point meets the start point, the object
completes.
Select "No paint" for the arrow head stroke.

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KaPPA-View4 Manual on User Map Creation

In the default setting, the clicked point snaps to a nearest intersection of the grid.
For more detailed setting of grid spacing and snapping, open a window byclicking "File" from the menu and then "Document Properties...", and set
conditions on "Grids" or "Snap" tab.

3) Place the line segment and the arrowhead suitably.

4) Group the two objects together.
Select the two objects simultaneously by dragging encircling the line and thearrowhead with

tool.

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4. Creating Map Objects

Group them together by clicking "Object" of the menu and select "Group".

In the XML editor the grouped objects is expressed as <svg:g>. A line and anarrowhead objects are saved in it as child objects.

Add an ID to a grouped object to change the color of an enzymatic reaction arrowaccording to the data.

) can be utilized to draw a complex curve. Grouping function
The Bezier tool (enables users to draw various expressions such as branched enzymatic reactions.

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KaPPA-View4 Manual on User Map Creation

Note:
Avoid creating multi-layered grouped objects when creating a complex enzymatic
reaction objects with more than three objects grouped together. Grouping
grouped objects together disturbs proper color expression.

OK
Each object is grouped only once.

NG
A grouped object includes other child groups. Propercolor expression may be disturbed.

Typical attributes of KaPPA-View enzymatic reaction objects are as follows.
KaPPA-View element

An arrow representing each enzymatic
reactionLine SVG Object

path （recommended） or line （only for dottedlines）

Attributestyle

Description

Value

fill

Color of the fill

No color

strokeColor of the#000000 Black

strokestroke-width

Stroke width

3.0 px

Arrowhead SVG Object

path （required）

Attribute

Description

Value

fill

Color of the fill#000000 Black

strokeColor of the

No colorstyle

strokeRefer to 5-5. Creating Line and circle Objects with Inkscape for line objects
creation.

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4. Creating Map Objects

4-4-2. Adding IDs
Add an enzymatic reaction object ID to a grouped object following the format
shown below.
ID format of enzymatic reaction objects

R+number

Description

Enzymatic reaction IDs used in the system

example）

R0000101

To look up the enzymatic reaction IDs used in the system, download Enzyme
information file from the Download function of KaPPA-View4 after logging-in.
Genes assigned to enzymatic reactions are listed in Gene Box information file foreach species.

4-5. Link to Another Map
On a User Maps users can add links to other associated maps. The link isrepresented by a round-cornered rectangle with the name of the linked map in it.
Users can jump to the other map by clicking the symbol. Efficient use of links
will help understanding of the relationship of metabolic pathways.

4-5-1. Creating Objects
1) Draw a square with "Create rectangles and squares" tool (control the roundness of the corners.

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KaPPA-View4 Manual on User Map Creation

Select a color, typically white, for the fill color but not blank. No paint of fill will
result in a KaPPA-View4 link symbol that can only be clicked on the line around.
1) Type in text with "Create and edit text objects" tool (

).

Note:
KaPPA-View4 cannot properly display a text object with newlines (returns)
inserted. To display more than one line of text properly, either convert the text
object to outlines or create one text object for each line.
3) Change fonts following the steps shown below.
After finishing typing the text, re-select the text with

tool.

Click the font setting button.

A Text and Font setting window will pop up. After setting font, style, size, etc.
click Apply.

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4. Creating Map Objects

Now the text reflects the font setting.

4) Convert the text object to outlines.
To convert the text to outlines, select the text object and click "Path" of the menu
and select "Object to Path".

Visually the text is unchanged, but by selecting the object withrecognized that the text is converted to outlines.

tool, it is

In fact, the outlined text is a "path" object. Users can recognize it with XML
editor.
5) Pile the round-cornered rectangle and the text and group them together.

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KaPPA-View4 Manual on User Map Creation

6) Add an ID to the grouped object. Assign the map ID of the linked map (see4-5-3. Adding an ID).

Typical attributes of a round-cornered rectangle representing a link tocontiguous map in KaPPA-View4 are as follows.
KaPPA-View element

A round-cornered square representing acontiguous map

SVG Object

A

rect

round-cornered（recommended）

rectangle partor path

Attribute

DescriptionValuerx （for rect）

Roundness of10

the corner
toward X-axisry （for rect）

Roundness of10

the corner
toward Y-axis
style

fill

Color of the fill

#FFFFFF White(except for no
paint)

strokeColor of the#000000 Black

stroke35

4. Creating Map Objects

stroke-width
SVG Object

Stroke width

1 px

A text part

path (outlined,
recommended) or
text

Attribute

Description

Value

style

font-family

Font family

Arial(before-inkscape-font-

Inkscape font

Arial

converting

specification

specification

tofont-size

Font size

12.5 px

outlines)

font-weight

Bald fontnormal （normal）

font-style

Italicizing

normal (normal）

4-5-2. About conversion of a text to outlines
We’ve introduced a way for converting a text object to outlines in the previous
section. There are two reasons for why we recommend this.
One is the limitation of the font. Since not all of the fonts described in SVG filecan be converted into Flash properly with KaPPA-View4 (see 5-2. Font), thedesign may corrupt. The text objects converted to outlines can prevent the designfrom collapsing.
The other is how the text is displayed on the map. When the cursor is placed on
the not-outlined-text on map link object, the cursor will be I shaped, on the other
hand, on the outlined-text object, the cursor will be finger shaped widely used toindicate a link. Functions are perfectly fine even for the not-outlined-text, but it
is not intuitively user-friendly.

Before conversion to outlines

After conversion to outlines

36

KaPPA-View4 Manual on User Map Creation

One of the disadvantages of conversion to outlines is that text cannot be
re-edited.
The link function on KaPPA-View4 is unaffected whether to do or not to do thetext conversion to outlines. Therefore the conversion is up to the users.

4-5-3. Adding IDs
Attach an ID to an object that indicates the link to other map following theformat below.
ID format of map link objects

3 letters+integer number(+1 letter)

Description

Map IDs used in the system

example）

Uni00001
Uni00034f
Lja00017

Attach an ID to the grouped object that includes a round-curved rectangle andthe text so that the link function is executed when the rectangle is clicked. To
place several links to the same contiguous map, carefully group them all so thatthe resulted group object doesn't include any child group object.
There are several methods to look up map IDs used in the system.
- Get Map Information file of each species from Download page.
The figure below is an example of a Map Information file.

37

4. Creating Map Objects

The map of map_level 3 in the first column (column A) is the lowermost layered
metabolic pathway map. The map name is written in the fifth column (column E)
and the corresponding map ID is on the second column (column B).
Example) In the figure above is Map Information file for a universal map. The
map ID of Calvin cycle in universal mode is Uni00112.

- Check the ID on the lower left corner of the map in each map mode.

38

KaPPA-View4 Manual on User Map Creation

5. Other Objects
5-1. Grouped Object
Inkscape can treat more than one object as one object. This function is calledgrouping. KaPPA-View4 colors objects according to experiment data by adding
IDs to them, but when the objects are grouped together, coloring target may belimited. This section covers what to be careful about when grouping objects
together.

5-1-1. Grouping Objects Together
Using
tool, click objects while pressing Shift key to select several objects atthe same time.

Click "Object" of the menu and select "Group" to group the selected objects
together.

39

5. Other Objects

To ungroup the grouped objects, click "Object" and "Ungroup".
Grouping and ungrouping can also be done from the toolbar.

In XML editor, the objects that had been grouped together are now child objects
that belong to the grouped object <svg:g>.

5-1-2. Coloring Rule of Grouped Objects
When a grouped object has been assigned KaPPA-View4 map element IDs, i.e.,
ID of gene, gene box, compound, enzymatic reaction, or link to contiguous map,the child objects that belong to the grouped object will be processed based on therules shown below.
- When the child object has been assigned a valid ID, the child object will becolored according to the ID.
- When the child object hasn’t been assigned any valid IDs, it will be coloredaccording to the parent group ID. However if a parent grouped object (A)contained a child grouped object (B), the objects in group B will be excluded fromthe coloring according to the ID of A.

40

KaPPA-View4 Manual on User Map Creation

Therefore in other words, regarding coloring of the objects, the ID that added tothe object that is out of the group is prioritized, and when an ID is added to agrouped object, only the objects that directly belong to the group will be affected.

5-2. Font

5-2-1. Standard Font: Arial
Arial is the standard font for KaPPA-View4 maps. Since a User Map createdwith Arial is properly displayed on KaPPA-View4 as it seen on the Inkscape, westrongly recommend using Arial.

5-2-2. Using Other Fonts
Even if fonts other than Arial are used on a user map, the map is displayed on
KaPPA-View4 with no error when the very computer is used because thecomputer must have the same font installed. However Flash cannot properly
process some of special fonts such as Japanese font and may replace the font withsimilar one resulting in corrupted design or character. Special font may also
cause some trouble when the SVG file is opened on a different computer. We
strongly recommend using wide spread fonts such as Times New Roman otherthan Arial to prevent the corruption.

5-2-3. Conversion of a text to outlines
Even though text cannot be re-edited, by converting to outlines the text designand character corruption can be prevented, and it enables KaPPA-View4 to
display in exactly the same way as on Inkscape. When the User Map is going to
be sent to the KaPPA-View4 administrator, all the text on it must be converted tooutlines.
Click "Path" of the menu and select "Object to Path" while selecting the text
object.

41

5. Other Objects

The text doesn’t change visually, but by selecting it with
it is converted to outlines.

tool, users can see

Users can see with the XML editor that the outlined text has been converted intoa "path" object.

5-3. Text Object
In Inkscape text object, which is created withtool, users can insert a
newlines (returns) within the text. However, KaPPA-View4 doesn’t recognize theinserted newlines and display the text in one line. To avoid it, either convert the
text to outlines or create each lines as a separate text object.

5-4. Image
Images can be added into User Maps and they are displayed on KaPPA-View4
too, facilitates to create attractive presentation maps. The image file must be
embedded in the SVG file. The steps are shown below.
1) Add the image on the canvas.
Either copy and paste the image or click "File" of the menu and select "Import" toload the image.

42

KaPPA-View4 Manual on User Map Creation

2) Click "Effects" of the menu and select "Images" and then "Embed All Images..."to open a setting window.

To embed only the selected image, check "Embed only selected images" and click
Apply button.

A console similar to the command prompt of Windows pops up briefly. When the
console disappears, the embedding is completed.
3) Checking the image embedding.
The file size of the SVG file becomes larger after images embedding. Users cancheck if the image is properly displayed on the KaPPA-View4 according to aprocedure described in 6-1. User Map Operation Confirmation.

5-5. Creating Line and circle Objects with Inkscape
KaPPA-View4 default map contains dashed lines expressed with "line" objects
and compounds circles created with "circle" objects, but in Inkscape they are notcreated easily with simple tools. This section covers the steps of creating those43

5. Other Objects

objects. A dashed line created with a "path" objects cannot be properly expressedon KaPPA-View4. Use a line object to draw dashed lines.

5-5-1. Creating Line Objects
Line object is the only way to create a dashed line on KaPPA-View4, although it
cannot draw curves. Dashed lines can be used for links to contiguous maps andexpressing multiple steps of the metabolic pathways,
Open XML editor. Select <svg:svg id="*****"> on the highest rank and click"New element node" button.

A dialogue pops up. Type "svg:line" and click "Create" button.

An item '<svg:line id="*****">' is added, and a marker appears on the upper left
corner of the canvas.

44

KaPPA-View4 Manual on User Map Creation

Try dragging one of the controller for object enlarging on the screen.

New attributes for position of the object are automatically added to the line
object. Set each attribute value as below.
Attribute

Value

Descriptionx1

0

X coordinate of
the start point

x2

100

X coordinate of
the end pointy1

0

Y coordinate of
the start point

y2

100

Y coordinate of
the end point

They are displayed on the canvas as below.

Line objects become visible by setting the stroke paint.

45

5. Other Objects

Adjust them by dragging and transforming.
To make the line dashed, select "Stroke style" tab from "Fill and Stroke" setting
window, and select an item from "Dashes:".

46

KaPPA-View4 Manual on User Map Creation

5-5-2. Creating Circle Objects
Open XML editor, select '<svg:svg id="*****">' on the top and click "New elementnode" button.

A dialogue pops up. Type "svg:circle" and click "Create" button.

A new element will be added on XML editor, but the canvas still remains blank.

Select the element of '<svg:circle id="****">' and set attributes and values asfollows.
Attributes

ValuesDescriptioncx

0

X coordinate of the center47

5. Other Objectscy0

Y coordinate of the centerr

9radius

A black circle appears on the upper left corner of the canvas.

A circle object is now on the screen. Adjust the object just like other Inkscapeobjects.

48

KaPPA-View4 Manual on User Map Creation

5-5-3. Loading Templates
Users can download sample data (sampleFiles.zip) from the KaPPA-View4 top
page or from the main page that appears after logging in.

After unzipping the zip file, open "template_v***.svg" in "userMap" folder with
Inkscape (v*** indicates the version of the data). Basic objects such as "line" and"circle" objects can be obtained from the file.
Users can load the template object onto the current canvas too. Click "File" of themenu and select "Import..."Imported objects are grouped all together. Ungroup them before using.

49

7. Others

6. Using User Maps on KaPPA-View4
You may want to test your first SVG if it actually works correctly on
KaPPA-View4. When a good User Map is completed, it will be a great help foryour efficient analysis. You may want to share your carefully curated map withmany other people. You can send e-mail to the administrators by simple steps on
KaPPA-View4. We welcome any criticisms on our default map.
This chapter covers the operation of KaPPA-View4 regarding the use of user
maps. Refer to "Users' manual" for more detailed information of KaPPA-View4
operations.

6-1. Checking behavior of User Map
Uploading a user map to KaPPA-View4 is the best way to check the behavior ofit.

6-1-1. Accessing to KaPPA-View4
Go to KaPPA-View4 website.
http://kpv.kazusa.or.jp/kpv4/
Guests can log in simply by clicking "Enter". Power Users type "Name" and"Password" and click "Login" button to login.

50

KaPPA-View4 Manual on User Map Creation

for Guest Users
for Power Users

Power Users can save User Maps on KaPPA-View4 server and view them from
Pathway Tree anytime. Guests have to upload User Maps for every analysis. A
guest can easily become a Power User by clicking "Create Account" on the upper
right corner of the window and following simple steps.

6-1-2. Uploading User Map for checking
Click Temporary Upload in the main menu.

Select "User Map" for type of data.

Click "Browse" and select the SVG file created with Inkscape, then click "Upload"
button.

51

7. Others

The loaded SVG file is converted into Flash and displayed as Map Preview.

On the map preview, properly added valid IDs of objects such as genes,
compounds, enzymatic reactions will be seen as tool tips when a mouse cursor isplaces on the objects.

Users can test if the user map functions properly in this way.
Information pop-ups and inter-map jumping don’t function on preview. The
coloring based on experiment data is neither visually expressed on preview.
Tip:
Right click to show Flash context menu. "Go Full Screen" expands the map to thefull screen and will help users checking the details. "Zoom In" magnifies the map
area around the mouser cursor.

52

KaPPA-View4 Manual on User Map Creation

Once the user map is confirmed, upload the map to KaPPA-View4 server.
Type a map name and click "Submit". The comment box can be left blank.

The map name will be displayed under the Pathway Tree that appears on Map
View and Analysis screen.

6-1-3. Browsing User Maps on KaPPA-View4
The map name typed to upload will be displayed under the Pathway Tree thatcan be seen on Map View and Analysis screen. Select suitable species becauseuser maps cannot be used under the Universal Map Mode.

53

7. Others

Confirm inter-map jumping and data-based coloring.

6-1-4. Registering User Maps on KaPPA-View4 (for Power Users)
Power Users can register their own user map into their account and use themaps right after logging in.
From the Power User menu on the left of the main window, select User Map
Upload. Upload the maps from the form similar to Temporary Uploading. The
registered user maps can be used from the Pathway Tree just like temporarily
uploaded maps.

The registered maps are viewed in Personal Data List of Power User menu.
Users can delete the map from Personal Data List as well.

6-2. Sending User Maps to KaPPA-View4 Administrators (forPower Users）

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KaPPA-View4 Manual on User Map Creation

Despite our best effort, there may be information error or deficiency in thedefault map. Once user maps with corrected errors or species specific pathways
that default map didn’t cover are completed, consideration them to the public isgreatly appreciated.
Power Users can send their user map to the KaPPA-View4 administrator withsimple steps. The administrators will discuss on using the user map for
improving the default map. We acknowledge the map donor with a great
appreciation.

6-2-1. Sending a User Map
Register a user map as a Power User following 6-1-4. Registering User Maps on
KaPPA-View4 (for Power Users). List the registered map from Personal Data
List.

Check the User Maps to send and click "Send to Admin" button.

A new window pops up. Check the map and type message to the administrator.
Click "Submit" to send the User Map file and the message.

55

7. Others

The message can be either in English or Japanese. The administrator will e-mailthe user to discuss the treatment of the user map.

6-2-2. Note

•Notes on Creating a User Map
Convert all characters to outlines when the user map to be sent uses any fonts
other than Arial.

•Comments to the Administrator
Do not forget to send the following information.
- NameUsed for specifying the contribution.
- Affiliation
Used for specifying the contribution.

56

KaPPA-View4 Manual on User Map Creation- Contact e-mail address
The administrator may contact regarding the user map information.
- Use of the user map
1) Information addition to the default map
2) Curation of the default map
3) Adding a new map
Please let us know the suitable species and position on the Pathway Tree.

57

7. Others

7. Others
7-1. About Us
Team KaPPA-View
e-mail: kappa-view at kazusa.or.jp (replace at to @)The Administrators and developing team of KaPPA-View in Kazusa DNA
Research Institute (http://www.kazusa.or.jp/e/). Please send your all
inquiries to this e-mail address.

7-2. Acknowledgements
We are grateful to Miss Sumy Sekine and Mr. Atsushi Hiruta for translation
assistance of this manual into English. KaPPA-View was developed in Kazusa
DNA Research Institute with a support from the New Energy and Industrial
Technology Development Organization (NEDO), Japan under the research
project named "Development of Fundamental Technologies for Controlling theMaterial Production Process of Plants" (P02001).

7-3. References
KaPPA-View4: a metabolic pathway database for representation and analysis ofcorrelation networks of gene co-expression and metabolite co-accumulation andomics data. Sakurai et al., (2011) Nucleic Acids Research 39: D677-684

7-4. Manual Version
ver 1.0 (2010.12.30)
Initial English version released.

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KaPPA-View4 Manual on User Map Creation

Appendices
Appendix A. List of Recommended Settings of Objects
KaPPA-View element
SVG Object

A square representing each generect （required）

Attribute

Description

Value

width

Width

10

heightHeight10rx

Roundness0

toward X-axisryRoundness0

toward Y-axis
style

fill

Color of the fill

#FFFFFF White（except
for no paint）

strokeColor of the stroke#000000 Black

stroke-width

Stroke width

1.5 px

KaPPA-View element

A square representing a gene box

SVGObject

rect （Required）

Attribute

Description

Value

rx

Roundness

not defined （Required）

toward X-axisryRoundness

not defined （Required）

toward Y-axis
transform

Rotating the object

One of the below (Required）

etc.

・not defined (default)・scale(-1,-1)
・scale(1,-1)
・scale(-1,1)・matrix(0,1,1,0,0,0)59

Appendices・matrix(0,-1,1,0,0,0)・matrix(0,1,-1,0,0,0)・matrix(0,-1,-1,0,0,0)

KaPPA-View element

A circle representing a compound

SVG Object

rect （recommended）

Attribute

Description

Value

width

Width

20

heightHeight20

rx

Roundness

10

toward X-axisryRoundness

10

toward Y-axis
style

fill

Color of the fill

#FFFFFF White（except
for no paint）

strokeColor of the stroke#000000 Black

stroke-width

Stroke width

2.0 pxSVG Object

circle （Not recommended. Only used in
KaPPA-View default map）

Attribute

Description

Value

r

Radius9

Color of the fill

#FFFFFF White（except

style

fill

for no paint）
strokeColor of the stroke#000000 Black

stroke-width

Stroke width

2.0 px

KaPPA-View element

An arrow representing each enzymatic
reactionLine SVG Object

path （recommended） or line （only for dottedlines）

Attributestyle

Description

Value

fill

Color of the fill

No color

strokeColor of the#000000 Black

strokestroke-width

60

Stroke width

3.0 px

KaPPA-View4 Manual on User Map Creation

Arrowhead SVG Object

path （required）

Attribute

Description

Value

fill

Color of the fill#000000 Black

strokeColor of the

No colorstyle

strokeKaPPA-View element

A round-cornered square representing acontiguous map

SVG Object

A

rect

round-cornered（recommended）

rectangle partor path

Attribute

DescriptionValuerx （for rect）

Roundness of10

the corner
toward X-axisry （for rect）

Roundness of10

the corner
toward Y-axis
style

fill

Color of the fill

#FFFFFF White(except for no
paint)

strokeColor of the#000000 Black

strokestroke-width
SVG Object

Stroke width

1 px

A text part

path (outlined,
recommended) or
text

Attribute

Description

Value

style

font-family

Font family

Arial(before-inkscape-font-

Inkscape font

Arial

converting

specification

specification

tofont-size

Font size

12.5 px

outlines)

font-weight

Bald fontnormal （normal）

font-style

Italicizing

normal (normal）

61

Appendices

Appendix B. List of ID formats of Objects
ID format of gene objects
text

text+(integer number)_g

Gene IDs used in KaPPA-View4 system or user-defined ID
starting with "TMG"
Gene objects with a user-defined ID will be colored when the ID
and the corresponding experiment data are described in the
uploaded or POST transferred data file.

Integer number

Use different integer numbers to draw one gene on more than
one place of the same map.

example）

At1g12340(1)_g
TMG001(1)_g

ID format of a gene box object
numberB+numberCorresponding to the numeric part of enzymatic reaction ID
starting with "R"

example）

B00001

ID format of a compound object

KPC+number,C+number,G+number,D+number, OR
TMC+number

Description

KPC+number is compound ID format used in KaPPA-View4
Classic system.
C, G or D+number are compound ID format used in KaPPA-View4
KEGG.
TMC+number is a user-defined ID. If the IDs and corresponding
experiment values are described in the uploaded or POST
transferred file, the color will be displayed according to the data.

example）

KPC00005
TMC00001

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KaPPA-View4 Manual on User Map Creation

ID format of enzymatic reaction objects

R+number

Description

Enzymatic reaction IDs used in the system

example）

R0000101

ID format of map link objects

3 letters+integer number(+1 letter)

Description

Map IDs used in the system

example）

Uni00001
Uni00034f
Lja00017

63