Author: kono
Date: 2010-02-11 19:25:46 -0800 (Thu, 11 Feb 2010)
New Revision: 19312
Added:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGEntryType.java
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGRelationType.java
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/util/
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/util/ColorParser.java
csplugins/trunk/ucsd/kono/KGMLReader/testData/bsu00030.xml
Modified:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
Log:
New attributes added to nodes.
Added:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGEntryType.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGEntryType.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGEntryType.java
2010-02-12 03:25:46 UTC (rev 19312)
@@ -0,0 +1,16 @@
+package org.cytoscape.data.reader.kgml;
+
+public enum KEGGEntryType {
+ ORTHOLOG("ortholog"), ENZYME("enzyme"), GENE("gene"), GROUP("group"),
+ COMPOUND("compound"), MAP("map");
+
+ private String tag;
+
+ private KEGGEntryType(final String tag) {
+ this.tag = tag;
+ }
+
+ public String getTag() {
+ return this.tag;
+ }
+}
Added:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGRelationType.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGRelationType.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGRelationType.java
2010-02-12 03:25:46 UTC (rev 19312)
@@ -0,0 +1,16 @@
+package org.cytoscape.data.reader.kgml;
+
+public enum KEGGRelationType {
+ EC_REL("ECrel"), PP_REL("PPrel"), GE_REL("GErel"),
+ PC_REL("PCrel"), MAPLINK("maplink");
+
+ private final String tag;
+
+ private KEGGRelationType(final String tag) {
+ this.tag = tag;
+ }
+
+ public String getTag() {
+ return this.tag;
+ }
+}
Modified:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
2010-02-12 01:26:06 UTC (rev 19311)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
2010-02-12 03:25:46 UTC (rev 19312)
@@ -21,6 +21,7 @@
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.view.CyNetworkView;
+import cytoscape.visual.ArrowShape;
import cytoscape.visual.EdgeAppearanceCalculator;
import cytoscape.visual.GlobalAppearanceCalculator;
import cytoscape.visual.NodeAppearanceCalculator;
@@ -40,6 +41,14 @@
private int[] nodeIdx;
private int[] edgeIdx;
+
+ private static final String KEGG_NAME = "KEGG.name";
+ private static final String KEGG_ENTRY_TYPE = "KEGG.entry";
+ private static final String KEGG_LABEL = "KEGG.label";
+ private static final String KEGG_RELATION_TYPE = "KEGG.relation";
+
+
+ private static final String KEGG_LINK = "KEGG.link";
public PathwayMapper(final Pathway pathway) {
this.pathway = pathway;
@@ -66,8 +75,15 @@
if
(!comp.getGraphics().getType().equals(KEGGShape.LINE.getTag())) {
CyNode node = Cytoscape.getCyNode(pathwayID +
"-"
+ comp.getId(), true);
- nodeAttr.setAttribute(node.getIdentifier(),
"KEGG.name", comp
+ nodeAttr.setAttribute(node.getIdentifier(),
KEGG_NAME, comp
.getName());
+ nodeAttr.setAttribute(node.getIdentifier(),
KEGG_LINK, comp.getLink());
+ nodeAttr.setAttribute(node.getIdentifier(),
KEGG_ENTRY_TYPE, comp.getType());
+
+ final Graphics graphics = comp.getGraphics();
+ if(graphics != null && graphics.getName() !=
null) {
+
nodeAttr.setAttribute(node.getIdentifier(), KEGG_LABEL, graphics.getName());
+ }
nodeMap.put(comp.getId(), node);
entryMap.put(comp.getId(), comp);
}
@@ -85,6 +101,8 @@
final List<Relation> relations = pathway.getRelation();
final List<CyEdge> edges = new ArrayList<CyEdge>();
+ final CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
+
for(Relation rel: relations) {
final String ent1 = rel.getEntry1();
final String ent2 = rel.getEntry2();
@@ -93,14 +111,19 @@
final String type = rel.getType();
CyNode source = nodeMap.get(ent1);
CyNode target = nodeMap.get(ent2);
- CyNode compound = nodeMap.get(subs.get(0).getValue());
- System.out.println(source.getIdentifier());
- System.out.println(target.getIdentifier());
- System.out.println(compound.getIdentifier() + "\n\n");
- CyEdge edge1 = Cytoscape.getCyEdge(source, compound,
"interaction", type, true);
- CyEdge edge2 = Cytoscape.getCyEdge(compound, target,
"interaction", type, true);
- edges.add(edge1);
- edges.add(edge2);
+
+ for(Subtype sub: subs) {
+ CyNode hub = nodeMap.get(sub.getValue());
+ System.out.println(source.getIdentifier());
+ System.out.println(target.getIdentifier());
+ System.out.println(hub.getIdentifier() +
"\n\n");
+ CyEdge edge1 = Cytoscape.getCyEdge(source, hub,
"interaction", type, true);
+ CyEdge edge2 = Cytoscape.getCyEdge(hub, target,
"interaction", type, true);
+ edges.add(edge1);
+ edges.add(edge2);
+
+ edgeAttr.setAttribute(edge1.getIdentifier(),
this.KEGG_RELATION_TYPE, type);
+ }
}
edgeIdx = new int[edges.size()];
@@ -143,18 +166,21 @@
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FILL_COLOR,
nodeColor);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE,
- NodeShape.ELLIPSE);
-
nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_OPACITY,
- 220);
+ NodeShape.ROUND_RECT);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_COLOR,
nodeLineColor);
-
+
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LINE_WIDTH,
+ 2);
+
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_COLOR,
nodeLabelColor);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FONT_FACE,
nodeLabelFont);
+ //Default Edge appr
+
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_TGTARROW_SHAPE,
ArrowShape.DELTA);
+
final DiscreteMapping nodeWidth = new DiscreteMapping(30,
"ID", ObjectMapping.NODE_MAPPING);
final Calculator nodeWidthCalc = new BasicCalculator(vsName +
"-"
Added:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/util/ColorParser.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/util/ColorParser.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/util/ColorParser.java
2010-02-12 03:25:46 UTC (rev 19312)
@@ -0,0 +1,9 @@
+package org.cytoscape.data.reader.kgml.util;
+
+import java.awt.Color;
+
+public class ColorParser {
+ public static Color getColor(final String colorString) {
+ return null;
+ }
+}
Added: csplugins/trunk/ucsd/kono/KGMLReader/testData/bsu00030.xml
===================================================================
--- csplugins/trunk/ucsd/kono/KGMLReader/testData/bsu00030.xml
(rev 0)
+++ csplugins/trunk/ucsd/kono/KGMLReader/testData/bsu00030.xml 2010-02-12
03:25:46 UTC (rev 19312)
@@ -0,0 +1,803 @@
+<?xml version="1.0"?>
+<!DOCTYPE pathway SYSTEM "http://www.genome.jp/kegg/xml/KGML_v0.7.0_.dtd";>
+<!-- Creation date: Oct 7, 2009 14:31:05 +0900 (JST) -->
+<pathway name="path:bsu00030" org="bsu" number="00030"
+ title="Pentose phosphate pathway"
+ image="http://www.genome.jp/kegg/pathway/bsu/bsu00030.png";
+ link="http://www.genome.jp/kegg-bin/show_pathway?bsu00030";>
+ <entry id="1" name="cpd:C01151" type="compound"
+ link="http://www.kegg.jp/dbget-bin/www_bget?C01151";>
+ <graphics name="C01151" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="circle" x="692" y="552" width="8" height="8"/>
+ </entry>
+ <entry id="2" name="ko:K05774" type="ortholog" reaction="rn:R06836"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K05774";>
+ <graphics name="K05774" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="628" y="554" width="46" height="17"/>
+ </entry>
+ <entry id="3" name="cpd:C00668" type="compound"
+ link="http://www.kegg.jp/dbget-bin/www_bget?C00668";>
+ <graphics name="C00668" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="circle" x="201" y="303" width="8" height="8"/>
+ </entry>
+ <entry id="4" name="bsu:BSU31350" type="gene" reaction="rn:R02739"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU31350";>
+ <graphics name="pgi" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="258" y="304" width="46" height="17"/>
+ </entry>
+ <entry id="5" name="cpd:C00118" type="compound"
+ link="http://www.kegg.jp/dbget-bin/www_bget?C00118";>
+ <graphics name="C00118" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="circle" x="819" y="303" width="8" height="8"/>
+ </entry>
+ <entry id="6" name="cpd:C00022" type="compound"
+ link="http://www.kegg.jp/dbget-bin/www_bget?C00022";>
+ <graphics name="C00022" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="circle" x="790" y="228" width="8" height="8"/>
+ </entry>
+ <entry id="7" name="bsu:BSU22100" type="gene" reaction="rn:R05605"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU22100";>
+ <graphics name="kdgA" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="752" y="293" width="46" height="17"/>
+ </entry>
+ <entry id="8" name="path:bsu00010" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu00010";>
+ <graphics name="Glycolysis / Gluconeogenesis" fgcolor="#000000"
bgcolor="#FFFFFF"
+ type="roundrectangle" x="994" y="227" width="68" height="26"/>
+ </entry>
+ <entry id="9" name="bsu:BSU35920" type="gene" reaction="rn:R02750"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU35920";>
+ <graphics name="rbsK" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="401" y="612" width="46" height="17"/>
+ </entry>
+ <entry id="10" name="bsu:BSU23500" type="gene" reaction="rn:R02749"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU23500";>
+ <graphics name="drm" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="402" y="644" width="46" height="17"/>
+ </entry>
+ <entry id="11" name="bsu:BSU39420" type="gene" reaction="rn:R01066"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU39420";>
+ <graphics name="deoC" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="262" y="644" width="46" height="17"/>
+ </entry>
+ <entry id="12" name="bsu:BSU00510" type="gene" reaction="rn:R01049"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU00510";>
+ <graphics name="prs" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="529" y="516" width="46" height="17"/>
+ </entry>
+ <entry id="13" name="bsu:BSU23500" type="gene" reaction="rn:R01057"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU23500";>
+ <graphics name="drm" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="628" y="490" width="46" height="17"/>
+ </entry>
+ <entry id="14" name="bsu:BSU35920" type="gene" reaction="rn:R01051"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU35920";>
+ <graphics name="rbsK" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="628" y="469" width="46" height="17"/>
+ </entry>
+ <entry id="15" name="bsu:BSU17890" type="gene" reaction="rn:R01641"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU17890";>
+ <graphics name="tkt" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="420" y="509" width="46" height="17"/>
+ </entry>
+ <entry id="16" name="bsu:BSU36920" type="gene" reaction="rn:R01056"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU36920";>
+ <graphics name="ywlF" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="531" y="434" width="46" height="17"/>
+ </entry>
+ <entry id="17" name="bsu:BSU15790" type="gene" reaction="rn:R01529"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU15790";>
+ <graphics name="rpe" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="476" y="396" width="46" height="17"/>
+ </entry>
+ <entry id="18" name="bsu:BSU17890" type="gene" reaction="rn:R01830"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU17890";>
+ <graphics name="tkt" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="305" y="396" width="46" height="17"/>
+ </entry>
+ <entry id="19" name="bsu:BSU37120" type="gene" reaction="rn:R01070"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU37120";>
+ <graphics name="fbaA" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="200" y="511" width="46" height="17"/>
+ </entry>
+ <entry id="20" name="bsu:BSU29190" type="gene" reaction="rn:R04779"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU29190";>
+ <graphics name="pfkA" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="201" y="435" width="46" height="17"/>
+ </entry>
+ <entry id="21" name="bsu:BSU37090 bsu:BSU40190" type="gene"
reaction="rn:R04780"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU37090+bsu:BSU40190";>
+ <graphics name="ywjI..." fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="150" y="435" width="46" height="17"/>
+ </entry>
+ <entry id="22" name="bsu:BSU31350" type="gene" reaction="rn:R02740"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU31350";>
+ <graphics name="pgi" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="200" y="349" width="46" height="17"/>
+ </entry>
+ <entry id="23" name="ko:K00032" type="ortholog" reaction="rn:R02032
rn:R02034"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K00032";>
+ <graphics name="K00032" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="489" y="277" width="46" height="17"/>
+ </entry>
+ <entry id="24" name="ko:K11441" type="ortholog" reaction="rn:R02658"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K11441";>
+ <graphics name="K11441" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="450" y="241" width="46" height="17"/>
+ </entry>
+ <entry id="25" name="bsu:BSU23860 bsu:BSU25730 bsu:BSU40080" type="gene"
reaction="rn:R01528"
+
link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU23860+bsu:BSU25730+bsu:BSU40080";>
+ <graphics name="yqjI..." fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="529" y="350" width="46" height="17"/>
+ </entry>
+ <entry id="26" name="bsu:BSU13010" type="gene" reaction="rn:R02035"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU13010";>
+ <graphics name="ykgB" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="472" y="304" width="46" height="17"/>
+ </entry>
+ <entry id="27" name="bsu:BSU23850" type="gene" reaction="rn:R02736"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU23850";>
+ <graphics name="zwf" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="365" y="303" width="46" height="17"/>
+ </entry>
+ <entry id="29" name="bsu:BSU22110" type="gene" reaction="rn:R01541"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU22110";>
+ <graphics name="kdgK" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="691" y="241" width="46" height="17"/>
+ </entry>
+ <entry id="30" name="ko:K01690" type="ortholog" reaction="rn:R02036"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K01690";>
+ <graphics name="K01690" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="608" y="304" width="46" height="17"/>
+ </entry>
+ <entry id="31" name="bsu:BSU40060" type="gene" reaction="rn:R01737"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU40060";>
+ <graphics name="gntK" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="532" y="241" width="46" height="17"/>
+ </entry>
+ <entry id="32" name="ko:K05308" type="ortholog" reaction="rn:R01538"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K05308";>
+ <graphics name="K05308" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="608" y="156" width="46" height="17"/>
+ </entry>
+ <entry id="33" name="ko:K01053" type="ortholog" reaction="rn:R01519"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K01053";>
+ <graphics name="K01053" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="421" y="156" width="46" height="17"/>
+ </entry>
+ <entry id="34" name="ko:K00117" type="ortholog" reaction="rn:R06620"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K00117";>
+ <graphics name="K00117" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="267" y="214" width="46" height="17"/>
+ </entry>
+ <entry id="35" name="ko:K00115" type="ortholog" reaction="rn:R00305"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K00115";>
+ <graphics name="K00115" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="267" y="193" width="46" height="17"/>
+ </entry>
+ <entry id="37" name="bsu:BSU02830 bsu:BSU03930" type="gene"
reaction="rn:R01520 rn:R01521"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU02830+bsu:BSU03930";>
+ <graphics name="ycdF..." fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="267" y="125" width="46" height="17"/>
+ </entry>
+ <entry id="38" name="path:bsu00010" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu00010";>
+ <graphics name="Glycolysis / Gluconeogenesis" fgcolor="#000000"
bgcolor="#FFFFFF"
+ type="roundrectangle" x="50" y="426" width="64" height="276"/>
+ </entry>
+ <entry id="39" name="path:bsu00040" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu00040";>
+ <graphics name="Pentose and glucuronate interconversions"
fgcolor="#000000" bgcolor="#FFFFFF"
+ type="roundrectangle" x="429" y="356" width="136" height="34"/>
+ </entry>
+ <entry id="40" name="path:bsu00230" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu00230";>
+ <graphics name="Purine metabolism" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="roundrectangle" x="635" y="593" width="73" height="32"/>
+ </entry>
+ <entry id="41" name="path:bsu00030" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?pathway+bsu00030";>
+ <graphics name="TITLE:Pentose phosphate pathway" fgcolor="#000000"
bgcolor="#FFFFFF"
+ type="roundrectangle" x="165" y="58" width="249" height="25"/>
+ </entry>
+ <entry id="42" name="path:bsu00240" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu00240";>
+ <graphics name="Pyrimidine metabolism" fgcolor="#000000"
bgcolor="#FFFFFF"
+ type="roundrectangle" x="635" y="628" width="73" height="32"/>
+ </entry>
+ <entry id="43" name="path:bsu00340" type="map"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu00340";>
+ <graphics name="Histidine metabolism" fgcolor="#000000"
bgcolor="#FFFFFF"
+ type="roundrectangle" x="636" y="663" width="73" height="32"/>
+ </entry>
+ <entry id="45" name="ko:K06151 ko:K06152" type="ortholog"
reaction="rn:R01741"
+ link="http://www.kegg.jp/dbget-bin/www_bget?K06151+K06152";>
+ <graphics name="K06151..." fgcolor="#000000" bgcolor="#FFFFFF"
+ type="rectangle" x="451" y="185" width="46" height="17"/>
+ </entry>
+ <entry id="46" name="bsu:BSU37110" type="gene" reaction="rn:R01827"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU37110";>
+ <graphics name="ywjH" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="364" y="475" width="46" height="17"/>
+ </entry>
+ <entry id="47" name="bsu:BSU09310" type="gene" reaction="rn:R01057"
+ link="http://www.kegg.jp/dbget-bin/www_bget?bsu:BSU09310";>
+ <graphics name="pgcA" fgcolor="#000000" bgcolor="#BFFFBF"
+ type="rectangle" x="628" y="511" width="46" height="17"/>
+ </entry>
+ <entry id="48" name="cpd:C00257" type="compound"
+ link="http://www.kegg.jp/dbget-bin/www_bget?C00257";>
+ <graphics name="C00257" fgcolor="#000000" bgcolor="#FFFFFF"
+ type="circle" x="529" y="155" width="8" height="8"/>
+ </entry>
+ <entry id="49" name="cpd:C00198" type="compound"
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+ <substrate name="cpd:C00257"/>
+ <product name="cpd:C00204"/>
+ </reaction>
+ <reaction name="rn:R01519" type="irreversible">
+ <substrate name="cpd:C00198"/>
+ <product name="cpd:C00257"/>
+ </reaction>
+ <reaction name="rn:R06620" type="irreversible">
+ <substrate name="cpd:C00031"/>
+ <product name="cpd:C00198"/>
+ </reaction>
+ <reaction name="rn:R00305" type="irreversible">
+ <substrate name="cpd:C00031"/>
+ <product name="cpd:C00198"/>
+ </reaction>
+ <reaction name="rn:R01522" type="irreversible">
+ <substrate name="cpd:C00221"/>
+ <product name="cpd:C00198"/>
+ </reaction>
+ <reaction name="rn:R01520 rn:R01521" type="reversible">
+ <substrate name="cpd:C00221"/>
+ <product name="cpd:C00198"/>
+ </reaction>
+ <reaction name="rn:R01522" type="irreversible">
+ <substrate name="cpd:C00221"/>
+ <product name="cpd:C00198"/>
+ </reaction>
+ <reaction name="rn:R01741" type="irreversible">
+ <substrate name="cpd:C00257"/>
+ <product name="cpd:C06473"/>
+ </reaction>
+ <reaction name="rn:R01827" type="reversible">
+ <substrate name="cpd:C05382"/>
+ <substrate name="cpd:C00118"/>
+ <product name="cpd:C00279"/>
+ <product name="cpd:C05345"/>
+ </reaction>
+ <reaction name="rn:R01057" type="reversible">
+ <substrate name="cpd:C00620"/>
+ <product name="cpd:C00117"/>
+ </reaction>
+ <reaction name="rn:R06837" type="reversible">
+ <substrate name="cpd:C00620"/>
+ <product name="cpd:C01151"/>
+ </reaction>
+ <reaction name="rn:R08570" type="reversible">
+ <substrate name="cpd:C00204"/>
+ <product name="cpd:C00022"/>
+ <product name="cpd:C00577"/>
+ </reaction>
+ <reaction name="rn:R08571" type="irreversible">
+ <substrate name="cpd:C00577"/>
+ <product name="cpd:C00258"/>
+ </reaction>
+ <reaction name="rn:R08572" type="irreversible">
+ <substrate name="cpd:C00258"/>
+ <product name="cpd:C00631"/>
+ </reaction>
+ <reaction name="rn:R05605" type="reversible">
+ <substrate name="cpd:C04442"/>
+ <product name="cpd:C00022"/>
+ <product name="cpd:C00118"/>
+ </reaction>
+ <reaction name="rn:R01739" type="reversible">
+ <substrate name="cpd:C00257"/>
+ <product name="cpd:C06473"/>
+ </reaction>
+ <reaction name="rn:R01621" type="irreversible">
+ <substrate name="cpd:C00231"/>
+ <product name="cpd:C00118"/>
+ </reaction>
+</pathway>
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![http://www.genome.jp/kegg/pathway/bsu/bsu00030.png"](http://www.genome.jp/kegg/pathway/bsu/bsu00030.png"){kind=link}