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Last active September 2, 2024 05:09
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update.groovy
@Grab(group='io.github.egonw.bacting', module='managers-ui', version='1.0.1-SNAPSHOT')
@Grab(group='io.github.egonw.bacting', module='managers-libgpml', version='1.0.1-SNAPSHOT')
@Grab(group='io.github.egonw.bacting', module='managers-bridgedb', version='1.0.1-SNAPSHOT')
import org.bridgedb.Xref
workspaceRoot = ".."
bioclipse = new net.bioclipse.managers.BioclipseManager(workspaceRoot);
ui = new net.bioclipse.managers.UIManager(workspaceRoot);
gpml = new net.bioclipse.managers.LibGPMLManager(workspaceRoot);
bridgedb = new net.bioclipse.managers.BridgedbManager(workspaceRoot);
wpfile = args[0]
gpmlContent = gpml.loadModel("/worm/" + wpfile)
mapper = bridgedb.loadRelationalDatabase(
bioclipse.fullPath("/worm/Ce_Derby_Ensembl_108.bridge")
);
agilent = bridgedb.getSourceFromName("Agilent");
for (node : gpmlContent.getDataNodes()) {
oldxref = node.getXref()
if (oldxref && oldxref.dataSource && oldxref.dataSource.systemCode == "W") {
newxref = new Xref(oldxref.id, agilent)
enxref = bridgedb.map(mapper, newxref, "En");
if (enxref.size() == 1) {
node.setXref(enxref.getAt(0))
println "${oldxref} -> ${newxref} -> ${enxref}"
} else if (enxref.size() == 0) {
println "${oldxref} -> no Ensembl mapping, keeping as is"
} else {
println "${oldxref} -> multiple Ensembl mappings, keeping as is"
}
} else {
println "${oldxref} -> keeping as is"
}
}
gpml.saveModelAsGPML2013a("/worm/" + wpfile + ".new", gpmlContent)
Raw
WP2223.diff
diff --git a/WP2223.gpml b/WP2223.gpml.new
index 8d01090..d2897db 100644
--- a/WP2223.gpml
+++ b/WP2223.gpml.new
@@ -1,183 +1,187 @@
<?xml version="1.0" encoding="UTF-8"?>
<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="LIN-12/Notch Lateral Signaling" Data-Source="WikiPathways" Version="WP2223_r135294" Author="[Kyook, MaintBot, RaatsS, Khanspers]" Last-Modified="20240815205238" Organism="Caenorhabditis elegans">
<Comment Source="WikiPathways-description">Lateral signaling targets and negative regulation of LET-23 signaling. The LIN-12/Notch pathway plays two related roles in vulval development; to prevent adjacent induced vulval precursor cells (VPCs) from both becoming 1° VPCs and to induce VPCs adjacent to the 1°VPC to take a 2° cell fate.
-See figure 14 in http://www.wormbook.org/chapters/www_vulvaldev/vulvaldev.pdf.
-</Comment>
+See figure 14 in http://www.wormbook.org/chapters/www_vulvaldev/vulvaldev.pdf.</Comment>
<BiopaxRef>ea2</BiopaxRef>
<Graphics BoardWidth="708.5" BoardHeight="455.0" />
<DataNode TextLabel="LIN-12" GraphId="cbf8f" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="231.0" CenterY="163.0" Width="65.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="R107.8" />
+ <Xref Database="Ensembl" ID="WBGene00003001" />
</DataNode>
<DataNode TextLabel="lst-1" GraphId="bef29" Type="GeneProduct" GroupRef="a9676">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="316.0" Width="65.0" Height="20.0" ZOrder="32770" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="T22A3.3" />
+ <Xref Database="Ensembl" ID="WBGene00003083" />
</DataNode>
<DataNode TextLabel="lst-2" GraphId="f7cc5" Type="GeneProduct" GroupRef="a9676">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="352.0" Width="65.0" Height="20.0" ZOrder="32771" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="R160.7" />
+ <Xref Database="Ensembl" ID="WBGene00003084" />
</DataNode>
<DataNode TextLabel="lst-4" GraphId="eab9e" Type="GeneProduct" GroupRef="a9676">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="386.0" Width="65.0" Height="20.0" ZOrder="32772" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="Y37A1B.2" />
+ <Xref Database="Ensembl" ID="WBGene00003086" />
</DataNode>
<DataNode TextLabel="ark-1" GraphId="b2902" Type="GeneProduct" GroupRef="c5e03">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="146.0" Width="65.0" Height="20.0" ZOrder="32774" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="C01C7.1" />
+ <Xref Database="Ensembl" ID="WBGene00000186" />
</DataNode>
<DataNode TextLabel="lip-1" GraphId="a3f88" Type="GeneProduct" GroupRef="c5e03">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="183.0" Width="65.0" Height="20.0" ZOrder="32775" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="C05B10.1" />
+ <Xref Database="Ensembl" ID="WBGene00003043" />
</DataNode>
<DataNode TextLabel="dpy-23" GraphId="ec4bd" Type="GeneProduct" GroupRef="c5e03">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="217.0" Width="65.0" Height="20.0" ZOrder="32776" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="R160.1" />
+ <Xref Database="Ensembl" ID="WBGene00001082" />
</DataNode>
<DataNode TextLabel="lst-3" GraphId="fd955" Type="GeneProduct" GroupRef="c5e03">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="366.0" CenterY="248.0" Width="65.0" Height="20.0" ZOrder="32777" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="Y37A1B.1" />
+ <Xref Database="Ensembl" ID="WBGene00003085" />
</DataNode>
<DataNode TextLabel="LET-23" GraphId="f7a4a" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="500.0" CenterY="146.0" Width="65.0" Height="20.0" ZOrder="32778" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="ZK1067.1" />
+ <Xref Database="Ensembl" ID="WBGene00002299" />
</DataNode>
<DataNode TextLabel="LET-60" GraphId="c5b29" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="500.0" CenterY="227.0" Width="65.0" Height="20.0" ZOrder="32779" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="ZK792.6" />
+ <Xref Database="Ensembl" ID="WBGene00002335" />
</DataNode>
<DataNode TextLabel="MPK-1" GraphId="a3b9f" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="500.0" CenterY="353.0" Width="65.0" Height="20.0" ZOrder="32780" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="F43C1.2" />
+ <Xref Database="Ensembl" ID="WBGene00003401" />
</DataNode>
<DataNode TextLabel="sli-1" GraphId="a7c35" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="646.0" CenterY="146.0" Width="65.0" Height="20.0" ZOrder="32782" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="M02A10.3" />
+ <Xref Database="Ensembl" ID="WBGene00004829" />
</DataNode>
<DataNode TextLabel="unc-101" GraphId="a51a4" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="646.0" CenterY="186.0" Width="65.0" Height="20.0" ZOrder="32783" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="K11D2.3" />
+ <Xref Database="Ensembl" ID="WBGene00006829" />
</DataNode>
<DataNode TextLabel="apm-1" GraphId="ac57a" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="646.0" CenterY="220.0" Width="65.0" Height="20.0" ZOrder="32784" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="F55A12.7" />
+ <Xref Database="Ensembl" ID="WBGene00000150" />
</DataNode>
<DataNode TextLabel="gap-1" GraphId="b4884" Type="GeneProduct">
<BiopaxRef>fa4</BiopaxRef>
<Graphics CenterX="646.0" CenterY="251.0" Width="65.0" Height="20.0" ZOrder="32785" FontSize="10" Valign="Middle" />
- <Xref Database="WormBase" ID="T24C12.2" />
+ <Xref Database="Ensembl" ID="WBGene00001515" />
</DataNode>
<Interaction GraphId="c1289">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="500.0" Y="353.0" GraphRef="a3b9f" RelX="0.0" RelY="0.0" />
- <Point X="500.0" Y="425.0" ArrowHead="Arrow" />
+ <Point GraphId="c9ebb" X="500.0" Y="353.0" GraphRef="a3b9f" RelX="0.0" RelY="0.0" />
+ <Point GraphId="a0df7" X="500.0" Y="425.0" ArrowHead="Arrow" />
<Anchor Position="0.5277777777777778" Shape="None" GraphId="c88ed" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id10038c63">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="613.5" Y="146.0" GraphRef="a7c35" RelX="-1.0" RelY="0.0" />
- <Point X="532.5" Y="146.0" GraphRef="f7a4a" RelX="1.0" RelY="0.0" ArrowHead="TBar" />
+ <Point GraphId="bb840" X="613.5" Y="146.0" GraphRef="a7c35" RelX="-1.0" RelY="0.0" />
+ <Point GraphId="d9b5b" X="532.5" Y="146.0" GraphRef="f7a4a" RelX="1.0" RelY="0.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id2bcc0724">
<Graphics ConnectorType="Elbow" ZOrder="12288" LineThickness="1.0">
- <Point X="398.5" Y="352.0" GraphRef="f7cc5" RelX="1.0" RelY="0.0" />
- <Point X="500.0" Y="391.0" GraphRef="c88ed" RelX="0.0" RelY="0.0" ArrowHead="TBar" />
+ <Point GraphId="da8a0" X="398.5" Y="352.0" GraphRef="f7cc5" RelX="1.0" RelY="0.0" />
+ <Point GraphId="ca3e7" X="500.0" Y="391.0" GraphRef="c88ed" RelX="0.0" RelY="0.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id4db865e3">
<Graphics ConnectorType="Elbow" ZOrder="12288" LineThickness="1.0">
- <Point X="613.5" Y="251.0" GraphRef="b4884" RelX="-1.0" RelY="0.0" />
- <Point X="516.25" Y="237.0" GraphRef="c5b29" RelX="0.5" RelY="1.0" ArrowHead="TBar" />
+ <Point GraphId="e399b" X="613.5" Y="251.0" GraphRef="b4884" RelX="-1.0" RelY="0.0" />
+ <Point GraphId="dc1c3" X="516.25" Y="237.0" GraphRef="c5b29" RelX="0.5" RelY="1.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id590c64af">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="500.0" Y="237.0" GraphRef="c5b29" RelX="0.0" RelY="1.0" />
- <Point X="500.0" Y="343.0" GraphRef="a3b9f" RelX="0.0" RelY="-1.0" ArrowHead="Arrow" />
+ <Point GraphId="ac03b" X="500.0" Y="237.0" GraphRef="c5b29" RelX="0.0" RelY="1.0" />
+ <Point GraphId="adf7a" X="500.0" Y="343.0" GraphRef="a3b9f" RelX="0.0" RelY="-1.0" ArrowHead="Arrow" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id84acafa9">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="398.5" Y="352.0" GraphRef="f7cc5" RelX="1.0" RelY="0.0" />
- <Point X="467.5" Y="353.0" GraphRef="a3b9f" RelX="-1.0" RelY="0.0" ArrowHead="TBar" />
+ <Point GraphId="e2080" X="398.5" Y="352.0" GraphRef="f7cc5" RelX="1.0" RelY="0.0" />
+ <Point GraphId="bfa48" X="467.5" Y="353.0" GraphRef="a3b9f" RelX="-1.0" RelY="0.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id8bad0f31">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="500.0" Y="156.0" GraphRef="f7a4a" RelX="0.0" RelY="1.0" />
- <Point X="500.0" Y="217.0" GraphRef="c5b29" RelX="0.0" RelY="-1.0" ArrowHead="Arrow" />
+ <Point GraphId="f21f4" X="500.0" Y="156.0" GraphRef="f7a4a" RelX="0.0" RelY="1.0" />
+ <Point GraphId="ac6a0" X="500.0" Y="217.0" GraphRef="c5b29" RelX="0.0" RelY="-1.0" ArrowHead="Arrow" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="idbf666215">
<Graphics ConnectorType="Elbow" ZOrder="12288" LineThickness="1.0">
- <Point X="231.0" Y="173.0" GraphRef="cbf8f" RelX="0.0" RelY="1.0" />
- <Point X="325.5" Y="324.5" GraphRef="dc68c" RelX="-1.0" RelY="-0.5" ArrowHead="Arrow" />
+ <Point GraphId="c0545" X="231.0" Y="173.0" GraphRef="cbf8f" RelX="0.0" RelY="1.0" />
+ <Point GraphId="ab8c0" X="325.5" Y="324.5" GraphRef="a9676" RelX="-1.0" RelY="-0.5" ArrowHead="Arrow" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="idc9b440f8">
<Graphics ConnectorType="Elbow" ZOrder="12288" LineThickness="1.0">
- <Point X="500.0" Y="136.0" GraphRef="f7a4a" RelX="0.0" RelY="-1.0" />
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- <Point X="160.0" Y="233.5" />
- <Point X="325.5" Y="351.0" GraphRef="dc68c" RelX="-1.0" RelY="0.0" ArrowHead="TBar" />
+ <Point GraphId="c7104" X="500.0" Y="136.0" GraphRef="f7a4a" RelX="0.0" RelY="-1.0" />
+ <Point GraphId="ad7a4" X="330.0" Y="116.0" />
+ <Point GraphId="b2247" X="160.0" Y="233.5" />
+ <Point GraphId="c1c2b" X="325.5" Y="351.0" GraphRef="a9676" RelX="-1.0" RelY="0.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="iddc0fcf4d">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="263.5" Y="163.0" GraphRef="cbf8f" RelX="1.0" RelY="0.0" />
- <Point X="325.5" Y="162.5" GraphRef="d5ca8" RelX="-1.0" RelY="-0.5" ArrowHead="Arrow" />
+ <Point GraphId="fb313" X="263.5" Y="163.0" GraphRef="cbf8f" RelX="1.0" RelY="0.0" />
+ <Point GraphId="ed702" X="325.5" Y="162.5" GraphRef="c5e03" RelX="-1.0" RelY="-0.5" ArrowHead="Arrow" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="idfd3c96c6">
<Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="398.5" Y="146.0" GraphRef="b2902" RelX="1.0" RelY="0.0" />
- <Point X="467.5" Y="146.0" GraphRef="f7a4a" RelX="-1.0" RelY="0.0" ArrowHead="TBar" />
+ <Point GraphId="a1840" X="398.5" Y="146.0" GraphRef="b2902" RelX="1.0" RelY="0.0" />
+ <Point GraphId="d875b" X="467.5" Y="146.0" GraphRef="f7a4a" RelX="-1.0" RelY="0.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id67fe0239">
<Graphics ConnectorType="Elbow" ZOrder="32786" LineThickness="1.0">
- <Point X="613.5" Y="186.0" GraphRef="a51a4" RelX="-1.0" RelY="0.0" />
- <Point X="516.25" Y="156.0" GraphRef="f7a4a" RelX="0.5" RelY="1.0" ArrowHead="TBar" />
+ <Point GraphId="ae8d3" X="613.5" Y="186.0" GraphRef="a51a4" RelX="-1.0" RelY="0.0" />
+ <Point GraphId="b5018" X="516.25" Y="156.0" GraphRef="f7a4a" RelX="0.5" RelY="1.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
<Interaction GraphId="id1c9d7524">
<Graphics ZOrder="32787" LineThickness="1.0">
- <Point X="398.5" Y="183.0" GraphRef="a3f88" RelX="1.0" RelY="0.0" />
- <Point X="483.75" Y="343.0" GraphRef="a3b9f" RelX="-0.5" RelY="-1.0" ArrowHead="TBar" />
+ <Point GraphId="d55b3" X="398.5" Y="183.0" GraphRef="a3f88" RelX="1.0" RelY="0.0" />
+ <Point GraphId="dc533" X="483.75" Y="343.0" GraphRef="a3b9f" RelX="-0.5" RelY="-1.0" ArrowHead="mim-inhibition" />
</Graphics>
<Xref Database="" ID="" />
</Interaction>
- <Group GroupId="c5e03" GraphId="d5ca8" />
- <Group GroupId="a9676" GraphId="dc68c" />
+ <Group GroupId="c5e03" GraphId="c5e03" />
+ <Group GroupId="a9676" GraphId="a9676" />
<InfoBox CenterX="0.0" CenterY="0.0" />
<Biopax>
+ <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
+ <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Notch signaling pathway</bp:TERM>
+ <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000204</bp:ID>
+ <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
+ </bp:openControlledVocabulary>
<bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="ea2">
<bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">14752159</bp:ID>
<bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
@@ -188,11 +192,6 @@ See figure 14 in http://www.wormbook.org/chapters/www_vulvaldev/vulvaldev.pdf.
<bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bais C</bp:AUTHORS>
<bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Greenwald I</bp:AUTHORS>
</bp:PublicationXref>
- <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
- <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Notch signaling pathway</bp:TERM>
- <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000204</bp:ID>
- <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
- </bp:openControlledVocabulary>
<bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="fa4">
<bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">18050418</bp:ID>
<bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
@@ -203,4 +202,3 @@ See figure 14 in http://www.wormbook.org/chapters/www_vulvaldev/vulvaldev.pdf.
</bp:PublicationXref>
</Biopax>
</Pathway>
-
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