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Nantia Leonidou
committed
Integrate alternative version of CURIEs within URIs
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‎models/Annotated_Models/iYO844_SBOannotated.xml

+17-17
Original file line numberDiff line numberDiff line change
@@ -32371,7 +32371,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU32830"/>
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</fbc:geneProductAssociation>
3237332373
</reaction>
32374-
<reaction metaid="R_ACACT3r" sboTerm="SBO:0000402" id="R_ACACT3r" name="Acetyl-CoA C-acyltransferase (hexanoyl-CoA) (r)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
32374+
<reaction metaid="R_ACACT3r" sboTerm="SBO:0000215" id="R_ACACT3r" name="Acetyl-CoA C-acyltransferase (hexanoyl-CoA) (r)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_ACACT3r">
@@ -32648,7 +32648,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU08860"/>
3264932649
</fbc:geneProductAssociation>
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</reaction>
32651-
<reaction metaid="R_ACACT1r" sboTerm="SBO:0000402" id="R_ACACT1r" name="Acetyl-CoA C-acetyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
32651+
<reaction metaid="R_ACACT1r" sboTerm="SBO:0000215" id="R_ACACT1r" name="Acetyl-CoA C-acetyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_ACACT1r">
@@ -32967,7 +32967,7 @@
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<speciesReference species="M_lipt_e" stoichiometry="1" constant="true"/>
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</listOfReactants>
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</reaction>
32970-
<reaction metaid="R_ACGS" sboTerm="SBO:0000402" id="R_ACGS" name="N-acetylglutamate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
32970+
<reaction metaid="R_ACGS" sboTerm="SBO:0000215" id="R_ACGS" name="N-acetylglutamate synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_ACGS">
@@ -34621,7 +34621,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU00760"/>
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</fbc:geneProductAssociation>
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</reaction>
34624-
<reaction metaid="R_ADD" sboTerm="SBO:0000376" id="R_ADD" name="Adenine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
34624+
<reaction metaid="R_ADD" sboTerm="SBO:0000401" id="R_ADD" name="Adenine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_ADD">
@@ -39709,7 +39709,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU27260"/>
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</fbc:geneProductAssociation>
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</reaction>
39712-
<reaction metaid="R_DCYTD" sboTerm="SBO:0000376" id="R_DCYTD" name="Deoxycytidine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
39712+
<reaction metaid="R_DCYTD" sboTerm="SBO:0000401" id="R_DCYTD" name="Deoxycytidine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
3971339713
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_DCYTD">
@@ -39954,7 +39954,7 @@
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</fbc:or>
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</fbc:geneProductAssociation>
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</reaction>
39957-
<reaction metaid="R_CYTD" sboTerm="SBO:0000376" id="R_CYTD" name="Cytidine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
39957+
<reaction metaid="R_CYTD" sboTerm="SBO:0000401" id="R_CYTD" name="Cytidine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_CYTD">
@@ -41158,7 +41158,7 @@
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<speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
4115941159
</listOfProducts>
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</reaction>
41161-
<reaction metaid="R_DCMPDA" sboTerm="SBO:0000376" id="R_DCMPDA" name="DCMP deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
41161+
<reaction metaid="R_DCMPDA" sboTerm="SBO:0000401" id="R_DCMPDA" name="DCMP deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
4116241162
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_DCMPDA">
@@ -41232,7 +41232,7 @@
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<speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
4123341233
</listOfProducts>
4123441234
</reaction>
41235-
<reaction metaid="R_CMPDAi" sboTerm="SBO:0000376" id="R_CMPDAi" name="CMP deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
41235+
<reaction metaid="R_CMPDAi" sboTerm="SBO:0000401" id="R_CMPDAi" name="CMP deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_CMPDAi">
@@ -44455,7 +44455,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU23850"/>
4445644456
</fbc:geneProductAssociation>
4445744457
</reaction>
44458-
<reaction metaid="R_G6PDA" sboTerm="SBO:0000376" id="R_G6PDA" name="Glucosamine-6-phosphate deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
44458+
<reaction metaid="R_G6PDA" sboTerm="SBO:0000401" id="R_G6PDA" name="Glucosamine-6-phosphate deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_G6PDA">
@@ -47268,7 +47268,7 @@
4726847268
<fbc:geneProductRef fbc:geneProduct="G_BSU37060"/>
4726947269
</fbc:geneProductAssociation>
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</reaction>
47271-
<reaction metaid="R_GUAD" sboTerm="SBO:0000376" id="R_GUAD" name="Guanine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
47271+
<reaction metaid="R_GUAD" sboTerm="SBO:0000401" id="R_GUAD" name="Guanine deaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
4727247272
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_GUAD">
@@ -53424,7 +53424,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU24310"/>
5342553425
</fbc:geneProductAssociation>
5342653426
</reaction>
53427-
<reaction metaid="R_MALTATr" sboTerm="SBO:0000402" id="R_MALTATr" name="Maltose O-acetyltransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
53427+
<reaction metaid="R_MALTATr" sboTerm="SBO:0000215" id="R_MALTATr" name="Maltose O-acetyltransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
5342853428
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_MALTATr">
@@ -53772,7 +53772,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU31580"/>
5377353773
</fbc:geneProductAssociation>
5377453774
</reaction>
53775-
<reaction metaid="R_MCSNAH" sboTerm="SBO:0000376" id="R_MCSNAH" name="5-Methylcytosine aminohydrolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
53775+
<reaction metaid="R_MCSNAH" sboTerm="SBO:0000401" id="R_MCSNAH" name="5-Methylcytosine aminohydrolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_MCSNAH">
@@ -54128,7 +54128,7 @@
5412854128
<fbc:geneProductRef fbc:geneProduct="G_BSU11610"/>
5412954129
</fbc:geneProductAssociation>
5413054130
</reaction>
54131-
<reaction metaid="R_ORNTAC_1" sboTerm="SBO:0000402" id="R_ORNTAC_1" name="Ornithine transacetylase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
54131+
<reaction metaid="R_ORNTAC_1" sboTerm="SBO:0000215" id="R_ORNTAC_1" name="Ornithine transacetylase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
5413254132
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_ORNTAC_1">
@@ -55755,7 +55755,7 @@
5575555755
<speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
5575655756
</listOfProducts>
5575755757
</reaction>
55758-
<reaction metaid="R_PTAr" sboTerm="SBO:0000402" id="R_PTAr" name="Phosphotransacetylase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
55758+
<reaction metaid="R_PTAr" sboTerm="SBO:0000215" id="R_PTAr" name="Phosphotransacetylase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_PTAr">
@@ -58175,7 +58175,7 @@
5817558175
<fbc:geneProductRef fbc:geneProduct="G_BSU19710"/>
5817658176
</fbc:geneProductAssociation>
5817758177
</reaction>
58178-
<reaction metaid="R_SERAT" sboTerm="SBO:0000402" id="R_SERAT" name="Serine O-acetyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
58178+
<reaction metaid="R_SERAT" sboTerm="SBO:0000215" id="R_SERAT" name="Serine O-acetyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
5817958179
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_SERAT">
@@ -59337,7 +59337,7 @@
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<fbc:geneProductRef fbc:geneProduct="G_BSU13730"/>
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</fbc:geneProductAssociation>
5933959339
</reaction>
59340-
<reaction metaid="R_SPMDAT1" sboTerm="SBO:0000402" id="R_SPMDAT1" name="Spermidine acetyltransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
59340+
<reaction metaid="R_SPMDAT1" sboTerm="SBO:0000215" id="R_SPMDAT1" name="Spermidine acetyltransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_SPMDAT1">
@@ -64194,7 +64194,7 @@
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</fbc:or>
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</fbc:geneProductAssociation>
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</reaction>
64197-
<reaction metaid="R_URIC" sboTerm="SBO:0000200" id="R_URIC" name="Uricase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
64197+
<reaction metaid="R_URIC" sboTerm="SBO:0000233" id="R_URIC" name="Uricase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#R_URIC">

‎src/sboannotator/SBOannotator.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -144,7 +144,7 @@ def getECNums(react):
144144
ECNums = []
145145
for line in lines:
146146
if 'ec-code' in line:
147-
ECNums.append(line.split('ec-code')[1][1:])
147+
ECNums.append(line.split('ec-code')[1][1:][:-3])
148148
return ECNums
149149

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