Commit f7859e99 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

Merge branch 'issue-9' into 'master'

Update conversion script

Closes #9

See merge request !227
parents 2adedfbd c95de239
......@@ -25,11 +25,15 @@ for currentpath, folders, files in os.walk(fullPath_modelDir):
print('(exception)')
# move both output files to the respective folders (note: files are overwritten)
fileName_sif = file[:-4] + '.sbml.sif'
fileName_sif = file[:-4] + '.sif'
fileName_raw = file[:-4] + '_raw.sif'
fileName_sbml = file[:-4] + '.sbml'
file_sif = os.path.join(currentpath, fileName_sif)
file_raw = os.path.join(currentpath, fileName_raw)
file_sbml = os.path.join(currentpath, fileName_sbml)
if os.path.isfile(file_sif) and os.path.isfile(file_sbml):
if os.path.isfile(file_sif) and os.path.isfile(file_sbml)and os.path.isfile(file_raw):
shutil.move(file_sif, os.path.join(outputDir, 'sif', fileName_sif))
shutil.move(file_raw, os.path.join(outputDir, 'sif', fileName_raw))
shutil.move(file_sbml, os.path.join(outputDir, 'sbml', fileName_sbml))
print(' Done.')
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......@@ -57,7 +57,7 @@
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006915" />
</rdf:Bag>
</bqbiol:isEncodedBy>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:BCL2_phosphorylated" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s20" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:!BCL2_phosphorylated" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s20" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
</rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="Autophagy_phenotype" qual:constant="false" qual:id="sa18"><annotation><rdf:RDF>
<rdf:Description rdf:about="#s21">
......@@ -245,7 +245,7 @@
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......
This diff is collapsed.
......@@ -84,7 +84,7 @@
<rdf:li rdf:resource="urn:miriam:hgnc:7562" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:TLR4" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s53" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:TLR4&amp;IRF6&amp;MYD88_cytoplasm" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s53" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
</rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="P65/P015_complex" qual:constant="false" qual:id="csa7"><annotation><rdf:RDF>
<rdf:Description rdf:about="#s165">
......@@ -273,7 +273,7 @@
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:TRIM14/TRIM23_complex" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s91" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
</rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="NFKB1:NFKNIA_complex" qual:constant="false" qual:id="csa21"><annotation><rdf:RDF><rdf:Description rdf:about="#s184"><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:NFKB1&amp;!CACTIN" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s184" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description></rdf:RDF></annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="Orf3a" qual:constant="true" qual:id="sa1"><annotation><rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="NFKB1:NFKNIA_complex" qual:constant="false" qual:id="csa21"><annotation><rdf:RDF><rdf:Description rdf:about="#s184"><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:NFKB1&amp;NFKBIA_phosphorylated_ubiquitinated_ubiquitinated_ubiquitinated&amp;!CACTIN" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s184" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description></rdf:RDF></annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="Orf3a" qual:constant="true" qual:id="sa1"><annotation><rdf:RDF>
<rdf:Description rdf:about="#s1">
<bqbiol:isVersionOf>
<rdf:Bag>
......@@ -338,7 +338,7 @@
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:TICAM1" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s13" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
</rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="CASP1" qual:constant="true" qual:id="sa25"><annotation><rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="CASP1" qual:constant="false" qual:id="sa25"><annotation><rdf:RDF>
<rdf:Description rdf:about="#s31">
<bqbiol:isDescribedBy>
<rdf:Bag>
......@@ -350,7 +350,7 @@
<rdf:li rdf:resource="urn:miriam:hgnc:1499" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:CASP1" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s31" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
<bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:function:PYCARD_ubiquitinated_ubiquitinated_ubiquitinated&amp;NLRP3" /></rdf:Bag></bqbiol:isDescribedBy><bqbiol:isDescribedBy><rdf:Bag><rdf:li rdf:resource="urn:casq:cdid:s31" /></rdf:Bag></bqbiol:isDescribedBy></rdf:Description>
</rdf:RDF>
</annotation></qual:qualitativeSpecies><qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:name="TRAF6_cytoplasm" qual:constant="false" qual:id="sa38"><annotation><rdf:RDF>
<rdf:Description rdf:about="#s54">
......@@ -691,7 +691,7 @@ HMOX1 PMID:19590927
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF></annotation></qual:transition><qual:transition qual:id="tr_csa8"><qual:listOfInputs><qual:input qual:qualitativeSpecies="sa142" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa8_in_0" /></qual:listOfInputs><qual:listOfOutputs><qual:output qual:qualitativeSpecies="csa8" qual:transitionEffect="assignmentLevel" qual:id="tr_csa8_out" /></qual:listOfOutputs><qual:listOfFunctionTerms><qual:defaultTerm qual:resultLevel="0" /><qual:functionTerm qual:resultLevel="1"><math xmlns="http://www.w3.org/1998/Math/MathML"><apply><eq /><ci>sa142</ci><cn type="integer">1</cn></apply></math></qual:functionTerm></qual:listOfFunctionTerms><annotation><rdf:RDF><rdf:Description rdf:about="#re112">
</rdf:RDF></annotation></qual:transition><qual:transition qual:id="tr_csa8"><qual:listOfInputs><qual:input qual:qualitativeSpecies="sa142" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa8_in_0" /><qual:input qual:qualitativeSpecies="sa141" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa8_in_1" /><qual:input qual:qualitativeSpecies="sa143" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa8_in_2" /></qual:listOfInputs><qual:listOfOutputs><qual:output qual:qualitativeSpecies="csa8" qual:transitionEffect="assignmentLevel" qual:id="tr_csa8_out" /></qual:listOfOutputs><qual:listOfFunctionTerms><qual:defaultTerm qual:resultLevel="0" /><qual:functionTerm qual:resultLevel="1"><math xmlns="http://www.w3.org/1998/Math/MathML"><apply><and /><apply><eq /><ci>sa142</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa141</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa143</ci><cn type="integer">1</cn></apply></apply></math></qual:functionTerm></qual:listOfFunctionTerms><annotation><rdf:RDF><rdf:Description rdf:about="#re112">
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<rdf:li rdf:resource="urn:miriam:pubmed:28829373" />
......@@ -794,7 +794,7 @@ TRIM23 PMID:20724660
</rdf:Bag>
</bqmodel:isDescribedBy>
</rdf:Description>
</rdf:RDF></annotation></qual:transition><qual:transition qual:id="tr_csa21"><qual:listOfInputs><qual:input qual:qualitativeSpecies="sa81" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa21_in_0" /><qual:input qual:qualitativeSpecies="sa138" qual:transitionEffect="none" qual:sign="negative" qual:id="tr_csa21_in_1" /></qual:listOfInputs><qual:listOfOutputs><qual:output qual:qualitativeSpecies="csa21" qual:transitionEffect="assignmentLevel" qual:id="tr_csa21_out" /></qual:listOfOutputs><qual:listOfFunctionTerms><qual:defaultTerm qual:resultLevel="0" /><qual:functionTerm qual:resultLevel="1"><math xmlns="http://www.w3.org/1998/Math/MathML"><apply><and /><apply><eq /><ci>sa81</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa138</ci><cn type="integer">0</cn></apply></apply></math></qual:functionTerm></qual:listOfFunctionTerms><annotation><rdf:RDF><rdf:Description rdf:about="#re93">
</rdf:RDF></annotation></qual:transition><qual:transition qual:id="tr_csa21"><qual:listOfInputs><qual:input qual:qualitativeSpecies="sa81" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa21_in_0" /><qual:input qual:qualitativeSpecies="sa65" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_csa21_in_1" /><qual:input qual:qualitativeSpecies="sa138" qual:transitionEffect="none" qual:sign="negative" qual:id="tr_csa21_in_2" /></qual:listOfInputs><qual:listOfOutputs><qual:output qual:qualitativeSpecies="csa21" qual:transitionEffect="assignmentLevel" qual:id="tr_csa21_out" /></qual:listOfOutputs><qual:listOfFunctionTerms><qual:defaultTerm qual:resultLevel="0" /><qual:functionTerm qual:resultLevel="1"><math xmlns="http://www.w3.org/1998/Math/MathML"><apply><and /><apply><eq /><ci>sa81</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa65</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa138</ci><cn type="integer">0</cn></apply></apply></math></qual:functionTerm></qual:listOfFunctionTerms><annotation><rdf:RDF><rdf:Description rdf:about="#re93">
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......@@ -832,6 +832,13 @@ A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Pote
</rdf:Bag>
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</rdf:RDF></annotation></qual:transition><qual:transition qual:id="tr_sa25"><qual:listOfInputs><qual:input qual:qualitativeSpecies="sa14" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_sa25_in_0" /><qual:input qual:qualitativeSpecies="sa10" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_sa25_in_1" /></qual:listOfInputs><qual:listOfOutputs><qual:output qual:qualitativeSpecies="sa25" qual:transitionEffect="assignmentLevel" qual:id="tr_sa25_out" /></qual:listOfOutputs><qual:listOfFunctionTerms><qual:defaultTerm qual:resultLevel="0" /><qual:functionTerm qual:resultLevel="1"><math xmlns="http://www.w3.org/1998/Math/MathML"><apply><and /><apply><eq /><ci>sa14</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa10</ci><cn type="integer">1</cn></apply></apply></math></qual:functionTerm></qual:listOfFunctionTerms><annotation><rdf:RDF><rdf:Description rdf:about="#re24">
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</rdf:RDF></annotation></qual:transition><qual:transition qual:id="tr_sa38"><qual:listOfInputs><qual:input qual:qualitativeSpecies="sa101" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_sa38_in_0" /><qual:input qual:qualitativeSpecies="sa49" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_sa38_in_1" /><qual:input qual:qualitativeSpecies="sa52" qual:transitionEffect="none" qual:sign="negative" qual:id="tr_sa38_in_2" /><qual:input qual:qualitativeSpecies="sa70" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_sa38_in_3" /></qual:listOfInputs><qual:listOfOutputs><qual:output qual:qualitativeSpecies="sa38" qual:transitionEffect="assignmentLevel" qual:id="tr_sa38_out" /></qual:listOfOutputs><qual:listOfFunctionTerms><qual:defaultTerm qual:resultLevel="0" /><qual:functionTerm qual:resultLevel="1"><math xmlns="http://www.w3.org/1998/Math/MathML"><apply><and /><apply><or /><apply><eq /><ci>sa49</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa70</ci><cn type="integer">1</cn></apply></apply><apply><eq /><ci>sa101</ci><cn type="integer">1</cn></apply><apply><eq /><ci>sa52</ci><cn type="integer">0</cn></apply></apply></math></qual:functionTerm></qual:listOfFunctionTerms><notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title /></head><body><p>TRAF6 PMID:20724660
TRIM 38 PMID: 22539786
TRIM 23 PMID: 20724660
......
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FADD POSITIVE FAS/FASL_complex
FAS/FASL_complex POSITIVE FADD
BAD/BBC3/BCL2L11_complex POSITIVE BAX
BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex
BAX POSITIVE BAD/BBC3/BCL2L11_complex
Orf7a POSITIVE BCL2/MCL1/BCL2L1_complex
E POSITIVE BCL2/MCL1/BCL2L1_complex
BAD NEGATIVE BCL2/MCL1/BCL2L1_complex
BAX NEGATIVE BCL2/MCL1/BCL2L1_complex
BCL2/MCL1/BCL2L1_complex NEGATIVE BAX
Apoptosome_complex POSITIVE CASP9_Cytoplasm
CYCS POSITIVE Apoptosome_complex
AKT1 NEGATIVE Apoptosome_complex
APAF1 POSITIVE Apoptosome_complex
CASP9_Cytoplasm POSITIVE Apoptosome_complex
MAPK14 POSITIVE CYCS
CASP9_Cytoplasm NEGATIVE AKT1
M NEGATIVE AKT1
BAD NEGATIVE AKT1
TRADD/FADD_complex POSITIVE TNF/TNFRSF1A_complex
AKT1 NEGATIVE Apoptosome_complex
AKT1 NEGATIVE CASP9_Cytoplasm
AKT1 NEGATIVE BAD
TNF/TNFRSF1A_complex POSITIVE TRADD/FADD_complex
TRADD/FADD_complex POSITIVE CASP8
FADD POSITIVE TRADD/FADD_complex
FADD POSITIVE CASP8
TRADD POSITIVE TRADD/FADD_complex
CASP8 POSITIVE TRADD/FADD_complex
CASP8 POSITIVE FADD
CASP3 POSITIVE CASP8
BID POSITIVE CASP8
CASP7 POSITIVE CASP8
Orf7a POSITIVE BCL2/MCL1/BCL2L1_complex
E POSITIVE BCL2/MCL1/BCL2L1_complex
BAD NEGATIVE BCL2/MCL1/BCL2L1_complex
CASP8 POSITIVE CASP3
CASP8 POSITIVE BID
CASP8 POSITIVE CASP7
CASP3 POSITIVE Apoptosis_phenotype
CASP9_Cytoplasm POSITIVE CASP3
Apoptosis_phenotype POSITIVE CASP3
CASP7 POSITIVE CASP9_Cytoplasm
BAX POSITIVE BID
Orf3a POSITIVE MAPK14
Apoptosis_phenotype POSITIVE CASP7
CASP9_Cytoplasm POSITIVE CASP7
BID POSITIVE BAX
MAPK14 POSITIVE CYCS
M NEGATIVE AKT1
CASP7 POSITIVE Apoptosis_phenotype
Orf3b POSITIVE Apoptosis_phenotype
Orf8a POSITIVE Apoptosis_phenotype
N POSITIVE Apoptosis_phenotype
S POSITIVE Apoptosis_phenotype
Orf9b POSITIVE Apoptosis_phenotype
Orf6 POSITIVE Apoptosis_phenotype
Orf3a POSITIVE MAPK14
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