A collection of canonical pre build Pattern to query BIOPAX datasets¶
imports¶
In [1]:
import logging
logging.getLogger().setLevel(logging.INFO)
In [2]:
from biopax_explorer.pattern.rack import Rack
from biopax_explorer.pattern.pattern import PatternExecutor
import json
In [3]:
from biopax_explorer.pattern.view import writePatternGraphView
from IPython.display import Image
In [4]:
rk=Rack()
In [5]:
print("#----------------------")
print("patterns")
print("#----------------------")
for pname,p in rk.patterns.items():
print("%s : %s"%(pname,p().description))
print("#----------------------")
print("sub patterns(building block)")
print("#----------------------")
for pname in rk.subpatterns.keys():
print(pname)
#----------------------
patterns
#----------------------
controlsMetabolicCatalysis :
Pattern for a Protein controlling a reaction whose participant is a small molecule.
The controller is in a Complex
notBlackboxComplexInComplex :
Pattern to detect inconsistant complex (recursive complexes of complexes)
inComplexWith :
A Pattern that defines two proteins have states that are members of the same complex. Handles nested complexes and
homologies. Also guarantees that relationship to the complex is through different direct
complex members.
inSameComplex :
Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
Complex membership can be through multiple nesting and/or through homology relations.
controlsExpressionWithTemplateReac :
a Pattern defining the control of a TemplateReation and the related products
usedToProduce :
A Pattern that associate 2 small molecules, product and substrat of a
biochemical reaction.
reactsWith :
Constructs a pattern where first and last small molecules are substrates to the same
biochemical reaction.
controlsPhosphorylation :
a Pattern that define the Control of Phosphorylation, including
Complex management
modifierConv :
a Pattern matching EntityReferences participating to Conversions
stateChange : Pattern matching State changes for conversions: a Conversion with an input and an output (PhysicalEntity)
that related to the same EntityReference. Complexes are excluded here
molecularInteraction :
inSameComplexEffectingControl :
a Complex that is the controller of a Control Interaction with the related Components
bindsTo :
a Complex with a least 2 Components, connects the entities
#----------------------
sub patterns(building block)
#----------------------
controlsMetabolicCatalysisBothSimple
controlsMetabolicCatalysisControllerComplex
controlsMetabolicCatalysisControlledComplex
controlsMetabolicCatalysisBothComplex
stateChangeSimple
stateChangeComplex
usedToProduceNoComplex
usedToProduceLeftComplex
usedToProduceRightComplex
usedToProduceBothComplex
reactsWithNoComplex
reactsWithComplex
controlsPhosphorylationRightSimple
controlsPhosphorylationControllerComplex
controlsPhosphorylationLeftComplex
controlsPhosphorylationRightComplex
controlsPhosphorylationBothComplex
controlsPhosphorylationBothComplexAndComplexController
controlsPhosphorylationControllerAndLeftComplex
controlsPhosphorylationControllerAndRightComplex
modifierConvNoComplex
modifierConvComplex
stateChangeNoComplex
controlsStateChangeSimple
controlsStateChangeComplexController
controlsStateChangeBothComplex
controlsStateChangeComplexControllerAndBothComplex
molecularInteractionNoComplex
molecularInteractionComplex
inSameActiveComplexMolecularInteraction
inSameActiveComplexOtherInteraction
Constants for database (change "localhost" for "db" if necessary)¶
In [6]:
datasetN = "netpath"
datasetP = "panther"
db = "http://db:3030" # with local triple store deployed with docker-compose
#db = "https://rdf-ds.genouest.org" # using an online default triple store
r = Rack()
peN = PatternExecutor(db,datasetN) # create a Pattern executor for a dataset
#peN.verbose() # display logs
peP = PatternExecutor(db,datasetP) # create a Pattern executor for a dataset
#peP.verbose() # display logs
# Function to print the URI of the 10 first lines of the results.
def first_lines_pk(res:list,size=10):
if len(res)==0:
print("-- no result in this dataset--")
else:
print("-- %s results in this dataset --" %(len(res)))
for tab in res[:size]:
for res in tab:
print(res.pk, end=', ')
print("")
def first_lines(res:list,size=10):
if len(res)==0:
print("-- no result in this dataset --")
else:
print("-- %s results in this dataset --" %(len(res)))
for tab in res[:size]:
for res in tab:
m={"uri":res.pk,"class":res.cls}
print(json.dumps(m))
print("")
Pattern 1 : controlsMetabolicCatalysis¶
In [7]:
p = r.controlsMetabolicCatalysis()
In [8]:
res_P1 = peP.executePattern(p)
first_lines(res_P1)
print("corresponding generated SPARQL queries (multiple here):")
print("#------------------------")
for q in peP.querylist:
print("###")
print(q)
print("###")
print("#------------------------")
-- 3275 results in this dataset --
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_bf734355b89c655065b642b8754aa36c", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#ComplexAssembly_efa6e8280aac983ec6be651e757cd78b", "class": "ComplexAssembly"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_63b519b626488d0507c012caf5ba35b0", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_8f856925befe1621671616de4e12a743", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_c50e1ff7775e9794c5069e26b936434c", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_2b00e35fa97280d9debaccf3c7c47949", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_8fa3b76da2bdd01480b77cb5d52a38e7", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_2e0b8e21985f121cd2beca5562a24e3c", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_01d50d0fb681063f6a793f3cb96e4e90", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_426e49fd9771d671dac83a7c5e6dc96a", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_cdcda9c01f126306f2b726a7611a2944", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_8730a53e4782012efda650e948164eda", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_70b40fb84e6f56a1b8c383541e387d74", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_7a80a9137f398accafa7fafbc590b59e", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_278c755335f2a60a24cf629df3147f10", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_3bee47256e65e3eff2d5bf04a0e4188e", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_1faa5595236a8a059d990caaeaa6efe3", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_8d0c4774249096fa3a53c07f38b99f21", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_8285213520a595441eeaa7c4c8424f11", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_6f36b46af192e8ce857e854c2c0948c4", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_1faa5595236a8a059d990caaeaa6efe3", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_8d0c4774249096fa3a53c07f38b99f21", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_8285213520a595441eeaa7c4c8424f11", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_88814a717e1a4c22061bd99ba8aacc68", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_1faa5595236a8a059d990caaeaa6efe3", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_8d0c4774249096fa3a53c07f38b99f21", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_8285213520a595441eeaa7c4c8424f11", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_a26ace79698aff1d911dac162224b216", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_72f3b21029de4015165e5cbfd12f5d46", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_f3acddb8bc7ac8cf318b2ce9b4220660", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_d6383d2fcea3015e161a2538d0e02178", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_bccd8c7f2e13b06278886fc396a52e78", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_72f3b21029de4015165e5cbfd12f5d46", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_f3acddb8bc7ac8cf318b2ce9b4220660", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_d6383d2fcea3015e161a2538d0e02178", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_9b8ceee9f90e5bd4375f4a00f3237f3d", "class": "SmallMolecule"}
{"uri": "http://pathwaycommons.org/pc12/#Catalysis_20c5d638404170a3a48ffd6aca619a9c", "class": "Catalysis"}
{"uri": "http://pathwaycommons.org/pc12/#BiochemicalReaction_9ed3b0e620ce3aac238ec44a1aa70172", "class": "BiochemicalReaction"}
{"uri": "http://pathwaycommons.org/pc12/#Protein_d2ab9888b77749d4eab57091313eca3d", "class": "Protein"}
{"uri": "http://pathwaycommons.org/pc12/#SmallMolecule_c32f873fe9f1dad2b69fc0b890145947", "class": "SmallMolecule"}
corresponding generated SPARQL queries (multiple here):
#------------------------
###
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bi: <http://www.biopax.org/release/biopax-level3.owl#>
select ?s2 ?o2 ?s4 ?o4 ?controlledn0I ?controllern0Controller ?asson1SM ?s2__rdft ?o2__rdft ?s4__rdft ?o4__rdft
where {
?s2 ?controlledn0I ?o2 .
?s2 ?controllern0Controller ?s4 .
?o2 ?asson1SM ?o4 .
?s2 rdf:type ?s2__rdft .
?o2 rdf:type ?o2__rdft .
?s4 rdf:type ?s4__rdft .
?o4 rdf:type ?o4__rdft .
{ ?o2 a bi:Conversion } UNION { ?o2 a bi:TransportWithBiochemicalReaction } UNION { ?o2 a bi:ComplexAssembly } UNION { ?o2 a bi:BiochemicalReaction } UNION { ?o2 a bi:Transport } UNION { ?o2 a bi:Degradation } .
{ ?o4 a bi:SmallMolecule } .
{ ?s2 a bi:Control } UNION { ?s2 a bi:Modulation } UNION { ?s2 a bi:Catalysis } UNION { ?s2 a bi:TemplateReactionRegulation } { ?s4 a bi:Protein }
FILTER ( ?controlledn0I = bi:controlled ) .
FILTER ( ?controllern0Controller = bi:controller ) .
FILTER ( ?asson1SM = bi:left || ?asson1SM = bi:right ) .
}
###
###
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bi: <http://www.biopax.org/release/biopax-level3.owl#>
select ?s2 ?o2 ?s4 ?o4 ?s6 ?controlledn0I ?controllern0complex ?componentn1Controller ?asson2SM ?s2__rdft ?o2__rdft ?s4__rdft ?o4__rdft ?s6__rdft
where {
?s2 ?controlledn0I ?s4 .
?s2 ?controllern0complex ?o2 .
?o2 ?componentn1Controller ?o4 .
?s4 ?asson2SM ?s6 .
?s2 rdf:type ?s2__rdft .
?o2 rdf:type ?o2__rdft .
?s4 rdf:type ?s4__rdft .
?o4 rdf:type ?o4__rdft .
?s6 rdf:type ?s6__rdft .
{ ?o2 a bi:Complex } .
{ ?o4 a bi:Protein } .
{ ?s2 a bi:Control } UNION { ?s2 a bi:Modulation } UNION { ?s2 a bi:Catalysis } UNION { ?s2 a bi:TemplateReactionRegulation } { ?s4 a bi:Conversion } UNION { ?s4 a bi:TransportWithBiochemicalReaction } UNION { ?s4 a bi:ComplexAssembly } UNION { ?s4 a bi:BiochemicalReaction } UNION { ?s4 a bi:Transport } UNION { ?s4 a bi:Degradation } { ?s6 a bi:SmallMolecule }
FILTER ( ?controlledn0I = bi:controlled ) .
FILTER ( ?controllern0complex = bi:controller ) .
FILTER ( ?componentn1Controller = bi:component ) .
FILTER ( ?asson2SM = bi:left || ?asson2SM = bi:right ) .
}
###
###
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bi: <http://www.biopax.org/release/biopax-level3.owl#>
select ?s2 ?o2 ?s4 ?o4 ?s6 ?controlledn0I ?controllern0Controller ?asson1Comp_cont ?componentn2SM ?s2__rdft ?o2__rdft ?s4__rdft ?o4__rdft ?s6__rdft
where {
?s2 ?controlledn0I ?o2 .
?s2 ?controllern0Controller ?o4 .
?o2 ?asson1Comp_cont ?s4 .
?s4 ?componentn2SM ?s6 .
?s2 rdf:type ?s2__rdft .
?o2 rdf:type ?o2__rdft .
?s4 rdf:type ?s4__rdft .
?o4 rdf:type ?o4__rdft .
?s6 rdf:type ?s6__rdft .
{ ?o2 a bi:Conversion } UNION { ?o2 a bi:TransportWithBiochemicalReaction } UNION { ?o2 a bi:ComplexAssembly } UNION { ?o2 a bi:BiochemicalReaction } UNION { ?o2 a bi:Transport } UNION { ?o2 a bi:Degradation } .
{ ?o4 a bi:Protein } .
{ ?s2 a bi:Control } UNION { ?s2 a bi:Modulation } UNION { ?s2 a bi:Catalysis } UNION { ?s2 a bi:TemplateReactionRegulation } { ?s4 a bi:Complex } { ?s6 a bi:SmallMolecule }
FILTER ( ?controlledn0I = bi:controlled ) .
FILTER ( ?controllern0Controller = bi:controller ) .
FILTER ( ?asson1Comp_cont = bi:left || ?asson1Comp_cont = bi:right ) .
FILTER ( ?componentn2SM = bi:component ) .
}
###
###
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bi: <http://www.biopax.org/release/biopax-level3.owl#>
select ?s2 ?o2 ?s4 ?o4 ?s6 ?o6 ?controllern0complex ?controlledn0I ?asson1Comp_cont ?componentn2Controller ?componentn3SM ?s2__rdft ?o2__rdft ?s4__rdft ?o4__rdft ?s6__rdft ?o6__rdft
where {
?s2 ?controllern0complex ?s4 .
?s2 ?controlledn0I ?o2 .
?o2 ?asson1Comp_cont ?o4 .
?s4 ?componentn2Controller ?s6 .
?o4 ?componentn3SM ?o6 .
?s2 rdf:type ?s2__rdft .
?o2 rdf:type ?o2__rdft .
?s4 rdf:type ?s4__rdft .
?o4 rdf:type ?o4__rdft .
?s6 rdf:type ?s6__rdft .
?o6 rdf:type ?o6__rdft .
{ ?o2 a bi:Conversion } UNION { ?o2 a bi:TransportWithBiochemicalReaction } UNION { ?o2 a bi:ComplexAssembly } UNION { ?o2 a bi:BiochemicalReaction } UNION { ?o2 a bi:Transport } UNION { ?o2 a bi:Degradation } .
{ ?o4 a bi:Complex } .
{ ?o6 a bi:SmallMolecule } .
{ ?s2 a bi:Control } UNION { ?s2 a bi:Modulation } UNION { ?s2 a bi:Catalysis } UNION { ?s2 a bi:TemplateReactionRegulation } { ?s4 a bi:Complex } { ?s6 a bi:Protein }
FILTER ( ?controllern0complex = bi:controller ) .
FILTER ( ?controlledn0I = bi:controlled ) .
FILTER ( ?asson1Comp_cont = bi:left || ?asson1Comp_cont = bi:right ) .
FILTER ( ?componentn2Controller = bi:component ) .
FILTER ( ?componentn3SM = bi:component ) .
}
###
#------------------------
Pattern 2 : inComplexWith¶
In [9]:
p = r.inComplexWith()
img="data/output/inComplexWith.svg"
writePatternGraphView(p,img,format="svg")
img="data/output/inComplexWith.png"
writePatternGraphView(p,img, format="png") # other format : svg
Image(img)
Out[9]:
In [10]:
res_P2 = peN.executePattern(p)
print("first result; object oriented instance manipulation")
print("first 10 results (uris)")
first_lines_pk(res_P2)
first result; object oriented instance manipulation first 10 results (uris) -- 3260 results in this dataset -- http://pathwaycommons.org/pc12/#Complex_151ed4c4ece14ff69a6d51679cb7ead7, http://pathwaycommons.org/pc12/#Protein_866d2e8479f1c4c1f92d8e5ad2214783, http://pathwaycommons.org/pc12/#Protein_b8221ae4aa1927b358e88d6eb6621650, http://identifiers.org/uniprot/P16471, http://identifiers.org/uniprot/O60674, http://pathwaycommons.org/pc12/#Complex_e06d3622e685e82d46a2edd9ccffc090, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_e56e82e7ef21b5799328ee719d6d47f6, http://identifiers.org/uniprot/Q9NQC7, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_06d601b603de842d87c35b35ad33865a, http://identifiers.org/uniprot/O43318, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_e8a68ac9ae711ea979d21b6cc0f6f6e8, http://identifiers.org/uniprot/Q15750, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_b1323a0b4e9f34d6985eca1fae5ab88e, http://identifiers.org/uniprot/Q9NYJ8, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_06d601b603de842d87c35b35ad33865a, http://identifiers.org/uniprot/O43318, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_3541eb6e587ca9aa170ff9f17bbd51ef, http://identifiers.org/uniprot/Q15750, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_acc48b6077852a67807a4e53fb625202, http://identifiers.org/uniprot/Q9NYJ8, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_83bea0b7026f945de6fe49284563eba9, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_9611f4ea83e9080927d39eac047f3b4f, http://identifiers.org/uniprot/O15111, http://identifiers.org/uniprot/Q9Y4K3, http://pathwaycommons.org/pc12/#Complex_9695d8dca18d787a873ffda9d7430f9f, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_af9220325cab4d60894e78f7f308a89e, http://identifiers.org/uniprot/Q8N5C8, http://identifiers.org/uniprot/Q9Y4K3,
Pattern 3 : inSameComplex¶
In [11]:
p = r.inSameComplex()
res_P3 = peN.executePattern(p)
first_lines_pk(res_P3)
-- 3260 results in this dataset -- http://pathwaycommons.org/pc12/#Complex_151ed4c4ece14ff69a6d51679cb7ead7, http://pathwaycommons.org/pc12/#Protein_866d2e8479f1c4c1f92d8e5ad2214783, http://pathwaycommons.org/pc12/#Protein_b8221ae4aa1927b358e88d6eb6621650, http://identifiers.org/uniprot/O60674, http://identifiers.org/uniprot/P16471, http://pathwaycommons.org/pc12/#Complex_e06d3622e685e82d46a2edd9ccffc090, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_e56e82e7ef21b5799328ee719d6d47f6, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q9NQC7, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_06d601b603de842d87c35b35ad33865a, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/O43318, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_e8a68ac9ae711ea979d21b6cc0f6f6e8, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q15750, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_b1323a0b4e9f34d6985eca1fae5ab88e, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q9NYJ8, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_06d601b603de842d87c35b35ad33865a, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/O43318, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_3541eb6e587ca9aa170ff9f17bbd51ef, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q15750, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_acc48b6077852a67807a4e53fb625202, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q9NYJ8, http://pathwaycommons.org/pc12/#Complex_83bea0b7026f945de6fe49284563eba9, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_9611f4ea83e9080927d39eac047f3b4f, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/O15111, http://pathwaycommons.org/pc12/#Complex_9695d8dca18d787a873ffda9d7430f9f, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_af9220325cab4d60894e78f7f308a89e, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q8N5C8,
Pattern 4 : controlsExpressionWithTemplateReac¶
In [12]:
p = r.controlsExpressionWithTemplateReac()
res_P4 = peP.executePattern(p)
first_lines_pk(res_P4)
-- 186 results in this dataset -- http://pathwaycommons.org/pc12/#TemplateReactionRegulation_add65d7dcbc0fb64fc52416c02436599, http://pathwaycommons.org/pc12/#TemplateReaction_37ac8d251fe3fd2ea22d887ba5b8857f, http://pathwaycommons.org/pc12/#Protein_5d5c7c0d2e7914c18f27aaa341e2cdb7, http://pathwaycommons.org/pc12/#RnaRegion_f109fbc253f916f257db07b61d15d295, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_1be59a46ad3d359b55fa6b1ab01c5ee5, http://pathwaycommons.org/pc12/#TemplateReaction_37ac8d251fe3fd2ea22d887ba5b8857f, http://pathwaycommons.org/pc12/#Protein_3b4e32b8b764ba16cb98757ec6c19eb7, http://pathwaycommons.org/pc12/#RnaRegion_f109fbc253f916f257db07b61d15d295, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_06835df57c87a930dfa9f8a3feffc686, http://pathwaycommons.org/pc12/#TemplateReaction_37ac8d251fe3fd2ea22d887ba5b8857f, http://pathwaycommons.org/pc12/#Protein_8324c842a1e05e915f991efc894ea678, http://pathwaycommons.org/pc12/#RnaRegion_f109fbc253f916f257db07b61d15d295, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_5e0c4025ca1a333e86b30eb8384513bc, http://pathwaycommons.org/pc12/#TemplateReaction_97ef7a8129f069765e6249b4afb52eb7, http://pathwaycommons.org/pc12/#Protein_c867045130d2b7b30740a9aae5f6f494, http://pathwaycommons.org/pc12/#RnaRegion_200a9de4aaa90aa1161fad84c33f4a6d, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_130a64de8844e761d9da9780d850fd39, http://pathwaycommons.org/pc12/#TemplateReaction_860eaaa289530127c787af86b11e1448, http://pathwaycommons.org/pc12/#Protein_c680df97459f02ac22a5ec92d69a702b, http://pathwaycommons.org/pc12/#RnaRegion_e9d69b79854e5dff36b6f49f1033269d, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_7054bae9b2dbd5b9bc5d9273363ee45a, http://pathwaycommons.org/pc12/#TemplateReaction_860eaaa289530127c787af86b11e1448, http://pathwaycommons.org/pc12/#Protein_80563fb9cb9c29ebc001b816214a0f25, http://pathwaycommons.org/pc12/#RnaRegion_e9d69b79854e5dff36b6f49f1033269d, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_cdf61e247c26f90e9023e59eeaf2130a, http://pathwaycommons.org/pc12/#TemplateReaction_860eaaa289530127c787af86b11e1448, http://pathwaycommons.org/pc12/#Protein_64cc20b39c2f00be1c83b57a800c81fc, http://pathwaycommons.org/pc12/#RnaRegion_e9d69b79854e5dff36b6f49f1033269d, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_cfff4f9277ce613f5be84761276adeea, http://pathwaycommons.org/pc12/#TemplateReaction_860eaaa289530127c787af86b11e1448, http://pathwaycommons.org/pc12/#Protein_bbf0c1cf3835eb05635108a5e5380d61, http://pathwaycommons.org/pc12/#RnaRegion_e9d69b79854e5dff36b6f49f1033269d, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_6d3e98e35b5ae7b7541cd6d756fe3e7c, http://pathwaycommons.org/pc12/#TemplateReaction_02877f9518dfb68cdaa721dc0c4459e5, http://pathwaycommons.org/pc12/#Protein_5b97596607aa8c3b7ed00d7acdd0f913, http://pathwaycommons.org/pc12/#RnaRegion_fb2fba6ee82767f69dd08f11a8b3b894, http://pathwaycommons.org/pc12/#TemplateReactionRegulation_abd5e1c199852e823f234e3e4a9f5de8, http://pathwaycommons.org/pc12/#TemplateReaction_90fbec469fd9944e593c934cceeac9d2, http://pathwaycommons.org/pc12/#Complex_83e47b7d07a1abb74999a2f43e1cd461, http://pathwaycommons.org/pc12/#RnaRegion_917475ef07dc93b84b9ee5bd75a35419,
Pattern 5 : usedToProduce¶
In [13]:
p = r.usedToProduce()
res_P5 = peP.executePattern(p)
first_lines_pk(res_P5)
-- 2187 results in this dataset -- http://pathwaycommons.org/pc12/#BiochemicalReaction_815ee23e669b10849643f993bdbdc3af, http://pathwaycommons.org/pc12/#SmallMolecule_066bc5ddd20dbef88d54e189b9f716bf, http://pathwaycommons.org/pc12/#SmallMolecule_3d85ded276e55e2e7ec06ee6bb2be135, http://pathwaycommons.org/pc12/#SmallMoleculeReference_5750bd948616539b8647edb46f9aa539, http://pathwaycommons.org/pc12/#SmallMoleculeReference_686ef261203d10c67957192ddd952738, http://pathwaycommons.org/pc12/#BiochemicalReaction_2097515ad5b19f4e233ac6fa3d6b2f55, http://pathwaycommons.org/pc12/#SmallMolecule_b67e77bc899d7ee3f7bf4200f6e0508f, http://pathwaycommons.org/pc12/#SmallMolecule_048629e5e56fe4832bcf5abde167fdd1, http://pathwaycommons.org/pc12/#SmallMoleculeReference_90d32d835a981139866261bc79543575, http://pathwaycommons.org/pc12/#SmallMoleculeReference_65852063d330bbe7d28860361a8610dd, http://pathwaycommons.org/pc12/#BiochemicalReaction_6b0855cf708ec67bf82d12a055656edd, http://pathwaycommons.org/pc12/#SmallMolecule_b67e77bc899d7ee3f7bf4200f6e0508f, http://pathwaycommons.org/pc12/#SmallMolecule_640691e04875e8aadbbb789920d78f38, http://pathwaycommons.org/pc12/#SmallMoleculeReference_90d32d835a981139866261bc79543575, http://pathwaycommons.org/pc12/#SmallMoleculeReference_2fe329aa93c03f9bd83901ccc6548b1e, http://pathwaycommons.org/pc12/#BiochemicalReaction_6b0855cf708ec67bf82d12a055656edd, http://pathwaycommons.org/pc12/#SmallMolecule_b67e77bc899d7ee3f7bf4200f6e0508f, http://pathwaycommons.org/pc12/#SmallMolecule_425d6230f92a99bea1650f3e7fd71442, http://pathwaycommons.org/pc12/#SmallMoleculeReference_90d32d835a981139866261bc79543575, http://pathwaycommons.org/pc12/#SmallMoleculeReference_ae3e69f3ae3d42aa3d6ea4e48c1ec5c3, http://pathwaycommons.org/pc12/#TransportWithBiochemicalReaction_e9498c0682dbc58c43108093e0be2182, http://pathwaycommons.org/pc12/#SmallMolecule_59db4cf232af4075775e8f97c4dbc293, http://pathwaycommons.org/pc12/#SmallMolecule_0683fff7d3a426c84aebe76e0f8ddd45, http://pathwaycommons.org/pc12/#SmallMoleculeReference_f98a47f6a022bed71581d08cd6bfb20b, http://pathwaycommons.org/pc12/#SmallMoleculeReference_3c50f14385739b1cc571c4add5d78868, http://pathwaycommons.org/pc12/#BiochemicalReaction_33ce6cac9c9c0a738ec0ee42e9d49146, http://pathwaycommons.org/pc12/#SmallMolecule_9d76a86423840bb15c93e0e9cdc0e596, http://pathwaycommons.org/pc12/#SmallMolecule_ead51a2707fa93d7f85053d65a27ab16, http://pathwaycommons.org/pc12/#SmallMoleculeReference_fcbb7e7ae3dcb88435fcd4340bc0a806, http://identifiers.org/chebi/CHEBI:15377, http://pathwaycommons.org/pc12/#BiochemicalReaction_33ce6cac9c9c0a738ec0ee42e9d49146, http://pathwaycommons.org/pc12/#SmallMolecule_9d76a86423840bb15c93e0e9cdc0e596, http://pathwaycommons.org/pc12/#SmallMolecule_fa20650ce11e392c092c4a45f699090b, http://pathwaycommons.org/pc12/#SmallMoleculeReference_fcbb7e7ae3dcb88435fcd4340bc0a806, http://pathwaycommons.org/pc12/#SmallMoleculeReference_5d09f859ee9a3a73b8efae4f7d9df583, http://pathwaycommons.org/pc12/#BiochemicalReaction_044fe89923ec7521535d8ea57d966de5, http://pathwaycommons.org/pc12/#SmallMolecule_1e41e6ac37c7bcbb9cafdd8cd201c802, http://pathwaycommons.org/pc12/#SmallMolecule_c50186bf1c98736d2f553516c59309f9, http://pathwaycommons.org/pc12/#SmallMoleculeReference_39bea8f8657229e7843d8f4e33fe939d, http://pathwaycommons.org/pc12/#SmallMoleculeReference_5e70acf8687382e1e0cfc068382bba58, http://pathwaycommons.org/pc12/#BiochemicalReaction_7c75e63fb2bfad20c27af5f3f83b1ec6, http://pathwaycommons.org/pc12/#SmallMolecule_d462c87fb86ef87f2f483190dfc3a4d5, http://pathwaycommons.org/pc12/#SmallMolecule_a3d636b58d324dc18bff85af9fc6c97d, http://pathwaycommons.org/pc12/#SmallMoleculeReference_15ccfaaca1b43869ec411dd592c031a7, http://pathwaycommons.org/pc12/#SmallMoleculeReference_ef19dfe4283283d543e8661f478aa880, http://pathwaycommons.org/pc12/#BiochemicalReaction_60cab5957435444bb0db2a65f4b7a7e5, http://pathwaycommons.org/pc12/#SmallMolecule_d462c87fb86ef87f2f483190dfc3a4d5, http://pathwaycommons.org/pc12/#SmallMolecule_a3d636b58d324dc18bff85af9fc6c97d, http://pathwaycommons.org/pc12/#SmallMoleculeReference_15ccfaaca1b43869ec411dd592c031a7, http://pathwaycommons.org/pc12/#SmallMoleculeReference_ef19dfe4283283d543e8661f478aa880,
Pattern 6 : reactsWith¶
In [14]:
p = r.reactsWith()
res_P6 = peP.executePattern(p)
first_lines_pk(res_P6)
-- 998 results in this dataset -- http://pathwaycommons.org/pc12/#BiochemicalReaction_6b0855cf708ec67bf82d12a055656edd, http://pathwaycommons.org/pc12/#SmallMolecule_b67e77bc899d7ee3f7bf4200f6e0508f, http://pathwaycommons.org/pc12/#SmallMolecule_d7efcaa9d1c288e5b3713eff1052ca77, http://pathwaycommons.org/pc12/#SmallMoleculeReference_90d32d835a981139866261bc79543575, http://pathwaycommons.org/pc12/#SmallMoleculeReference_abaf546f7ef829143f9f8c11063d43ef, http://pathwaycommons.org/pc12/#BiochemicalReaction_48bef198676d2676d363dedec8cc7d0b, http://pathwaycommons.org/pc12/#SmallMolecule_237a205a845e789bc5c8e5ca10b590e1, http://pathwaycommons.org/pc12/#SmallMolecule_b6a213c137b4e3c2c49ba78eed4dde9f, http://pathwaycommons.org/pc12/#SmallMoleculeReference_0634987c3518b8a291024af3a7901f8c, http://pathwaycommons.org/pc12/#SmallMoleculeReference_fa9256047ab86f2827b316defbc5512d, http://pathwaycommons.org/pc12/#BiochemicalReaction_6f9ee54c9cbd61375919c3b4a4094e00, http://pathwaycommons.org/pc12/#SmallMolecule_2db23e4841261b98b7bf1f69430eb23e, http://pathwaycommons.org/pc12/#SmallMolecule_b8a3715331796c6cfad4ffc359024884, http://identifiers.org/chebi/CHEBI:15440, http://pathwaycommons.org/pc12/#SmallMoleculeReference_2d6593d106f3b53963f88d0f15287f3d, http://pathwaycommons.org/pc12/#BiochemicalReaction_9f920da611af2c80ab80f2fada79ea30, http://pathwaycommons.org/pc12/#SmallMolecule_739f11c0781284f58d90adcf4b53830e, http://pathwaycommons.org/pc12/#SmallMolecule_8bbbdd8720f2d1c2585b63c838d9de27, http://identifiers.org/chebi/CHEBI:15377, http://pathwaycommons.org/pc12/#SmallMoleculeReference_3248319a736b4d7579a8203fe8526406, http://pathwaycommons.org/pc12/#BiochemicalReaction_39bc687fae06aee25b01ba2edfee09a5, http://pathwaycommons.org/pc12/#SmallMolecule_03c161ff7a1d37ebdaafa78be0a96fc2, http://pathwaycommons.org/pc12/#SmallMolecule_b08e26fe1b6595b22b27028f7361fd7e, http://identifiers.org/chebi/CHEBI:15377, http://pathwaycommons.org/pc12/#SmallMoleculeReference_919af35598fcd386802ba6ef214a8efd, http://pathwaycommons.org/pc12/#BiochemicalReaction_39bc687fae06aee25b01ba2edfee09a5, http://pathwaycommons.org/pc12/#SmallMolecule_b08e26fe1b6595b22b27028f7361fd7e, http://pathwaycommons.org/pc12/#SmallMolecule_03c161ff7a1d37ebdaafa78be0a96fc2, http://pathwaycommons.org/pc12/#SmallMoleculeReference_919af35598fcd386802ba6ef214a8efd, http://identifiers.org/chebi/CHEBI:15377, http://pathwaycommons.org/pc12/#BiochemicalReaction_51509f0a033c6fb27ee9deb8e3df4eec, http://pathwaycommons.org/pc12/#SmallMolecule_39ff56d2ab8319f6f08a115bf91a2a56, http://pathwaycommons.org/pc12/#SmallMolecule_cc195586d2f74f757d7dbc665889733e, http://pathwaycommons.org/pc12/#SmallMoleculeReference_04792497eaecb608d3113fd1b000ec7b, http://pathwaycommons.org/pc12/#SmallMoleculeReference_3f9e3edc0b730528abedbb86dfdd0ea2, http://pathwaycommons.org/pc12/#BiochemicalReaction_0f68011dc4f1874d3616950dd98c3108, http://pathwaycommons.org/pc12/#SmallMolecule_e194d6329900104ae996ee567e0ff42f, http://pathwaycommons.org/pc12/#SmallMolecule_32a595a688808adb1e810037b5d6efba, http://identifiers.org/chebi/CHEBI:15377, http://identifiers.org/chebi/CHEBI:17769, http://pathwaycommons.org/pc12/#BiochemicalReaction_0f68011dc4f1874d3616950dd98c3108, http://pathwaycommons.org/pc12/#SmallMolecule_e194d6329900104ae996ee567e0ff42f, http://pathwaycommons.org/pc12/#SmallMolecule_b705c0f828cdcd099f4510f2f9c4cdb0, http://identifiers.org/chebi/CHEBI:15377, http://pathwaycommons.org/pc12/#SmallMoleculeReference_3b2fa0170d13f8fa13c6237362803d65, http://pathwaycommons.org/pc12/#BiochemicalReaction_e8d4f477e3c0176324f1a6bc9d3591d7, http://pathwaycommons.org/pc12/#SmallMolecule_b6280301b757081f4833d0e77bf43560, http://pathwaycommons.org/pc12/#SmallMolecule_6535eca9955e86e9d6188a260185f721, http://pathwaycommons.org/pc12/#SmallMoleculeReference_a1702407967b7a5af99fb0fab1af49d4, http://pathwaycommons.org/pc12/#SmallMoleculeReference_01ea1c23d7372a485be4946b1ec768e1,
Pattern 7 : controlsPhosphorylation¶
In [15]:
p = r.controlsPhosphorylation()
res_P7 = peP.executePattern(p)
first_lines_pk(res_P7)
-- 1072 results in this dataset -- http://pathwaycommons.org/pc12/#Catalysis_b0ad8734438b714c57af7cb0251ce9a5, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_fe52684ca9f539eaaad8d810077e2763, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_f1317f5ca6ac5be1281a7e8f81a3714d, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_b0ad8734438b714c57af7cb0251ce9a5, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_fe52684ca9f539eaaad8d810077e2763, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_93f83f5bfc38cd41abf33ce92368e35b, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_a1cc330e94ec6c45034bb51de1f09427, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_f78e3806c7c8b4722885dd321fab439b, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_f1317f5ca6ac5be1281a7e8f81a3714d, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_a1cc330e94ec6c45034bb51de1f09427, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_f78e3806c7c8b4722885dd321fab439b, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_93f83f5bfc38cd41abf33ce92368e35b, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_57dc30e9998d4587ab0ee890ce3d1231, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_64a24491038ff6567e7e7a73c9f3a612, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_f1317f5ca6ac5be1281a7e8f81a3714d, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_57dc30e9998d4587ab0ee890ce3d1231, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_64a24491038ff6567e7e7a73c9f3a612, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_93f83f5bfc38cd41abf33ce92368e35b, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_7b96923624fe62f24d8d7149ecbc6e5d, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_e7c461d6c86f241a39a4a5f6f44ee883, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_f1317f5ca6ac5be1281a7e8f81a3714d, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_7b96923624fe62f24d8d7149ecbc6e5d, http://pathwaycommons.org/pc12/#BiochemicalReaction_c2c31839b509e5b522ab2d830d170cfd, http://pathwaycommons.org/pc12/#Protein_e7c461d6c86f241a39a4a5f6f44ee883, http://pathwaycommons.org/pc12/#Protein_c5339551528b55a0a1d463cdc6547d67, http://pathwaycommons.org/pc12/#Protein_18dd08a268a592a72d3a06674b4b3b00, http://identifiers.org/uniprot/Q15139, http://identifiers.org/uniprot/Q15139, http://pathwaycommons.org/pc12/#ModificationFeature_93f83f5bfc38cd41abf33ce92368e35b, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_504cfcec81e9d00614cf051e77ad5ebb, http://pathwaycommons.org/pc12/#BiochemicalReaction_a30fc526797ea47e4b6da614134c8919, http://pathwaycommons.org/pc12/#Protein_a0a42138b4dbda3670341b30e6b6a560, http://pathwaycommons.org/pc12/#Protein_114e3ea7ac66671c3e447aaafd88276c, http://pathwaycommons.org/pc12/#Protein_3f15bc282189bf416d38a6cc1bb40d7e, http://identifiers.org/uniprot/Q99558, http://identifiers.org/uniprot/Q99558, http://pathwaycommons.org/pc12/#ModificationFeature_ddfad583f93920aae45d797e8b999f1e, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a, http://pathwaycommons.org/pc12/#Catalysis_e3e8bf85f400454e33da440ccefa8b99, http://pathwaycommons.org/pc12/#BiochemicalReaction_17f676ac0c135441c3261bb443bc5296, http://pathwaycommons.org/pc12/#Protein_008b881b83e8df5cc18bb452d0c764c9, http://pathwaycommons.org/pc12/#Protein_008b881b83e8df5cc18bb452d0c764c9, http://pathwaycommons.org/pc12/#Protein_afe84d83fcc9d0dda46e9b48419cf72a, http://identifiers.org/uniprot/Q9H6Q3, http://identifiers.org/uniprot/Q9H6Q3, http://pathwaycommons.org/pc12/#ModificationFeature_c64577a9bd29502051da7ed17bcdb42b, http://pathwaycommons.org/pc12/#SequenceModificationVocabulary_9154163cbf19483e42047bb3e4b24f1a,
Pattern 8 : modifierConv¶
In [16]:
p = r.modifierConv()
res_P8 = peN.executePattern(p)
first_lines_pk(res_P8)
-- 4872 results in this dataset -- http://pathwaycommons.org/pc12/#BiochemicalReaction_62f7ae47833be6077a61c0ddde84c917, http://pathwaycommons.org/pc12/#Protein_97a295df2ce7640ba4b4cb9f7afd7b5a, http://identifiers.org/uniprot/P10911, http://pathwaycommons.org/pc12/#BiochemicalReaction_6bea1a1ac392ba528c7e695e3b93a2db, http://pathwaycommons.org/pc12/#Protein_8d5fb5187319f27988b0da64aa78f27a, http://identifiers.org/uniprot/P46108, http://pathwaycommons.org/pc12/#BiochemicalReaction_6271a6d580d3e399b631e2e625ee8ff0, http://pathwaycommons.org/pc12/#Protein_57aa30744f37edbc717cd99605280e70, http://identifiers.org/uniprot/P28482, http://pathwaycommons.org/pc12/#BiochemicalReaction_b892991189fbca87ef55e70584793cc0, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_324cadcff5e64e13633623f039a406b5, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_8cf86c76ee338ceb3dc0ed6913538a81, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_7ee4de755f8857798377c821374adaf4, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_4bbb65e68352dbc43dd75c749d5c95bf, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_103591e64a73e96623a839af84bfc419, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_373ab172d5f1e419873ff6fe5b24f9f0, http://pathwaycommons.org/pc12/#Protein_a0b15919e4be3f2d601c5462414fda33, http://identifiers.org/uniprot/P07332,
Pattern 9 : stateChange¶
In [17]:
p = r.stateChange()
res_P9 = peN.executePattern(p)
first_lines_pk(res_P9)
-- 2384 results in this dataset -- http://pathwaycommons.org/pc12/#BiochemicalReaction_62f7ae47833be6077a61c0ddde84c917, http://pathwaycommons.org/pc12/#Protein_97a295df2ce7640ba4b4cb9f7afd7b5a, http://pathwaycommons.org/pc12/#Protein_7a654be983aa80d020c8b6c3617abb59, http://identifiers.org/uniprot/P10911, http://identifiers.org/uniprot/P10911, http://pathwaycommons.org/pc12/#BiochemicalReaction_6bea1a1ac392ba528c7e695e3b93a2db, http://pathwaycommons.org/pc12/#Protein_8d5fb5187319f27988b0da64aa78f27a, http://pathwaycommons.org/pc12/#Protein_15cba89b6f8236780573d3db8ef8e13b, http://identifiers.org/uniprot/P46108, http://identifiers.org/uniprot/P46108, http://pathwaycommons.org/pc12/#BiochemicalReaction_6271a6d580d3e399b631e2e625ee8ff0, http://pathwaycommons.org/pc12/#Protein_57aa30744f37edbc717cd99605280e70, http://pathwaycommons.org/pc12/#Protein_b424629aa340138e90806183e0d4e884, http://identifiers.org/uniprot/P28482, http://identifiers.org/uniprot/P28482, http://pathwaycommons.org/pc12/#BiochemicalReaction_b892991189fbca87ef55e70584793cc0, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_4a8a145108f9fa59685c6190430fbeed, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_324cadcff5e64e13633623f039a406b5, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_4a8a145108f9fa59685c6190430fbeed, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_8cf86c76ee338ceb3dc0ed6913538a81, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_7d9d48263c3e50b88fd7c24e51cae5e7, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_7ee4de755f8857798377c821374adaf4, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_4a8a145108f9fa59685c6190430fbeed, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_4bbb65e68352dbc43dd75c749d5c95bf, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_1f1a49472ae0a0c6dcb54e3372d2c060, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_103591e64a73e96623a839af84bfc419, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_4a8a145108f9fa59685c6190430fbeed, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://pathwaycommons.org/pc12/#BiochemicalReaction_373ab172d5f1e419873ff6fe5b24f9f0, http://pathwaycommons.org/pc12/#Protein_a0b15919e4be3f2d601c5462414fda33, http://pathwaycommons.org/pc12/#Protein_4e432defa142bafd41516f97a56c6a19, http://identifiers.org/uniprot/P07332, http://identifiers.org/uniprot/P07332,
Pattern 10 : controlsStateChange¶
In [18]:
p = r.controlsStateChange()
res_P10 = peN.executePattern(p)
first_lines_pk(res_P10)
-- 676 results in this dataset -- http://pathwaycommons.org/pc12/#Catalysis_84b80f728dd3f89bea7345778bb4eb94, http://pathwaycommons.org/pc12/#BiochemicalReaction_b892991189fbca87ef55e70584793cc0, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_4a8a145108f9fa59685c6190430fbeed, http://pathwaycommons.org/pc12/#Protein_79856ff790bab5a19b49069093957a14, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P35568, http://identifiers.org/uniprot/P52333, http://pathwaycommons.org/pc12/#Catalysis_2bfcf2717ebcae1ac6cf016a18f378aa, http://pathwaycommons.org/pc12/#BiochemicalReaction_08ca73a5dd4bf0ce213249092a677cac, http://pathwaycommons.org/pc12/#Protein_0639838efa23abff14ceebf9b544fc43, http://pathwaycommons.org/pc12/#Protein_45a55c65b8a1e11d00324e8d63afaefa, http://pathwaycommons.org/pc12/#Protein_55c11ec747711fe7bd4b1b4677035292, http://identifiers.org/uniprot/P29353, http://identifiers.org/uniprot/P29353, http://identifiers.org/uniprot/P43403, http://pathwaycommons.org/pc12/#Catalysis_761d59b001b4e13419d4206cf6187594, http://pathwaycommons.org/pc12/#BiochemicalReaction_fd6f906a21b3216114e2b4a70aa5d36d, http://pathwaycommons.org/pc12/#Protein_fb3e4401d929c9bb9841a234957d19ea, http://pathwaycommons.org/pc12/#Protein_f153d8cc57f3d9a501c57bfa42cf432c, http://pathwaycommons.org/pc12/#Protein_cad5314057182882d22eaf60245812c2, http://identifiers.org/uniprot/O14939, http://identifiers.org/uniprot/O14939, http://identifiers.org/uniprot/Q00535, http://pathwaycommons.org/pc12/#Catalysis_745bba12cdf996d59a99cd2de8e91003, http://pathwaycommons.org/pc12/#BiochemicalReaction_e1f7939035dbee2e05d723e07a556e7d, http://pathwaycommons.org/pc12/#Protein_7198db590ea2aaf658c8e37d27c065fe, http://pathwaycommons.org/pc12/#Protein_d58331cdc1bcdc08496ba471fb5bf9ad, http://pathwaycommons.org/pc12/#Protein_22ad8b1fa026b0aed99a4445c1fe6c07, http://identifiers.org/uniprot/P18846, http://identifiers.org/uniprot/P18846, http://identifiers.org/uniprot/O75582, http://pathwaycommons.org/pc12/#Catalysis_1d5260bd721a4b83f714cc1f9e4ca007, http://pathwaycommons.org/pc12/#BiochemicalReaction_9ef85ced26b313819ca0cebb97a90ee8, http://pathwaycommons.org/pc12/#Protein_b6632a752d40186d303ac0c1261ead91, http://pathwaycommons.org/pc12/#Protein_d4ec3f7fad1ae35ab4b5b747606e8c16, http://pathwaycommons.org/pc12/#Protein_5cb6d7be3209fed9891cd985fb1ce0ed, http://identifiers.org/uniprot/O15162, http://identifiers.org/uniprot/O15162, http://identifiers.org/uniprot/P12931, http://pathwaycommons.org/pc12/#Catalysis_7700d38bbc890a9bf0095ea6b177c12e, http://pathwaycommons.org/pc12/#BiochemicalReaction_516cdf6bfc0d3e04fefb7bcbaff23af3, http://pathwaycommons.org/pc12/#Protein_55e467ef775ba5cc92066c8c731fd487, http://pathwaycommons.org/pc12/#Protein_93c51abd5ecedd9e93fcb82292eef98b, http://pathwaycommons.org/pc12/#Protein_12775a2f3365f7d5eaee3610ee1f5f75, http://identifiers.org/uniprot/P41134, http://identifiers.org/uniprot/P41134, http://identifiers.org/uniprot/Q9HAU4, http://pathwaycommons.org/pc12/#Catalysis_c460e466bbdae472354e13d7b223f4aa, http://pathwaycommons.org/pc12/#BiochemicalReaction_ce27bcdb23f7a26af42814846816f3fe, http://pathwaycommons.org/pc12/#Protein_7cba5a4c7545c0e08f814aa003c8d261, http://pathwaycommons.org/pc12/#Protein_2298e5b46ee475c6a7698085c9ce5a18, http://pathwaycommons.org/pc12/#Protein_b8b4f4861a1e59ce97feac424f1ec5a6, http://identifiers.org/uniprot/P40763, http://identifiers.org/uniprot/P40763, http://identifiers.org/uniprot/P28482, http://pathwaycommons.org/pc12/#Catalysis_a94f519e31216294a6073aba4d6fba26, http://pathwaycommons.org/pc12/#BiochemicalReaction_df522ce983f0dff4a3db3754df3ced56, http://pathwaycommons.org/pc12/#Protein_2005883355a8609a17be4b54e0b5f73f, http://pathwaycommons.org/pc12/#Protein_f3fc47f46f8716412a3cf8c7f0bac3bd, http://pathwaycommons.org/pc12/#Protein_55c11ec747711fe7bd4b1b4677035292, http://identifiers.org/uniprot/Q9UQQ2, http://identifiers.org/uniprot/Q9UQQ2, http://identifiers.org/uniprot/P43403, http://pathwaycommons.org/pc12/#Catalysis_57bdef806563526ff8dc4e495f429f3d, http://pathwaycommons.org/pc12/#BiochemicalReaction_e5d80cd72822ffe406d7b802324c7942, http://pathwaycommons.org/pc12/#Protein_3c1e9eef0f33ff34ee9e5539b3d6dfa1, http://pathwaycommons.org/pc12/#Protein_4cdefd119aee72f1ca45f03405b40119, http://pathwaycommons.org/pc12/#Protein_5746733e748a27c14e1b13258d71e8b4, http://identifiers.org/uniprot/P55957, http://identifiers.org/uniprot/P55957, http://identifiers.org/uniprot/Q14790, http://pathwaycommons.org/pc12/#Catalysis_753b64ba6c21adc72686b7ab612934dd, http://pathwaycommons.org/pc12/#BiochemicalReaction_869ab20977b30dd90f3ff3a38b063e84, http://pathwaycommons.org/pc12/#Protein_4ab23bb106edaebea60b860972e83ba8, http://pathwaycommons.org/pc12/#Protein_ecaba4708d7295532d35845004424662, http://pathwaycommons.org/pc12/#Protein_845f7a062ac28e4284e9c93a9e98af7e, http://identifiers.org/uniprot/P10721, http://identifiers.org/uniprot/P10721, http://identifiers.org/uniprot/P07948,
Pattern 11 : molecularInteraction¶
In [19]:
p = r.molecularInteraction()
res_P11 = peN.executePattern(p)
first_lines_pk(res_P11)
-- 7522 results in this dataset -- http://pathwaycommons.org/pc12/#MolecularInteraction_80c95f96dad6f7b9542d8e910c4664c1, http://pathwaycommons.org/pc12/#Protein_8d5fb5187319f27988b0da64aa78f27a, http://pathwaycommons.org/pc12/#Protein_d0976de0c58cc6a122d08813459f3002, http://pathwaycommons.org/pc12/#MolecularInteraction_85fe7c3c360b17b6b0a9ddc18f4b04a5, http://pathwaycommons.org/pc12/#Protein_8d5fb5187319f27988b0da64aa78f27a, http://pathwaycommons.org/pc12/#Protein_76d01375b298d35fc317778e607a3f25, http://pathwaycommons.org/pc12/#MolecularInteraction_72be02573aebde4815d83be983430225, http://pathwaycommons.org/pc12/#Protein_8d5fb5187319f27988b0da64aa78f27a, http://pathwaycommons.org/pc12/#Protein_baede168dc071d910013b95d7ce60464, http://pathwaycommons.org/pc12/#MolecularInteraction_e036a4817c58f424dddd01fbb11a3874, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_c7854957a663c0d5a92da62454dfc16f, http://pathwaycommons.org/pc12/#MolecularInteraction_2c43a8a17f6672561bf711ecef421a03, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_60b3d4c46dc674b1e02b92c827800a63, http://pathwaycommons.org/pc12/#MolecularInteraction_0732763747de62de3da8deda91d228fd, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_e1b9cd743f8243e8afc274d80ce050a4, http://pathwaycommons.org/pc12/#MolecularInteraction_2474cd8de89088a1c2d6b273ed79b3bc, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_1fa39d736fe7072917748f3d8b09979f, http://pathwaycommons.org/pc12/#MolecularInteraction_9ae4047db3ba8bf8e5f0969c1a8c273e, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_35918f7b4e5cd9e517ceaa7f98029136, http://pathwaycommons.org/pc12/#MolecularInteraction_c2ac66e66db28cdb649e6a20f1520247, http://pathwaycommons.org/pc12/#Protein_91fee738b6774d6585fde871d14e25da, http://pathwaycommons.org/pc12/#Protein_a3b1b2f901eb2b86c21fcf5063fd5e93, http://pathwaycommons.org/pc12/#MolecularInteraction_9f394e6525ddd5aa29b4cb9600e91ce6, http://pathwaycommons.org/pc12/#Protein_a0b15919e4be3f2d601c5462414fda33, http://pathwaycommons.org/pc12/#Protein_d8ce087a273d476f3d40171f1bd5f194,
Pattern 12 : inSameActiveComplex¶
In [20]:
p = r.inSameActiveComplex()
res_P12 = peN.executePattern(p)
first_lines_pk(res_P12)
-- 2872 results in this dataset -- http://pathwaycommons.org/pc12/#MolecularInteraction_0cf2e610ce9807eb3632dd9fd1146475, http://pathwaycommons.org/pc12/#Complex_b4b7527f5a1beedd0e2c64b4388884ee, http://pathwaycommons.org/pc12/#Protein_5eed98296a729764f7c7d3a1a95b9aed, http://pathwaycommons.org/pc12/#Protein_ccfac61571656a21a570ac2516fc7dd1, http://pathwaycommons.org/pc12/#MolecularInteraction_0cf2e610ce9807eb3632dd9fd1146475, http://pathwaycommons.org/pc12/#Complex_b4b7527f5a1beedd0e2c64b4388884ee, http://pathwaycommons.org/pc12/#Protein_ccfac61571656a21a570ac2516fc7dd1, http://pathwaycommons.org/pc12/#Protein_5eed98296a729764f7c7d3a1a95b9aed, http://pathwaycommons.org/pc12/#MolecularInteraction_5b4f4d07922bfe9f5bffe5a3fc130dfb, http://pathwaycommons.org/pc12/#Complex_62dc9997327dec31a0984f15abe6efc6, http://pathwaycommons.org/pc12/#Protein_ca9c4c842d9c1691e6db3a3644433b70, http://pathwaycommons.org/pc12/#Protein_67b78f061b9963aeb7fe9e392787cec9, http://pathwaycommons.org/pc12/#MolecularInteraction_5b4f4d07922bfe9f5bffe5a3fc130dfb, http://pathwaycommons.org/pc12/#Complex_62dc9997327dec31a0984f15abe6efc6, http://pathwaycommons.org/pc12/#Protein_67b78f061b9963aeb7fe9e392787cec9, http://pathwaycommons.org/pc12/#Protein_ca9c4c842d9c1691e6db3a3644433b70, http://pathwaycommons.org/pc12/#MolecularInteraction_ec64f6a777c6adbfa0effb08c1ad1d4b, http://pathwaycommons.org/pc12/#Complex_20088d00ed7ed22f3526c50bd0bd26a9, http://pathwaycommons.org/pc12/#Protein_0eea9d53409ff5955ee0360fbb71b412, http://pathwaycommons.org/pc12/#Protein_3565d1b4dc97f737a478757b992e0829, http://pathwaycommons.org/pc12/#MolecularInteraction_ec64f6a777c6adbfa0effb08c1ad1d4b, http://pathwaycommons.org/pc12/#Complex_20088d00ed7ed22f3526c50bd0bd26a9, http://pathwaycommons.org/pc12/#Protein_3565d1b4dc97f737a478757b992e0829, http://pathwaycommons.org/pc12/#Protein_0eea9d53409ff5955ee0360fbb71b412, http://pathwaycommons.org/pc12/#MolecularInteraction_e30568156ba80806952010fecc88e904, http://pathwaycommons.org/pc12/#Complex_5fbf1f228bc97f0b503d07a2ac08cd11, http://pathwaycommons.org/pc12/#Protein_12d8fcdafbf47e5bcd22a63c84f8f0a5, http://pathwaycommons.org/pc12/#Protein_5059d46ea39b5be1224a1f59a660effd, http://pathwaycommons.org/pc12/#MolecularInteraction_e30568156ba80806952010fecc88e904, http://pathwaycommons.org/pc12/#Complex_5fbf1f228bc97f0b503d07a2ac08cd11, http://pathwaycommons.org/pc12/#Protein_5059d46ea39b5be1224a1f59a660effd, http://pathwaycommons.org/pc12/#Protein_12d8fcdafbf47e5bcd22a63c84f8f0a5, http://pathwaycommons.org/pc12/#MolecularInteraction_55177babe306a49240238ec8784040c5, http://pathwaycommons.org/pc12/#Complex_9e457dc83add7470161f60724e4443dc, http://pathwaycommons.org/pc12/#Protein_c0fbc6d5c7035aff7ce070f29d4c4561, http://pathwaycommons.org/pc12/#Protein_e4ce292ac21f33e70135d3529e364d4f, http://pathwaycommons.org/pc12/#MolecularInteraction_55177babe306a49240238ec8784040c5, http://pathwaycommons.org/pc12/#Complex_9e457dc83add7470161f60724e4443dc, http://pathwaycommons.org/pc12/#Protein_e4ce292ac21f33e70135d3529e364d4f, http://pathwaycommons.org/pc12/#Protein_c0fbc6d5c7035aff7ce070f29d4c4561,
Pattern 13 : inSameComplexEffectingControl¶
In [21]:
# No results neither in Netpath nor in Panther.
p = r.inSameComplexEffectingControl()
res_P13 = peN.executePattern(p)
first_lines_pk(res_P13)
-- 360 results in this dataset -- http://pathwaycommons.org/pc12/#Catalysis_41f0211d35bbdcdcbdfb963ae3c17404, http://pathwaycommons.org/pc12/#Complex_3c63da5f7e581c470e8f2ca551558302, http://pathwaycommons.org/pc12/#Protein_6e5c3b1dd2b890f17b63dcd1c6dcd774, http://pathwaycommons.org/pc12/#Protein_6e9eb16e84975dc47103b49c68613944, http://identifiers.org/uniprot/Q92793, http://identifiers.org/uniprot/Q09472, http://pathwaycommons.org/pc12/#Catalysis_41f0211d35bbdcdcbdfb963ae3c17404, http://pathwaycommons.org/pc12/#Complex_3c63da5f7e581c470e8f2ca551558302, http://pathwaycommons.org/pc12/#Protein_6e9eb16e84975dc47103b49c68613944, http://pathwaycommons.org/pc12/#Protein_6e5c3b1dd2b890f17b63dcd1c6dcd774, http://identifiers.org/uniprot/Q09472, http://identifiers.org/uniprot/Q92793, http://pathwaycommons.org/pc12/#Catalysis_2164519717fbd8ac420b838fe1f8e3c7, http://pathwaycommons.org/pc12/#Complex_f70fb481f0301dddb01b750eb5320991, http://pathwaycommons.org/pc12/#Protein_f5eb6fd7a4dfa7a8cd2d3b16e2ef2b21, http://pathwaycommons.org/pc12/#Protein_b61c37476d8e8101ce230a8c959e00b3, http://identifiers.org/uniprot/P61077, http://identifiers.org/uniprot/P62837, http://pathwaycommons.org/pc12/#Catalysis_2164519717fbd8ac420b838fe1f8e3c7, http://pathwaycommons.org/pc12/#Complex_f70fb481f0301dddb01b750eb5320991, http://pathwaycommons.org/pc12/#Protein_b61c37476d8e8101ce230a8c959e00b3, http://pathwaycommons.org/pc12/#Protein_f5eb6fd7a4dfa7a8cd2d3b16e2ef2b21, http://identifiers.org/uniprot/P62837, http://identifiers.org/uniprot/P61077, http://pathwaycommons.org/pc12/#Catalysis_ba3c7f260fa81264b2db4ae41a7086dc, http://pathwaycommons.org/pc12/#Complex_c8eebcc37ff58a7f7d3501f9213225c3, http://pathwaycommons.org/pc12/#Protein_7985a0e81b4b81f72615932c0c0aa8b1, http://pathwaycommons.org/pc12/#Protein_006441daf51e64e4a269b5baa164e04a, http://identifiers.org/uniprot/Q969H0, http://identifiers.org/uniprot/Q13616, http://pathwaycommons.org/pc12/#Catalysis_ba3c7f260fa81264b2db4ae41a7086dc, http://pathwaycommons.org/pc12/#Complex_c8eebcc37ff58a7f7d3501f9213225c3, http://pathwaycommons.org/pc12/#Protein_7985a0e81b4b81f72615932c0c0aa8b1, http://pathwaycommons.org/pc12/#Protein_499c4559f1c70204e6df7801ee8cc30e, http://identifiers.org/uniprot/Q969H0, http://identifiers.org/uniprot/P63208, http://pathwaycommons.org/pc12/#Catalysis_ba3c7f260fa81264b2db4ae41a7086dc, http://pathwaycommons.org/pc12/#Complex_c8eebcc37ff58a7f7d3501f9213225c3, http://pathwaycommons.org/pc12/#Protein_006441daf51e64e4a269b5baa164e04a, http://pathwaycommons.org/pc12/#Protein_7985a0e81b4b81f72615932c0c0aa8b1, http://identifiers.org/uniprot/Q13616, http://identifiers.org/uniprot/Q969H0, http://pathwaycommons.org/pc12/#Catalysis_ba3c7f260fa81264b2db4ae41a7086dc, http://pathwaycommons.org/pc12/#Complex_c8eebcc37ff58a7f7d3501f9213225c3, http://pathwaycommons.org/pc12/#Protein_006441daf51e64e4a269b5baa164e04a, http://pathwaycommons.org/pc12/#Protein_499c4559f1c70204e6df7801ee8cc30e, http://identifiers.org/uniprot/Q13616, http://identifiers.org/uniprot/P63208, http://pathwaycommons.org/pc12/#Catalysis_ba3c7f260fa81264b2db4ae41a7086dc, http://pathwaycommons.org/pc12/#Complex_c8eebcc37ff58a7f7d3501f9213225c3, http://pathwaycommons.org/pc12/#Protein_499c4559f1c70204e6df7801ee8cc30e, http://pathwaycommons.org/pc12/#Protein_7985a0e81b4b81f72615932c0c0aa8b1, http://identifiers.org/uniprot/P63208, http://identifiers.org/uniprot/Q969H0, http://pathwaycommons.org/pc12/#Catalysis_ba3c7f260fa81264b2db4ae41a7086dc, http://pathwaycommons.org/pc12/#Complex_c8eebcc37ff58a7f7d3501f9213225c3, http://pathwaycommons.org/pc12/#Protein_499c4559f1c70204e6df7801ee8cc30e, http://pathwaycommons.org/pc12/#Protein_006441daf51e64e4a269b5baa164e04a, http://identifiers.org/uniprot/P63208, http://identifiers.org/uniprot/Q13616,
Pattern 14 : bindsTo¶
In [22]:
p = r.bindsTo()
res_P14 = peN.executePattern(p)
first_lines_pk(res_P14)
-- 3260 results in this dataset -- http://pathwaycommons.org/pc12/#Complex_151ed4c4ece14ff69a6d51679cb7ead7, http://pathwaycommons.org/pc12/#Protein_866d2e8479f1c4c1f92d8e5ad2214783, http://pathwaycommons.org/pc12/#Protein_b8221ae4aa1927b358e88d6eb6621650, http://identifiers.org/uniprot/O60674, http://identifiers.org/uniprot/P16471, http://pathwaycommons.org/pc12/#Complex_e06d3622e685e82d46a2edd9ccffc090, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_e56e82e7ef21b5799328ee719d6d47f6, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q9NQC7, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_06d601b603de842d87c35b35ad33865a, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/O43318, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_e8a68ac9ae711ea979d21b6cc0f6f6e8, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q15750, http://pathwaycommons.org/pc12/#Complex_eb3e971c804489c19078182a7ac70459, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_b1323a0b4e9f34d6985eca1fae5ab88e, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q9NYJ8, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_06d601b603de842d87c35b35ad33865a, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/O43318, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_3541eb6e587ca9aa170ff9f17bbd51ef, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q15750, http://pathwaycommons.org/pc12/#Complex_a9df06bd8b85da204ce9e83f7b6cea0a, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_acc48b6077852a67807a4e53fb625202, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q9NYJ8, http://pathwaycommons.org/pc12/#Complex_83bea0b7026f945de6fe49284563eba9, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_9611f4ea83e9080927d39eac047f3b4f, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/O15111, http://pathwaycommons.org/pc12/#Complex_9695d8dca18d787a873ffda9d7430f9f, http://pathwaycommons.org/pc12/#Protein_8a874f0ea831516e9c0728fdb76198bb, http://pathwaycommons.org/pc12/#Protein_af9220325cab4d60894e78f7f308a89e, http://identifiers.org/uniprot/Q9Y4K3, http://identifiers.org/uniprot/Q8N5C8,
Pattern for complex validation : notBlackboxComplexInComplex¶
In [23]:
p = r.notBlackboxComplexInComplex()
res_P8 = peP.executePattern(p)
first_lines_pk(res_P8)
print('\n'.join(map(str,peP.trace))) # display processing log (usefull for Pattern design)
print("corresponding SPARQL query:")
print("#------------------------")
print(peP.querylist[0])
print("#------------------------")
-- 174 results in this dataset --
http://pathwaycommons.org/pc12/#Complex_579bb103ee0f0793438b03948e6e761f, http://pathwaycommons.org/pc12/#Complex_9701b7f04c04463e71ef2649927b4b19, http://pathwaycommons.org/pc12/#Complex_48c9d96b3ebb96af4af73dc161a6fb34,
http://pathwaycommons.org/pc12/#Complex_579bb103ee0f0793438b03948e6e761f, http://pathwaycommons.org/pc12/#Complex_9701b7f04c04463e71ef2649927b4b19, http://pathwaycommons.org/pc12/#Complex_82de90a4d69084412cb281fa7aacc325,
http://pathwaycommons.org/pc12/#Complex_9701b7f04c04463e71ef2649927b4b19, http://pathwaycommons.org/pc12/#Complex_48c9d96b3ebb96af4af73dc161a6fb34, http://pathwaycommons.org/pc12/#Protein_ae5422a9f331d287be33b875130243dd,
http://pathwaycommons.org/pc12/#Complex_2c59ca198864fca3a6f6aa135fb9c0f7, http://pathwaycommons.org/pc12/#Complex_d85f4c436c475149211d8b755b6fc1d2, http://pathwaycommons.org/pc12/#Protein_ad0125246c6db14c23d33eb1d4c8c287,
http://pathwaycommons.org/pc12/#Complex_15cf0ce0222559e1fc0ef3131703a607, http://pathwaycommons.org/pc12/#Complex_f81c0645f718b1cd99f16ce28879050f, http://pathwaycommons.org/pc12/#Protein_5f3c2236ef151a2abc188d772111f724,
http://pathwaycommons.org/pc12/#Complex_5e2e3b070737fbfade133deeb52dba58, http://pathwaycommons.org/pc12/#Complex_c5b57357ca85272db4b1547a501ee246, http://pathwaycommons.org/pc12/#Protein_46df743f008ca40d28482585689aa540,
http://pathwaycommons.org/pc12/#Complex_2c59ca198864fca3a6f6aa135fb9c0f7, http://pathwaycommons.org/pc12/#Complex_ae75374b02476f5504736cb9a9c511da, http://pathwaycommons.org/pc12/#Protein_3161f25014f1c3d347e4d0a9621e2e61,
http://pathwaycommons.org/pc12/#Complex_8a106438d5c413eaac118212b806fcc3, http://pathwaycommons.org/pc12/#Complex_01df64c2356ca50570c9a4272aae8093, http://pathwaycommons.org/pc12/#Protein_f881da01a1dde73c60fb573f84c1bcbc,
http://pathwaycommons.org/pc12/#Complex_b807e6a833a66700623d79fd2241fac3, http://pathwaycommons.org/pc12/#Complex_e5c489203e0ce661ac94a38cfe2bf942, http://pathwaycommons.org/pc12/#Protein_e5895fd6619c3621b4b75cd14ab95eb4,
http://pathwaycommons.org/pc12/#Complex_a040b9844d3defb3a93ea4be40dcc79b, http://pathwaycommons.org/pc12/#Complex_785867333e5c29b8b5c97c77f4dccb2f, http://pathwaycommons.org/pc12/#Protein_9f9a41fa074e1df43361df687653f8e8,
('STEP N°1/1',)
('SIZE OF RESULT : 174',)
corresponding SPARQL query:
#------------------------
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix bi: <http://www.biopax.org/release/biopax-level3.owl#>
select ?s2 ?o2 ?s4 ?componentn0C2 ?componentn1PE ?s2__rdft ?o2__rdft ?s4__rdft
where {
?s2 ?componentn0C2 ?o2 .
?o2 ?componentn1PE ?s4 .
?s2 rdf:type ?s2__rdft .
?o2 rdf:type ?o2__rdft .
?s4 rdf:type ?s4__rdft .
{ ?o2 a bi:Complex } .
{ ?s2 a bi:Complex } { ?s4 a bi:PhysicalEntity } UNION { ?s4 a bi:SmallMolecule } UNION { ?s4 a bi:DnaRegion } UNION { ?s4 a bi:RnaRegion } UNION { ?s4 a bi:Dna } UNION { ?s4 a bi:Rna } UNION { ?s4 a bi:Protein } UNION { ?s4 a bi:Complex }
FILTER ( ?componentn0C2 = bi:component ) .
FILTER ( ?componentn1PE = bi:component ) .
}
#------------------------
a Pattern can be made of multiple sub patterns associated with Set Operator¶
see https://forgemia.inra.fr/pegase/biopax-explorer/-/blob/main/src/biopax_explorer/pattern/rack.py for more details
In [24]:
p = r.reactsWith()
img="data/output/reactsWith.png"
writePatternGraphView(p,img, format="png") # other format : svg
Image(img)
Out[24]:
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In [ ]:
In [ ]: