Reactome biopax level 3 structure
library(rBiopaxParser)
biopaxfile3 <- "./Reactome/R-HSA-169911_level3.owl"
biopax <- readBiopax(biopaxfile3, verbose = F)
pw_list = listInstances(biopax, class = "bp:Pathway")
pw_list
## id name
## 1 Pathway1 Regulation of Apoptosis
## 2 Pathway2 Regulation of activated PAK-2p34 by proteasome mediated degradation
## 3 Pathway3 Regulation of PAK-2p34 activity by PS-GAP/RHG10
selectInstances(biopax, id = "Pathway1")[property=="pathwayComponent",.(property_attr_value)]
## property_attr_value
## 1: #Pathway2
## 2: #Pathway3
## 3: #BiochemicalReaction5
br_5_components = selectInstances(biopax,id="BiochemicalReaction5")
br_5_components[property=="displayName",.(property_value)]
## property_value
## 1: OMA1 hydrolyses OPA1
p_left <- br_5_components[property=="left",]
p_right <- br_5_components[property=="right",]
p_left
## class id property property_attr
## 1: BiochemicalReaction BiochemicalReaction5 left rdf:resource
## 2: BiochemicalReaction BiochemicalReaction5 left rdf:resource
## property_attr_value property_value
## 1: #SmallMolecule1
## 2: #Protein64
p_right
## class id property property_attr
## 1: BiochemicalReaction BiochemicalReaction5 right rdf:resource
## 2: BiochemicalReaction BiochemicalReaction5 right rdf:resource
## property_attr_value property_value
## 1: #Protein65
## 2: #Protein66
selectInstances(biopax,id="Protein64")[property=="displayName",.(property_value)]
## property_value
## 1: OPA1
selectInstances(biopax,id=p_left$property_attr_value)[property=="displayName",.(property_value)]
## property_value
## 1: OPA1
## 2: H2O
selectInstances(biopax,id=p_right$property_attr_value)[property=="displayName",.(property_value)]
## property_value
## 1: OPA1_HUMAN
## 2: OPA1_HUMAN
selectInstances(biopax,id=p_right$property_attr_value)[property=="name",.(property_value)]
## property_value
## 1: OPA1(88-194)
## 2: Dynamin-like 120 kDa protein, mitochondrial ecNumber3.6.5.5/ecNumber
## 3: OPA1(195-960)
## 4: Dynamin-like 120 kDa protein, mitochondrial ecNumber3.6.5.5/ecNumber
g1 <- pathway2RegulatoryGraph(biopax, pwid="Pathway1", expandSubpathways=F,splitComplexMolecules=F, useIDasNodenames = T, verbose=F)
g2 <- pathway2Graph(biopax, pwid="Pathway1", expandSubpathways=F ,splitComplexMolecules=F, useIDasNodenames = F, verbose=F)
pw_1graph_laidout = layoutRegulatoryGraph(g1)
pw_2graph_laidout = layoutRegulatoryGraph(g2)
g1
## A graphNEL graph with directed edges
## Number of Nodes = 10
## Number of Edges = 9
head(edges(g1),3)
## $PhysicalEntity1
## [1] "Protein1" "Protein2" "Protein17"
##
## $Protein1
## character(0)
##
## $Protein2
## character(0)
# plot(pw_1graph_laidout)
g2
## A graphNEL graph with directed edges
## Number of Nodes = 13
## Number of Edges = 18
edges(g2)
## $Protein1
## [1] "Protein17" "Complex2"
##
## $Protein2
## [1] "Protein17"
##
## $Protein17
## character(0)
##
## $Protein63
## [1] "Complex2"
##
## $Complex2
## [1] "Complex3"
##
## $Complex3
## character(0)
##
## $SmallMolecule1
## [1] "Protein65" "Protein66"
##
## $Protein64
## [1] "Protein65" "Protein66"
##
## $Protein65
## character(0)
##
## $Protein66
## character(0)
##
## $PhysicalEntity1
## [1] "Protein1" "Protein2" "Protein17"
##
## $Complex1
## [1] "Protein17" "Protein2"
##
## $Protein67
## [1] "SmallMolecule1" "Protein64" "Protein65" "Protein66"
plot(g2)
Biopax level 3 to table
library(rBiopaxParser)
biopaxfile3 <- "./Reactome/R-HSA-169911_level3.owl"
biopax <- readBiopax(biopaxfile3, verbose = F)
listPathways(biopax)
## id name
## 1 Pathway1 Regulation of Apoptosis
## 2 Pathway2 Regulation of activated PAK-2p34 by proteasome mediated degradation
## 3 Pathway3 Regulation of PAK-2p34 activity by PS-GAP/RHG10
unique(listPathwayComponents(biopax, id="Pathway1"))
## id
## 1 BiochemicalReaction1
## 2 BiochemicalReaction2
## 3 BiochemicalReaction3
## 4 BiochemicalReaction4
## 5 BiochemicalReaction5
## 6 Pathway2
## 7 Pathway3
## 8 Catalysis1
## 14 Catalysis2
## 20 Catalysis3
## 26 PathwayStep1
## 29 PathwayStep2
## 31 PathwayStep3
## 32 PathwayStep4
## 34 PathwayStep5
## 35 PathwayStep6
## 36 PathwayStep7
## name
## 1 Ubiquitination of PAK-2p34
## 2 Proteasome mediated degradation of PAK-2p34
## 3 Rho GTPase-activating protein 10 (RHG10) interacts with caspase-activated PAK-2p34
## 4 Interaction of PAK-2p34 with RGH10/ PS-GAP results in accumulation of PAK-2p34 in the perinuclear region
## 5 OMA1 hydrolyses OPA1
## 6 Regulation of activated PAK-2p34 by proteasome mediated degradation
## 7 Regulation of PAK-2p34 activity by PS-GAP/RHG10
## 8
## 14
## 20
## 26
## 29
## 31
## 32
## 34
## 35
## 36
listInteractionComponents(biopax, id="BiochemicalReaction5")
## id name
## 1 Protein64 OPA1
## 2 Protein65 OPA1_HUMAN
## 3 Protein66 OPA1_HUMAN
## 4 SmallMolecule1 H2O
pw_list = listInstances(biopax, class = "bp:Pathway")
path_df <- data.frame(biopax=biopaxfile3, relation="has_pathway", pw_list)
path_df
## biopax relation id
## 1 ./Reactome/R-HSA-169911_level3.owl has_pathway Pathway1
## 2 ./Reactome/R-HSA-169911_level3.owl has_pathway Pathway2
## 3 ./Reactome/R-HSA-169911_level3.owl has_pathway Pathway3
## name
## 1 Regulation of Apoptosis
## 2 Regulation of activated PAK-2p34 by proteasome mediated degradation
## 3 Regulation of PAK-2p34 activity by PS-GAP/RHG10
pw_component_list <- NULL
for(pw in pw_list$id){
pw_c <- selectInstances(biopax, id = pw)[property=="pathwayComponent",.(property_attr_value)]
pw_c_df <- data.frame(pathway=pw, relation="has_pathwayComponent", pw_c)
pw_component_list[[pw]] <- pw_c_df
}
pw_component <- rbindlist(pw_component_list)
pw_component
## pathway relation property_attr_value
## 1: Pathway1 has_pathwayComponent #Pathway2
## 2: Pathway1 has_pathwayComponent #Pathway3
## 3: Pathway1 has_pathwayComponent #BiochemicalReaction5
## 4: Pathway2 has_pathwayComponent #BiochemicalReaction1
## 5: Pathway2 has_pathwayComponent #BiochemicalReaction2
## 6: Pathway3 has_pathwayComponent #BiochemicalReaction3
## 7: Pathway3 has_pathwayComponent #BiochemicalReaction4
br_components_list <- NULL
brs <- unique(sub("^#","",pw_component[grep("BiochemicalReaction", property_attr_value),]$property_attr_value))
for(br in brs) {
# cat(br)
br_components = selectInstances(biopax, id = br)
br_c_name <-
br_components[property == "displayName", .(property_value)]$property_value
p_left <- br_components[property == "left", ]
p_right <- br_components[property == "right", ]
p_right$property_attr_value
br_comp_df <-
rbind(
data.frame(
ID = br,
Name = br_c_name,
relation = "has_left",
Molecula = p_left$property_attr_value
),
data.frame(
ID = br,
Name = br_c_name,
relation = "has_right",
Molecula = p_right$property_attr_value
)
)
br_components_list[[br]] <- br_comp_df
}
br_components_df <- rbindlist(br_components_list)
br_components_df
## ID
## 1: BiochemicalReaction5
## 2: BiochemicalReaction5
## 3: BiochemicalReaction5
## 4: BiochemicalReaction5
## 5: BiochemicalReaction1
## 6: BiochemicalReaction1
## 7: BiochemicalReaction1
## 8: BiochemicalReaction2
## 9: BiochemicalReaction2
## 10: BiochemicalReaction3
## 11: BiochemicalReaction3
## 12: BiochemicalReaction3
## 13: BiochemicalReaction4
## 14: BiochemicalReaction4
## Name
## 1: OMA1 hydrolyses OPA1
## 2: OMA1 hydrolyses OPA1
## 3: OMA1 hydrolyses OPA1
## 4: OMA1 hydrolyses OPA1
## 5: Ubiquitination of PAK-2p34
## 6: Ubiquitination of PAK-2p34
## 7: Ubiquitination of PAK-2p34
## 8: Proteasome mediated degradation of PAK-2p34
## 9: Proteasome mediated degradation of PAK-2p34
## 10: Rho GTPase-activating protein 10 (RHG10) interacts with caspase-activated PAK-2p34
## 11: Rho GTPase-activating protein 10 (RHG10) interacts with caspase-activated PAK-2p34
## 12: Rho GTPase-activating protein 10 (RHG10) interacts with caspase-activated PAK-2p34
## 13: Interaction of PAK-2p34 with RGH10/ PS-GAP results in accumulation of PAK-2p34 in the perinuclear region
## 14: Interaction of PAK-2p34 with RGH10/ PS-GAP results in accumulation of PAK-2p34 in the perinuclear region
## relation Molecula
## 1: has_left #SmallMolecule1
## 2: has_left #Protein64
## 3: has_right #Protein65
## 4: has_right #Protein66
## 5: has_left #Protein1
## 6: has_left #Protein2
## 7: has_right #Protein17
## 8: has_left #Protein17
## 9: has_right #Protein2
## 10: has_left #Protein1
## 11: has_left #Protein63
## 12: has_right #Complex2
## 13: has_left #Complex2
## 14: has_right #Complex3
moleculas <- unique(sub("^#","",br_components_df$Molecula))
moleculas_name_list <- list()
for(m in moleculas){
name <- selectInstances(biopax,id=m)[property=="displayName",.(property_value)]$property_value
moleculas_name_list[[m]] <- data.frame(Molecula=m, relation="has_displayName", name)
}
moleculas_name_df <- rbindlist(moleculas_name_list)
moleculas_name_df
## Molecula relation name
## 1: SmallMolecule1 has_displayName H2O
## 2: Protein64 has_displayName OPA1
## 3: Protein65 has_displayName OPA1_HUMAN
## 4: Protein66 has_displayName OPA1_HUMAN
## 5: Protein1 has_displayName p-T402-PAK-2p34
## 6: Protein2 has_displayName Ub
## 7: Protein17 has_displayName K48polyUb-p-T402-PAK-2p43
## 8: Protein63 has_displayName ARHGAP10
## 9: Complex2 has_displayName PAK-2p34:RHG10 complex
## 10: Complex3 has_displayName perinuclear PAK-2p34:RHG10 complex
# Name not display name
moleculas_name_list <- list()
for(m in grep("Complex",moleculas,value = T, invert = T)){
cat(m)
name <- selectInstances(biopax,id=m)[property=="name",.(property_value)]$property_value
moleculas_name_list[[m]] <- data.frame(Molecula=m, relation="has_name", name)
}
## SmallMolecule1Protein64Protein65Protein66Protein1Protein2Protein17Protein63
moleculas_name_df <- rbindlist(moleculas_name_list)
moleculas_name_df
## Molecula relation
## 1: SmallMolecule1 has_name
## 2: Protein64 has_name
## 3: Protein64 has_name
## 4: Protein65 has_name
## 5: Protein65 has_name
## 6: Protein66 has_name
## 7: Protein66 has_name
## 8: Protein1 has_name
## 9: Protein1 has_name
## 10: Protein2 has_name
## 11: Protein17 has_name
## 12: Protein63 has_name
## name
## 1: water
## 2: Dynamin-like 120 kDa protein, mitochondrial ecNumber3.6.5.5/ecNumber
## 3: OPA1_HUMAN
## 4: OPA1(88-194)
## 5: Dynamin-like 120 kDa protein, mitochondrial ecNumber3.6.5.5/ecNumber
## 6: OPA1(195-960)
## 7: Dynamin-like 120 kDa protein, mitochondrial ecNumber3.6.5.5/ecNumber
## 8: p-T402-PAK2(213-524)
## 9: phospho-PAK-2p34 (Thr 402)
## 10: ubiquitin
## 11: K48polyUb-phospho-PAK-2p34(Thr402)
## 12: Graf-2/ Arhgap10