Find things that could be protein states (Homo sapiens).

find.groovy

bioclipse.requireVersion("2.6.1")
// download all GPML files for a species, and save those in /WikiPathways/data/human/

dataMap = bioclipse.fullPath("/WikiPathways/data/human/")
gpmlFiles = new File(dataMap).listFiles()

gpmlFiles.each { file ->
  def data = new XmlParser().parse(file)
  def fName = file.getName();
  fName = fName.substring(fName.indexOf("_WP")+1);
  def pw = fName.substring(0,fName.indexOf("_"));
  pwName = data.@Name

  data.Shape.findAll{
    it.'@TextLabel' != null &&
    it.'@TextLabel'.trim().equals('P')
  }.each() { node ->
    println "$pw $pwName Shape -> " + node.'@GraphId'
  }
}

println "done"

Label "OH"

WP136 Phase I, non P450 Label "OH" -> db7
WP136 Phase I, non P450 Label "OH" -> e68
WP136 Phase I, non P450 Label "OH" -> e3d
WP136 Phase I, non P450 Label "OH" -> f1b
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> b92
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> aa2
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> d9a
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> a12
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> d94
WP237 Glucocorticoid & Mineralcorticoid Metabolism Label "OH" -> a25

Label "P"

WP411 mRNA Processing Label "P" -> cdd
WP313 Signaling of Hepatocyte Growth Factor Receptor Label "P" -> e70
WP313 Signaling of Hepatocyte Growth Factor Receptor Label "P" -> edd
WP313 Signaling of Hepatocyte Growth Factor Receptor Label "P" -> afe
WP710 DNA Damage Response (only ATM dependent) Label "P" -> d9199
WP2100 Arylhydrocarbon receptor (AhR) signaling pathway Label "P" -> dae33
WP2526 PDGF Pathway Label "P" -> b8938
WP2526 PDGF Pathway Label "P" -> c857c
WP2526 PDGF Pathway Label "P" -> b63b9
WP2526 PDGF Pathway Label "P" -> f8683
WP2526 PDGF Pathway Label "P" -> a037f
WP2526 PDGF Pathway Label "P" -> e6a99
WP2526 PDGF Pathway Label "P" -> d27a1
WP2526 PDGF Pathway Label "P" -> fb039
WP2526 PDGF Pathway Label "P" -> d9f5e
WP2526 PDGF Pathway Label "P" -> dc086
WP2526 PDGF Pathway Label "P" -> c7d5a
WP2526 PDGF Pathway Label "P" -> f8fe6
WP2526 PDGF Pathway Label "P" -> e158c
WP2516 ATM Signaling Pathway Label "P" -> bc294
WP2516 ATM Signaling Pathway Label "P" -> c4e11
WP2516 ATM Signaling Pathway Label "P" -> c958b
WP2516 ATM Signaling Pathway Label "P" -> b6133
WP2516 ATM Signaling Pathway Label "P" -> e11ac
WP2516 ATM Signaling Pathway Label "P" -> b8abd
WP2516 ATM Signaling Pathway Label "P" -> bbba7
WP2516 ATM Signaling Pathway Label "P" -> b90d8
WP2516 ATM Signaling Pathway Label "P" -> f4ff6
WP2516 ATM Signaling Pathway Label "P" -> aae5f
WP2516 ATM Signaling Pathway Label "P" -> c3821
WP2516 ATM Signaling Pathway Label "P" -> d3a66
WP2516 ATM Signaling Pathway Label "P" -> e116a
WP2516 ATM Signaling Pathway Label "P" -> e3091
WP2516 ATM Signaling Pathway Label "P" -> fc979
WP2516 ATM Signaling Pathway Label "P" -> caf78
WP2516 ATM Signaling Pathway Label "P" -> c95a9
WP2516 ATM Signaling Pathway Label "P" -> c04f7
WP2516 ATM Signaling Pathway Label "P" -> d4804
WP1434 Osteopontin Signaling Label "P" -> b42e7
WP1434 Osteopontin Signaling Label "P" -> f7ded
WP1434 Osteopontin Signaling Label "P" -> a3604
WP1434 Osteopontin Signaling Label "P" -> ea4ee
WP1434 Osteopontin Signaling Label "P" -> b0eab
WP619 Type II interferon signaling (IFNG) Label "P" -> b1eb8
WP619 Type II interferon signaling (IFNG) Label "P" -> ca06b
WP619 Type II interferon signaling (IFNG) Label "P" -> c6f35
WP619 Type II interferon signaling (IFNG) Label "P" -> a042e
WP428 Wnt Signaling Pathway Label "P" -> a2c
WP289 Myometrial Relaxation and Contraction Pathways Label "P" -> aaacd
WP581 EPO Receptor Signaling Label "P" -> d9320
WP581 EPO Receptor Signaling Label "P" -> ed225
WP581 EPO Receptor Signaling Label "P" -> a5151
WP581 EPO Receptor Signaling Label "P" -> d236a
WP581 EPO Receptor Signaling Label "P" -> ffb01
WP581 EPO Receptor Signaling Label "P" -> e07c7
WP581 EPO Receptor Signaling Label "P" -> b4af2
WP581 EPO Receptor Signaling Label "P" -> cf2f6
WP581 EPO Receptor Signaling Label "P" -> b7249
WP581 EPO Receptor Signaling Label "P" -> a969a
WP581 EPO Receptor Signaling Label "P" -> eda09
WP581 EPO Receptor Signaling Label "P" -> be2db
WP581 EPO Receptor Signaling Label "P" -> b7191
WP581 EPO Receptor Signaling Label "P" -> eaeb3
WP581 EPO Receptor Signaling Label "P" -> bdc08
WP581 EPO Receptor Signaling Label "P" -> b1bdf
WP581 EPO Receptor Signaling Label "P" -> ea249
WP262 EBV LMP1 signaling Label "P" -> edb5f
WP262 EBV LMP1 signaling Label "P" -> a7496
WP262 EBV LMP1 signaling Label "P" -> efbf0
WP262 EBV LMP1 signaling Label "P" -> b2244
WP262 EBV LMP1 signaling Label "P" -> bb7e3
WP1602 Nicotine Activity on Dopaminergic Neurons Label "P" -> f59f7
WP1602 Nicotine Activity on Dopaminergic Neurons Label "P" -> d7610
WP1602 Nicotine Activity on Dopaminergic Neurons Label "P" -> e69c7
WP536 Calcium Regulation in the Cardiac Cell Label "P" -> b87
WP536 Calcium Regulation in the Cardiac Cell Label "P" -> b0d

Shape "P"

WP49 IL-2 Signaling Pathway Shape "P" -> d0ac7
WP49 IL-2 Signaling Pathway Shape "P" -> e9d50
WP2324 AGE/RAGE pathway Shape "P" -> e8bc9
WP585 Interferon type I Shape "P" -> bc2ac
WP585 Interferon type I Shape "P" -> c193b
WP585 Interferon type I Shape "P" -> e105c
WP585 Interferon type I Shape "P" -> d25fd
WP585 Interferon type I Shape "P" -> d44a2
WP585 Interferon type I Shape "P" -> a8a58
WP585 Interferon type I Shape "P" -> a9fa8
WP585 Interferon type I Shape "P" -> b1603
WP585 Interferon type I Shape "P" -> f1a3e
WP585 Interferon type I Shape "P" -> dd379
WP585 Interferon type I Shape "P" -> f0eec
WP585 Interferon type I Shape "P" -> a0b24
WP585 Interferon type I Shape "P" -> a44d8
WP585 Interferon type I Shape "P" -> f1a80
WP585 Interferon type I Shape "P" -> b5d0c
WP585 Interferon type I Shape "P" -> eb992
WP585 Interferon type I Shape "P" -> b161a
WP585 Interferon type I Shape "P" -> e69c8
WP585 Interferon type I Shape "P" -> fe47e
WP585 Interferon type I Shape "P" -> ac9c8
WP585 Interferon type I Shape "P" -> f2336
WP585 Interferon type I Shape "P" -> ecaa2
WP585 Interferon type I Shape "P" -> dc4c7
WP2572 Primary Focal Segmental Glomerulosclerosis FSGS Shape "P" -> b9a0e
WP2572 Primary Focal Segmental Glomerulosclerosis FSGS Shape "P" -> a7015

Shape "Ub"

WP2324 AGE/RAGE pathway Shape "Ub" -> ddd3a