openbel-api 1.2.7-java → 1.2.8-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 60772f35d5cba63231bf2b925c748c58606af095
-  data.tar.gz: 8bc2ff556addbbf5abb156e39ced7a3ce1b8fd86
+  metadata.gz: 7476401d7e5a89338f83a7bc218c4e81684e5ba2
+  data.tar.gz: b88fe4f650867ee488cf7d9b37f5951a8063341b
 SHA512:
-  metadata.gz: 0c35fb15fb67b14b9a2b8fe3fc97187624c47bf281ab30d91f53b2104e7074366bd627fde75bdcd71a396da1a16c7a26c3ea43c84c026a0e4b677983dd398095
-  data.tar.gz: d2db63a059a447c718cb91c538645971122fda499cc981a668706948c6a8a5cf33b0974206b760442cd6e2c583280495f3dd02d8fac64d38fadf2eac63d0ad0c
+  metadata.gz: 3d296233b5a560807494fb12ea6ca5ce04f042bdb48f3b7c26f7ae0ef8e22cdabe4c8a02e6efccf011690d85c1cd030e9aacd20a27370e0f0e47bf3ec04c71ea
+  data.tar.gz: e29eb850020ce59dca864b2384c7a68c4aa9e4768024948566cc4385d0cef9155570d42711453f200533c8483126e5ff9b877d3bbb6816b29ba9b323b319d660

data/VERSION

@@ -1 +1 @@
-1.2.7
+1.2.8

data/app/openbel/api/routes/expressions.rb

@@ -176,8 +176,13 @@ module OpenBEL
         caret_position = (params[:caret_position] || bel.length).to_i
         halt 400 unless bel and caret_position
 
+        include_invalid_semantics = as_bool(params[:include_invalid_semantics])
+
         begin
-          completions = BELParser::Completion.complete(bel, @spec, @search, @supported_namespaces, caret_position)
+          completions =
+            BELParser::Completion.complete(
+              bel, @spec, @search, @supported_namespaces, caret_position, include_invalid_semantics
+            )
         rescue IndexError => ex
           halt(
             400,

data/app/openbel/api/routes/nanopubs.rb

@@ -336,7 +336,6 @@ module OpenBEL
         validate_nanopub!(original_bel_statement, nanopub.experiment_context) if strict
 
         facets                  = map_nanopub_facets(nanopub)
-        hash[:bel_statement]    = (hash[:bel_statement] || original_bel_statement).to_s
         nanopub                 = nanopub.to_h
         nanopub[:bel_statement] = nanopub.fetch(:bel_statement, nil).to_s
         nanopub[:facets]        = facets

data/bin/test_bel2_validation.py

@@ -6,13 +6,19 @@ Usage:  program.py <customer>
 
 """
 
-
 import requests
 import json
+import os.path
 
 base_url = "http://localhost:9292"
 
-files = ['bel2.0-example-statements.bel', 'bel2_document_examples.bel']
+# Pull these from the repo: openbel/language/version_2.0/*.bel
+# I softlink them into the bin dir
+
+files = [
+    f"{os.path.dirname(__file__)}/bel2.0-example-statements.bel",
+    f"{os.path.dirname(__file__)}/bel2_document_examples.bel"
+]
 
 
 def send_request(bel):
@@ -21,7 +27,7 @@ def send_request(bel):
 
     try:
         response = requests.get(
-            url=f"{base_url}/api/expressions/{bel}/validation",
+            url=f"{base_url}/api/expressions/{requests.utils.quote(bel)}/validation",
         )
         try:
             r = response.json()

data/config/config.yml

@@ -8,7 +8,7 @@ bel:
   #     (BEL version 1.0 specification)
   #   2.0
   #     (BEL version 2.0 specification)
-  version: 2.0
+  version: 1.0
 
 # Storage of nanopubs through the Mongo database.
 nanopub_store:

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 1.2.7
+  version: 1.2.8
 platform: java
 authors:
 - Anthony Bargnesi
@@ -365,8 +365,6 @@ dependencies:
 description: The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.
 email: abargnesi@selventa.com
 executables:
-- bel2.0-example-statements.bel
-- bel2_document_examples.bel
 - openbel-api
 - openbel-config
 - setup-docker.sh
@@ -425,8 +423,6 @@ files:
 - app/openbel/api/schemas/nanopub_resource.schema.json
 - app/openbel/api/util.rb
 - app/openbel/api/version.rb
-- bin/bel2.0-example-statements.bel
-- bin/bel2_document_examples.bel
 - bin/openbel-api
 - bin/openbel-config
 - bin/setup-docker.sh
@@ -473,7 +469,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5.1
+rubygems_version: 2.4.6
 signing_key: 
 specification_version: 4
 summary: The OpenBEL API provided over RESTful HTTP endpoints.

data/bin/bel2.0-example-statements.bel

@@ -1,344 +0,0 @@
-a(CHEBI:"2-oxoglutarate(2-)") directlyIncreases act(p(HGNC:EGLN1), ma(GO:"catalytic activity"))
-a(CHEBI:"3',5'-cyclic AMP") increases act(p(HGNC:RAP1A))
-a(CHEBI:"3',5'-cyclic GMP") increases surf(complex(p(HGNC:ITGAV),p(HGNC:ITGB5)))
-a(CHEBI:"arachidonic acid") increases act(p(MGI:Mpo), ma(DEFAULT:cat))
-a(CHEBI:"fatty acid") increases act(p(HGNC:UCP1))
-a(CHEBI:"nitric oxide") increases act(p(SFAM:"GUCY Family"), ma(GO:"catalytic activity"))
-a(CHEBI:"nitric oxide") decreases r(HGNC:CFTR, var("c.1521_1523delCTT"))
-a(CHEBI:"nitric oxide") increases surf(complex(p(HGNC:ITGA2),p(HGNC:ITGB1)))
-a(CHEBI:"okadaic acid") directlyDecreases act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity"))
-a(CHEBI:"okadaic acid") increases p(HGNC:IRS1,pmod(Ph,Ser))
-a(CHEBI:"oxidised LDL") increases act(p(HGNC:MMP2), ma(DEFAULT:cat))
-a(CHEBI:"oxidised LDL") increases surf(p(HGNC:MMP14))
-a(CHEBI:"phosphatidyl-L-serine") increases act(p(HGNC:F3), ma(GO:"peptidase activity"))
-a(CHEBI:"phosphatidyl-L-serine") increases act(p(SFAM:"PDE4 Long Family"), ma(GO:"catalytic activity"))
-a(CHEBI:"prostaglandin E2") increases act(p(HGNC:RAP1A))
-a(CHEBI:"prostaglandin E2") decreases p(HGNC:PRKCD,pmod(Ph))
-a(CHEBI:acetylcholine) increases act(p(HGNC:NOS3), ma(DEFAULT:cat))
-a(SCHEM:"LY 294002") causesNoChange act(p(HGNC:MAPK1), ma(DEFAULT:kin))
-act(complex(p(HGNC:CCND1),p(HGNC:CDK4)), ma(DEFAULT:kin)) directlyIncreases p(HGNC:RB1,pmod(Ph))
-act(complex(p(HGNC:F3),p(HGNC:F7)), ma(GO:"peptidase activity")) directlyIncreases act(p(HGNC:F10), ma(DEFAULT:pep))
-act(complex(SCOMP:"Calcineurin Complex"), ma(GO:"phosphatase activity")) increases act(p(SFAM:"MEF2 Family"), ma(GO:"nucleic acid binding transcription factor activity"))
-act(complex(SCOMP:"Calcineurin Complex"), ma(GO:"phosphatase activity")) causesNoChange r(MGI:Ppargc1a)
-act(complex(SCOMP:"IkappaB Kinase Complex"), ma(DEFAULT:kin)) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
-act(complex(SCOMP:"IkappaB Kinase Complex"), ma(DEFAULT:kin)) directlyIncreases deg(p(HGNC:NFKBIA))
-act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(DEFAULT:kin)) increases surf(p(HGNC:ATP1A2,pmod(Ph,Thr)))
-act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity")) increases bp(MESHPP:"Capillary Permeability")
-act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity")) directlyDecreases p(HGNC:RAF1,pmod(Ph,S))
-act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity")) directlyDecreases p(HGNC:RAF1,pmod(Ph,S,259))
-act(complex(SCOMP:"TORC1 Complex"), ma(DEFAULT:kin)) directlyIncreases p(MGI:Rps6kb1,pmod(Ph,Thr,412))
-act(complex(SCOMP:"TORC2 Complex"), ma(DEFAULT:kin)) directlyIncreases p(MGI:Eif4ebp1,pmod(Ph,Thr,36))
-act(p(fus(HGNC:BCR,?, HGNC:ABL1,?))) increases act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(DEFAULT:kin))
-act(p(fus(HGNC:BCR,?, HGNC:ABL1,?))) increases bp(GOBP:"cell adhesion")
-act(p(fus(HGNC:BCR,?, HGNC:ABL1,?))) increases p(HGNC:FOXO3,pmod(Ph,Ser,253))
-act(p(fus(HGNC:EWSR1,?, HGNC:FLI1,?))) directlyDecreases r(HGNC:CDKN1A)
-act(p(fus(HGNC:PAX3,?,HGNC:FOXO1,?)), ma(DEFAULT:tscript)) decreases r(HGNC:IGFBP5)
-act(p(fus(HGNC:TPR,?, HGNC:MET,?))) increases path(SDIS:"tumor growth")
-act(p(HGNC:"NKX2-5"), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:MIR143)
-act(p(HGNC:ADAMTS13), ma(GO:"peptidase activity")) increases deg(p(HGNC:VWF))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) decreases act(p(HGNC:FOXO3), ma(GO:"nucleic acid binding transcription factor activity"))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) increases act(p(HGNC:MDM2), ma(DEFAULT:cat))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) directlyDecreases act(p(HGNC:PAWR))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) directlyDecreases act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity"))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) decreases complex(p(HGNC:AKT1),p(HGNC:CREBBP))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) increases complex(p(HGNC:SKP2),p(SFAM:"FOXO Family"))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) increases tloc(p(HGNC:CDKN1A), fromLoc(MESHCS:"Cell Nucleus"), toLoc(MESHCS:Cytoplasm))
-act(p(HGNC:AKT1), ma(DEFAULT:kin)) decreases tloc(p(SFAM:"FOXO Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
-act(p(HGNC:CASP3), ma(GO: "catalytic activity")) decreases act(p(HGNC:PARP1), ma(DEFAULT:ribo))
-act(p(HGNC:CDK1), ma(DEFAULT:kin)) directlyIncreases act(complex(SCOMP:"Anaphase Promoting Complex"), ma(GO: "catalytic activity"))
-act(p(HGNC:CDK2), ma(DEFAULT:kin)) directlyIncreases p(HGNC:CDKN1B,pmod(Ph,Thr,187))
-act(p(HGNC:CTNNB1), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:CCND1)
-act(p(HGNC:CYP7A1), ma(DEFAULT:cat)) rateLimitingStepOf deg(a(CHEBI:cholesterol))
-act(p(HGNC:EGLN3), ma(DEFAULT:cat)) directlyIncreases p(HGNC:HIF1A,pmod(Hy,Pro,564))
-act(p(HGNC:F2), ma(GO:"peptidase activity")) directlyIncreases act(p(HGNC:F2R))
-act(p(HGNC:F2), ma(GO:"peptidase activity")) increases bp(GOBP:"blood coagulation")
-act(p(HGNC:F9), ma(DEFAULT:pep)) increases act(p(HGNC:F2), ma(GO:"peptidase activity"))
-act(p(HGNC:HIF1AN), ma(GO:"catalytic activity")) directlyIncreases p(HGNC:HIF1A,pmod(Hy,Asn,803))
-act(p(HGNC:HMGA1)) increases surf(p(HGNC:INSR))
-act(p(HGNC:HMOX1), ma(DEFAULT:cat)) directlyIncreases rxn(reactants(a(CHEBI:heme)),products(a(SCHEM:Biliverdine),a(CHEBI:"carbon monoxide")))
-act(p(HGNC:HRAS), ma(DEFAULT:gtp)) increases surf(p(HGNC:CDH5))
-act(p(HGNC:JUN), ma(GO:"nucleic acid binding transcription factor activity")) increases path(MESHD:"Carcinoma, Squamous Cell")
-act(p(HGNC:JUN), ma(GO:"nucleic acid binding transcription factor activity")) increases path(SDIS:"tumor growth")
-act(p(HGNC:KDR), ma(GO:"kinase activity")) directlyIncreases p(HGNC:KDR,pmod(Ph,Y,951))
-act(p(HGNC:KDR), ma(GO:"kinase activity")) directlyIncreases p(HGNC:KDR,pmod(Ph,Y,996))
-act(p(HGNC:KDR), ma(DEFAULT:kin)) association bp(GOBP:"cell death")
-act(p(HGNC:KLF9), ma(DEFAULT:tscript)) association bp(GOBP:"DNA replication")
-act(p(HGNC:LEF1), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:CCND1)
-act(p(HGNC:MAP2K1), ma(DEFAULT:kin)) increases surf(p(HGNC:ITGB3))
-act(p(HGNC:MYD88), ma(GO:"catalytic activity")) directlyIncreases complex(p(HGNC:MYD88),p(HGNC:IRAK1),p(HGNC:IRAK4))
-act(p(HGNC:NAA10), ma(DEFAULT:cat)) directlyIncreases p(HGNC:HIF1A,pmod(Ac,K,532))
-act(p(HGNC:PAK3), ma(GO:"kinase activity")) directlyIncreases p(HGNC:RAF1,pmod(Ph,S,338))
-act(p(HGNC:PDPK1), ma(GO:"kinase activity")) directlyIncreases p(SFAM:"AKT Family",pmod(MOD:PhosRes,Tyr,308))
-act(p(HGNC:PIM1)) increases surf(p(HGNC:KDR))
-act(p(HGNC:PLCG1)) directlyIncreases rxn(reactants(a(SCHEM:"1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate")),products(a(SCHEM:Diacylglycerol),a(SCHEM:"Inositol 1,4,5-trisphosphate")))
-act(p(HGNC:PRKCZ), ma(GO:"kinase activity")) increases tloc(p(HGNC:SLC2A4), fromLoc(MESHCS:"Intracellular Space"), toLoc(MESHCS:"Cell Membrane"))
-act(p(HGNC:PTEN), ma(DEFAULT:phos)) decreases act(p(HGNC:AKT1), ma(DEFAULT:kin))
-act(p(HGNC:PTPRJ), ma(DEFAULT:phos)) directlyDecreases act(p(HGNC:KDR), ma(DEFAULT:kin))
-act(p(HGNC:RANBP2), ma(GO:"catalytic activity")) directlyIncreases p(HGNC:HDAC4,pmod(Sumo,Lys,559))
-act(p(HGNC:ROCK1), ma(DEFAULT:kin)) association path(SDIS:"cardiomyocyte hypertrophy")
-act(p(HGNC:SGK1), ma(DEFAULT:kin)) directlyIncreases p(HGNC:RAF1,pmod(Ph,S,259))
-act(p(HGNC:SOD2), ma(DEFAULT:cat)) increases rxn(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide")))
-act(p(HGNC:SRC), ma(DEFAULT:kin)) increases act(p(SFAM:"RAF Family"), ma(GO:"kinase activity"))
-act(p(HGNC:SRC), ma(DEFAULT:kin)) directlyIncreases p(HGNC:CDH5,pmod(Ph,Y))
-act(p(HGNC:SRF), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:MIR143)
-act(p(HGNC:TIMP2), ma(DEFAULT:pep)) decreases p(HGNC:MMP9)
-act(p(HGNC:TNFRSF1A)) regulates act(complex(SCOMP:"AP-1 Complex"), ma(DEFAULT:tscript))
-act(p(HGNC:TNFRSF1A)) increases act(p(SFAM:"PRKC Family"), ma(GO:"kinase activity"))
-act(p(HGNC:USF1), ma(DEFAULT:tscript)) causesNoChange r(HGNC:IGF2R)
-act(p(HGNC:VHL), ma(DEFAULT:cat)) directlyIncreases deg(p(HGNC:PRKCI))
-act(p(MGI:Akt1), ma(DEFAULT:kin)) directlyDecreases act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity"))
-act(p(MGI:Akt1), ma(DEFAULT:kin)) directlyIncreases p(MGI:Foxo3,pmod(Ph,Thr,32))
-act(p(MGI:Akt1), ma(DEFAULT:kin)) directlyIncreases p(MGI:Tsc2,pmod(Ph,Ser,939))
-act(p(MGI:Akt1), ma(DEFAULT:kin)) decreases r(MGI:Cdkn1b)
-act(p(MGI:Cebpd), ma(DEFAULT:tscript)) association bp(MESHPP:Apoptosis)
-act(p(MGI:Chuk), ma(DEFAULT:kin)) increases deg(p(MGI:Nfkbia))
-act(p(MGI:Ctnnb1), ma(GO:"nucleic acid binding transcription factor activity")) increases r(MGI:Myc)
-act(p(MGI:Epas1), ma(DEFAULT:tscript)) increases surf(complex(p(MGI:Itgav),p(MGI:Itgb3)))
-act(p(MGI:Fads1), ma(GO: "catalytic activity")) directlyIncreases rxn(reactants(a(CHEBI:"all-cis-icosa-8,11,14-trienoic acid")),products(a(CHEBI:"arachidonic acid")))
-act(p(MGI:Fads2), ma(GO: "catalytic activity")) increases a(CHEBI:"arachidonic acid")
-act(p(MGI:Foxp3), ma(DEFAULT:tscript)) decreases sec(p(MGI:Ifng))
-act(p(MGI:Hif1a), ma(DEFAULT:tscript)) increases bp(GOBP:angiogenesis)
-act(p(MGI:Hras,var("p.Gly12Val")), ma(DEFAULT:gtp)) increases act(complex(SCOMP:"NADPH Oxidase Complex"), ma(GO:"catalytic activity"))
-act(p(MGI:Ikbkb), ma(DEFAULT:kin)) increases deg(p(MGI:Nfkbia))
-act(p(MGI:Inppl1), ma(DEFAULT:phos)) negativeCorrelation path(MESHD:Hyperglycemia)
-act(p(MGI:Itch), ma(DEFAULT:cat)) directlyIncreases deg(p(MGI:Trp63))
-act(p(MGI:Lpl), ma(DEFAULT:cat)) rateLimitingStepOf path(SDIS:"VLDL biosynthesis")
-act(p(MGI:Mmp2), ma(DEFAULT:cat)) rateLimitingStepOf bp(GOBP:"cellular extravasation")
-act(p(MGI:Mtor), ma(DEFAULT:kin)) directlyIncreases p(MGI:Eif4ebp1,pmod(Ph,Thr,36))
-act(p(MGI:Mybl1), ma(DEFAULT:tscript)) association bp(GOBP:"G1/S transition of mitotic cell cycle")
-act(p(MGI:Ppargc1a), ma(DEFAULT:tscript)) directlyIncreases act(p(SFAM:"MEF2 Family"), ma(DEFAULT:tscript))
-act(p(MGI:Tcf3), ma(DEFAULT:tscript)) directlyIncreases r(MGI:Bmp4)
-act(p(MGI:Tlr2), ma(DEFAULT:cat)) increases sec(p(MGI:Ccl2))
-act(p(RGD:Hmox1), ma(DEFAULT:cat)) rateLimitingStepOf deg(a(CHEBI:heme))
-act(p(SFAM:"ACSL Family"), ma(GO: "catalytic activity")) directlyIncreases rxn(reactants(a(SCHEM:"Long-chain fatty acid")),products(a(SCHEM:"Long-chain fatty acyl CoA")))
-act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) directlyIncreases p(HGNC:GSK3B,pmod(MOD:PhosRes,Ser,9))
-act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity")) decreases bp(GOBP:"G1/S transition of mitotic cell cycle")
-act(p(SFAM:"FOXO Family"), ma(DEFAULT:tscript)) directlyDecreases r(HGNC:CCND1)
-act(p(SFAM:"JAK Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:RAF1,pmod(Ph,Tyr,341))
-act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:PDE4B,pmod(Ph,Ser))
-act(p(SFAM:"MAPK JNK Family"), ma(GO:"kinase activity")) increases tloc(p(HGNC:CYCS), fromLoc(MESHCS:"Mitochondrial Membranes"), toLoc(MESHCS:Cytoplasm))
-act(p(SFAM:"MAPK p38 Family"), ma(GO:"kinase activity")) decreases deg(p(HGNC:HBP1))
-act(p(SFAM:"MAPK p38 Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:CDKN1A,pmod(Ph,Ser,190))
-act(p(SFAM:"MAPK p38 Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:HBP1,pmod(Ph))
-act(p(SFAM:"NOS Family"), ma(DEFAULT:cat)) increases rxn(reactants(a(CHEBI:dioxygen),a(CHEBI:"L-arginine")),products(a(CHEBI:"nitric oxide")))
-act(p(SFAM:"PDE Family"), ma(GO: "catalytic activity")) directlyIncreases rxn(reactants(a(CHEBI:"3',5'-cyclic AMP")),products(a(CHEBI:AMP)))
-act(p(SFAM:"PRKA Family"), ma(GO:"kinase activity")) directlyDecreases act(p(HGNC:GSK3B), ma(DEFAULT:kin))
-act(p(SFAM:"PRKA Family"), ma(GO:"kinase activity")) directlyIncreases act(p(SFAM:"PDE4 Long Family"), ma(GO: "catalytic activity"))
-act(p(SFAM:"PRKA Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:CREB1,pmod(Ph,Ser,133))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(GO:"kinase activity"))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity"))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(p(SFAM:"RAC Family"), ma(DEFAULT:gtp))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) directlyIncreases act(p(SFAM:"RAF Family"), ma(GO:"kinase activity"))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(p(SFAM:"RHO Family"), ma(DEFAULT:gtp))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases bp(GOBP:"cell proliferation")
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases complex(p(HGNC:RAF1),p(HGNC:BRAF))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases p(HGNC:RAF1,pmod(Ph,S,338))
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) positiveCorrelation path(MESHD:"Carcinoma, Non-Small-Cell Lung")
-act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) directlyIncreases tloc(p(HGNC:BRAF), fromLoc(MESHCS:"Intracellular Space"), toLoc(MESHCS:"Cell Membrane"))
-act(p(SFAM:"SRC Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:RAF1,pmod(Ph,Tyr,341))
-bp(GOBP:"cellular response to electrical stimulus") increases tloc(p(MGI:Hdac4), fromLoc(MESHCS:"Cell Nucleus"), toLoc(MESHCS:Cytoplasm))
-bp(GOBP:"mitotic nuclear division") positiveCorrelation p(HGNC:CDC16,pmod(Ph,Ser,558))
-bp(GOBP:"mitotic nuclear division") positiveCorrelation p(HGNC:CDC23,pmod(Ph,Thr,556))
-bp(GOBP:"response to endoplasmic reticulum") increases a(CHEBI:"calcium(2+)", loc(GOCC:"endoplasmic reticulum"))
-bp(MESHPP:"Insulin Resistance") negativeCorrelation act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
-bp(MESHPP:Obesity) negativeCorrelation act(p(HGNC:SLC2A4), ma(DEFAULT:tport))
-bp(MESHPP:Obesity) positiveCorrelation act(p(MGI:Trp53), ma(DEFAULT:tscript))
-complex(p(HGNC:CTNNB1),p(HGNC:LEF1)) directlyIncreases act(p(HGNC:CTNNB1), ma(DEFAULT:tscript))
-complex(p(HGNC:CYCS),p(HGNC:APAF1)) increases act(p(HGNC:CASP9), ma(GO:"peptidase activity"))
-complex(p(HGNC:F3),p(HGNC:F7)) increases act(p(HGNC:F10), ma(DEFAULT:pep))
-complex(p(HGNC:HIF1A),p(HGNC:EP300)) directlyIncreases act(p(HGNC:HIF1A), ma(DEFAULT:tscript))
-complex(p(HGNC:ITGA6),p(HGNC:ITGB1)) increases act(p(HGNC:SYK), ma(DEFAULT:kin))
-complex(p(HGNC:ITGB1),p(HGNC:FN1)) increases act(p(HGNC:PRKCA), ma(DEFAULT:kin))
-complex(p(HGNC:MAP3K11),p(HGNC:SH3RF1)) increases act(p(SFAM:"MAPK JNK Family"), ma(GO:"kinase activity"))
-complex(p(HGNC:MAP3K11),p(HGNC:SH3RF1)) increases p(HGNC:JUN,pmod(Ph))
-complex(p(HGNC:RBL2),p(SFAM:"E2F Family")) decreases bp(GOBP:"G1/S transition of mitotic cell cycle")
-complex(p(HGNC:RBL2),p(SFAM:"E2F Family")) directlyDecreases complex(p(SFAM:"E2F Family"),p(HGNC:EP300))
-composite(a(SCHEM:Lipopolysaccharide),p(MGI:Ifng)) increases act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity"))
-composite(p(HGNC:RAF1),p(HGNC:AKT1)) regulates act(p(HGNC:CDK2), ma(DEFAULT:kin))
-composite(p(HGNC:VEGFA),p(HGNC:FN1)) increases act(p(HGNC:PRKCA), ma(DEFAULT:kin))
-composite(p(HGNC:VEGFA),p(HGNC:FN1)) increases surf(p(HGNC:PRKCA))
-g(REF:"NM_000492.3", var("c.1521_1523delCTT")) association bp(GOBP:"wound healing")
-p(HGNC:AKT1, loc(MESHCS:Cytoplasm)) increases p(HGNC:EGFR, loc(MESHCS: Cytoplasm))
-p(HGNC:APP, frag("?_*")) negativeCorrelation path(SDIS:"Alzheimers disease")
-p(HGNC:APP, frag(25_35)) association path(SDIS:"Alzheimers disease")
-p(HGNC:BCL2) causesNoChange act(p(HGNC:PAWR))
-p(HGNC:BCL2, loc(MESHCS:Mitochondria)) increases p(HGNC:CYCS, loc(MESHCS:Mitochondria))
-p(HGNC:BRAF,var("p.Val599Glu")) directlyIncreases act(p(HGNC:BRAF), ma(DEFAULT:kin))
-p(HGNC:CALM1) regulates act(p(HGNC:NOS3), ma(DEFAULT:cat))
-p(HGNC:CASP3) increases p(HGNC:APC, frag(1_?))
-p(HGNC:CASP3) increases p(HGNC:HTT, frag(?))
-p(HGNC:CASP8) increases p(HGNC:CFLAR, frag(?,36kD))
-p(HGNC:CASP9, frag(?,55kD)) increases bp(GOBP:"apoptotic process")
-p(HGNC:CAV1) directlyDecreases act(p(HGNC:KDR), ma(DEFAULT:kin))
-p(HGNC:CAV1,pmod(Ph,Y,14)) directlyDecreases complex(p(HGNC:CAV1),p(HGNC:KDR))
-p(HGNC:CDH5,pmod(Ph,Tyr)) directlyDecreases bp(GOBP:"single organismal cell-cell adhesion")
-p(HGNC:CDKN1A,pmod(Ph,Ser,190)) decreases deg(p(HGNC:CDKN1A))
-p(HGNC:CDKN1B,pmod(Ph,Thr,187)) directlyIncreases complex(p(HGNC:SKP2),p(HGNC:CDKN1B))
-p(HGNC:CDKN1B,pmod(Ub)) directlyIncreases deg(p(HGNC:CDKN1B))
-p(HGNC:CFTR, var("?"")) regulates p(HGNC:NFKBIA)
-p(HGNC:CFTR, var("="")) increases act(p(HGNC:SLC9A3))
-p(HGNC:CFTR, var("p.Phe508del")) decreases bp(GOBP:"wound healing")
-p(HGNC:CTNNB1,var("p.Thr41Ala")) directlyIncreases act(p(HGNC:CTNNB1), ma(DEFAULT:tscript))
-p(HGNC:CYCS, loc(MESHCS:Cytoplasm)) increases bp(GOBP:"apoptotic process")
-p(HGNC:EDN3) causesNoChange act(p(HGNC:EDNRA))
-p(HGNC:EGF) increases p(HGNC:EGFR), loc(GOCC:"cell surface"))
-p(HGNC:EGF) increases p(HGNC:JAK2,pmod(Ph,Tyr))
-p(HGNC:EGF) increases tloc(p(SFAM:"STAT5 Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
-p(HGNC:EGFR,pmod(Ub,K)) directlyIncreases deg(p(HGNC:EGFR))
-p(HGNC:ELANE) -> p(HGNC:MUC5AC,pmod(Glyco))
-p(HGNC:ELK1,var("p.Trp379Ala")) directlyDecreases act(p(HGNC:ELK1), ma(DEFAULT:tscript))
-p(HGNC:EPO) increases act(p(SFAM:"RAF Family"), ma(GO:"kinase activity"))
-p(HGNC:EPO) increases p(HGNC:RAF1,pmod(Ph,Tyr,341))
-p(HGNC:ERBB3) causesNoChange act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
-p(HGNC:ERBB3) causesNoChange p(SFAM:"AKT Family",pmod(MOD:PhosRes,Thr,493))
-p(HGNC:EZH2) positiveCorrelation complex(p(SFAM:"Histone H3 Family",pmod(Me,Lys,27)),g(HGNC:DKK1))
-p(HGNC:EZH2) positiveCorrelation complex(p(SFAM:"Histone H3 Family",pmod(Me,Lys,27)),g(HGNC:DKK1))
-p(HGNC:F2) increases sec(a(CHEBI:"nitric oxide"))
-p(HGNC:F2) increases sec(p(HGNC:VWF))
-p(HGNC:F2) increases surf(p(HGNC:F3))
-p(HGNC:F2) increases tloc(p(HGNC:SELP), fromLoc(MESHCS:"Cytoplasmic Granules"), toLoc(MESHCS:"Cell Membrane"))
-p(HGNC:GP6) regulates act(p(HGNC:SYK), ma(DEFAULT:kin))
-p(HGNC:GSK3A,pmod(Ph,Ser,21)) directlyDecreases act(p(HGNC:GSK3A), ma(DEFAULT:kin))
-p(HGNC:HDAC4,pmod(Sumo,Lys,559)) directlyIncreases act(p(HGNC:HDAC4), ma(DEFAULT:cat))
-p(HGNC:HIF1A,pmod(Ac,K,532)) directlyIncreases deg(p(HGNC:HIF1A))
-p(HGNC:HIF1A,pmod(Hy,Asn,863)) directlyDecreases act(p(HGNC:HIF1A), ma(DEFAULT:tscript))
-p(HGNC:HIF1A,pmod(Hy,Pro,402)) directlyIncreases complex(p(HGNC:VHL),p(HGNC:HIF1A))
-p(HGNC:HIF1A,pmod(Hy,Pro,564)) directlyIncreases complex(p(HGNC:VHL),p(HGNC:HIF1A))
-p(HGNC:HRAS,var(p.Gly12Val)) decreases bp(GOBP:"G1/S transition of mitotic cell cycle")
-p(HGNC:HRAS,var(p.Gly12Val)) decreases sec(p(HGNC:CASP3))
-p(HGNC:IGF1) directlyIncreases act(p(HGNC:IGF1R), ma(DEFAULT:kin))
-p(HGNC:IGF1) regulates p(SFAM:"AKT Family",pmod(Ph,Ser,473))
-p(HGNC:IKBKB,pmod(Ph)) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
-p(HGNC:IL13) increases r(HGNC:CFTR, var(r.1653_1655delcuu))
-p(HGNC:IL1B) increases deg(p(HGNC:NFKBIA))
-p(HGNC:IL4) increases act(p(SFAM:"PDE4 Family"), ma(GO:"catalytic activity"))
-p(HGNC:IL6) increases act(p(HGNC:JAK2), ma(GO:"kinase activity"))
-p(HGNC:IL6) increases act(p(HGNC:STAT3),  ma(GO:"nucleic acid binding transcription factor activity"))
-p(HGNC:IL6) increases act(p(HGNC:TYK2), ma(GO:"kinase activity"))
-p(HGNC:IRS1,pmod(Ph,Ser)) negativeCorrelation p(HGNC:IRS1,pmod(Ph,Tyr))
-p(HGNC:IRS1,pmod(Glyco,Ser)) directlyDecreases act(p(HGNC:IRS1), ma(DEFAULT:cat))
-p(HGNC:IRS2,pmod(Ph,Ser)) negativeCorrelation p(HGNC:IRS2,pmod(Ph,Tyr))
-p(HGNC:LRIG1) increases p(HGNC:EGFR,pmod(Ub,K))
-p(HGNC:MYD88) causesNoChange r(HGNC:IFNB1)
-p(HGNC:NRAS,var("p.Gln61Arg")) increases p(HGNC:RPS6KB1,pmod(Ph,Ser,447))
-p(HGNC:PAWR,pmod(Ph,Thr,163)) directlyIncreases act(p(HGNC:PAWR))
-p(HGNC:PLAU, frag(?)) decreases bp(GOBP:"cell migration")
-p(HGNC:PLAU, frag(?, 18kD)) decreases bp(GOBP:"cell proliferation")
-p(HGNC:PRKACA) increases p(HGNC:GSK3A,pmod(Ph,Ser,21))
-p(HGNC:PRKACA) increases p(HGNC:GSK3B,pmod(MOD:PhosRes,Ser,9))
-p(HGNC:PRPF4B,pmod(Ph)) directlyDecreases complex(p(HGNC:PRPF4B),p(HGNC:PRPF6))
-p(HGNC:PRPF4B,pmod(Ph)) directlyDecreases complex(p(HGNC:PRPF4B),p(HGNC:SMARCA4))
-p(HGNC:PTEN) negativeCorrelation p(SFAM:"AKT Family",pmod(Ph))
-p(HGNC:PTEN) negativeCorrelation p(SFAM:"AKT Family",pmod(Ph))
-p(HGNC:PTEN,var("p.Arg173Cys")) decreases p(HGNC:PTEN)
-p(HGNC:RAF1,pmod(Ph,Ser,621)) directlyDecreases act(p(HGNC:RAF1), ma(GO:"kinase activity"))
-p(HGNC:RAF1,pmod(Ph,Ser,621)) directlyIncreases complex(p(HGNC:RAF1),p(SFAM:"14-3-3 Family"))
-p(HGNC:RAF1,pmod(Ph,Y,341)) directlyIncreases act(p(HGNC:RAF1), ma(GO:"kinase activity"))
-p(HGNC:RELA,pmod(Ac,Lys,310)) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
-p(HGNC:SELE) increases p(HGNC:HSPB1,pmod(Ph))
-p(HGNC:SIRT1) negativeCorrelation complex(p(SFAM:"Histone H4 Family",pmod(Ac,Lys,16)),g(HGNC:DKK1))
-p(HGNC:SNRPC) causesNoChange act(p(fus(HGNC:EWSR1,?, HGNC:FLI1,?)))
-p(HGNC:SUZ12) positiveCorrelation complex(p(SFAM:"Histone H3 Family",pmod(Me,Lys,27)),g(HGNC:DKK1))
-p(HGNC:TGFA) directlyIncreases act(p(HGNC:EGFR), ma(GO:"kinase activity"))
-p(HGNC:TGFB1) increases p(HGNC:CFTR, var("p.Thr1220Lysfs"))
-p(HGNC:TGFB1) association p(HGNC:COL4A1, loc(GOCC:"extracellular matrix"))
-p(HGNC:TIRAP) causesNoChange r(HGNC:IFNB1)
-p(HGNC:TNF) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
-p(HGNC:TNF) directlyIncreases act(p(HGNC:TNFRSF1A))
-p(HGNC:TNF) increases surf(p(HGNC:MMP14))
-p(HGNC:TP53,var("p.Arg175Leu")) decreases p(HGNC:TP53)
-p(HGNC:TP53,var("p.Arg181His")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
-p(HGNC:TP53,var("p.Arg248Gln")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
-p(HGNC:TP53,var("p.Arg273His")) increases bp(GOBP:"cell proliferation")
-p(HGNC:TP53,var("p.Arg282Trp")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
-p(HGNC:TP53,var("p.Asn239Ser")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
-p(HGNC:TP53,var("p.Asp281Glu")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
-p(HGNC:TP53,var("p.Pro309Ser")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
-p(HGNC:TP63) increases composite(p(SFAM:"Histone H3 Family",pmod(Ac)),p(SFAM:"Histone H4 Family",pmod(Ac)))
-p(HGNC:TP73,var("p.Arg263Trp")) directlyDecreases act(p(HGNC:TP73), ma(DEFAULT:tscript))
-p(HGNC:UCP1,var("p.Met229Leu")) positiveCorrelation path(MESHD:"Diabetes Mellitus, Type 2")
-p(HGNC:UCP1,var("p.Met229Leu")) positiveCorrelation path(MESHD:"Diabetes Mellitus, Type 2")
-p(HGNC:VEGFA) increases p(HGNC:FLT1,pmod(Ph,Y))
-p(HGNC:VEGFA) increases p(HGNC:PTK2B,pmod(Ph))
-p(HGNC:VEGFA) regulates p(SFAM:"PIK3R Class IA Family",pmod(Ph,Tyr))
-p(HGNC:VHL) decreases act(p(HGNC:HIF1A), ma(DEFAULT:tscript))
-p(HGNC:VHL) directlyDecreases act(p(HGNC:PRKCD), ma(GO:"kinase activity"))
-p(HGNC:VHL) directlyIncreases deg(p(HGNC:HIF1A))
-p(HGNC:VHL) decreases surf(p(HGNC:CXCR4))
-p(HGNC:VHL,var("p.Ile180Asn")) decreases p(HGNC:VHL)
-p(HGNC:VTN) directlyIncreases act(complex(p(HGNC:ITGAV),p(HGNC:ITGB3)))
-p(HGNC:VWF) directlyDecreases deg(p(HGNC:F8))
-p(MGI:Akt1,pmod(Ph,Ser,473)) directlyIncreases p(MGI:Foxo3,pmod(Ph,Thr,32))
-p(MGI:Angpt1) directlyIncreases act(p(MGI:Tek), ma(DEFAULT:kin))
-p(MGI:Braf,var("p.Val600Glu") increases p(MGI:Sftpc)
-p(MGI:Ctnnb1) increases act(p(MGI:Mapk1), ma(DEFAULT:kin))
-p(MGI:Egf) regulates p(MGI:Akt1)
-p(MGI:Hck,var("p.Tyr499Phe")) directlyIncreases act(p(MGI:Hck), ma(DEFAULT:kin))
-p(MGI:Hck,var("p.Tyr499Phe")) increases p(MGI:Il5)
-p(MGI:Hck,var("p.Tyr499Phe")) increases path(MESHD:Inflammation)
-p(MGI:Il6st,var("p.Tyr757Phe")) directlyDecreases act(p(MGI:Il6st), ma(DEFAULT:cat))
-p(MGI:Il6st,var("p.Tyr759Phe")) decreases bp(MESHPP:Apoptosis)
-p(MGI:Irs1) causesNoChange p(MGI:Rps6kb2,pmod(Ph))
-p(MGI:Jak3,var("p.Ala572Val")) increases p(MGI:Bcl2)
-p(MGI:Kras,var("p.Gly12Asp")) increases path(MESHD:Neoplasms)
-p(MGI:Mapkap1) causesNoChange p(MGI:Akt1,pmod(MOD:PhosRes,Ser,308))
-p(MGI:Mapkap1) increases p(MGI:Akt1,pmod(MOD:PhosRes,Ser,473))
-p(MGI:Mapkap1) increases p(MGI:Foxo3,pmod(Ph,Thr,32))
-p(MGI:Pgf) directlyIncreases act(p(MGI:Flt1), ma(DEFAULT:kin))
-p(MGI:Pias1) directlyDecreases act(p(MGI:Stat1), ma(GO:"nucleic acid binding transcription factor activity"))
-p(MGI:Pias3) directlyDecreases act(p(HGNC:STAT3), ma(GO:"nucleic acid binding transcription factor activity"))
-p(MGI:Rela,pmod(Ac,Lys,310)) directlyIncreases act(p(MGI:Rela), ma(DEFAULT:tscript))
-p(MGI:Vegfb) causesNoChange bp(GOBP:"vasculature development")
-p(MGI:Wnt7b) increases bp(GOBP:"lung epithelium development")
-p(REF:"NP_000483.3", var("p.Phe508del")) increases act(p(SFAM:"SREBF Family"), ma(DEFAULT:tscript))
-p(RGD:Chuk,pmod(MOD:PhosRes,Ser,180)) directlyIncreases act(p(RGD:Chuk), ma(DEFAULT:kin))
-p(RGD:Igf1) regulates act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity"))
-p(RGD:Igf1) increases act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp))
-p(RGD:Igf1) increases act(p(SFAM:"RPS6KB Family"), ma(GO:"kinase activity"))
-p(RGD:Igf1) increases p(SFAM:"RPS6KB Family",pmod(Ph,Thr,412))
-p(RGD:Igf1) causesNoChange r(RGD:Myog)
-p(RGD:Ikbkb,pmod(MOD:PhosRes,Ser,177)) directlyIncreases act(p(RGD:Ikbkb), ma(DEFAULT:kin))
-p(RGD:Itgb4,pmod(Ph,Tyr)) directlyIncreases complex(p(RGD:Itga6),p(RGD:Itgb4),p(RGD:Shc1))
-p(SFAM:"AKT Family") increases p(HGNC:IRAK1,pmod(Ph,Thr,100))
-p(SFAM:"AKT Family",pmod(Ph,Ser,473)) positiveCorrelation p(SFAM:"AKT Family",pmod(MOD:PhosRes,Tyr,308))
-p(SFAM:"AKT Family",pmod(Ph,Ser,473)) positiveCorrelation path(MESHD:"Carcinoma, Non-Small-Cell Lung")
-p(SFAM:"AKT Family",pmod(Ph,Thr,308)) positiveCorrelation act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
-p(SFAM:"AKT Family",var("p.Lys179Met")) directlyDecreases act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
-p(SFAM:"AKT Family",var("p.Lys179Met")) increases bp(GOBP:"apoptotic process")
-p(SFAM:"FOXO Family",pmod(Ac)) directlyDecreases act(p(SFAM:"FOXO Family"), , ma(GO:"nucleic acid binding transcription factor activity"))
-p(SFAM:"FOXO Family",pmod(Ph)) increases tloc(p(SFAM:"FOXO Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
-p(SFAM:"Histone H3 Family",pmod(Ac)) increases act(p(HGNC:SREBF1), ma(DEFAULT:tscript))
-p(SFAM:"Histone H4 Family",pmod(Me,Arg,3)) increases act(p(HGNC:YY1), ma(DEFAULT:tscript))
-p(SFAM:"IL1 Family") increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
-p(SFAM:"IL1 Family") increases act(p(HGNC:IRAK1), ma(DEFAULT:kin))
-p(SFAM:"IL1 Family") increases r(HGNC:SELE)
-p(SFAM:"INS Family") increases p(MGI:Akt1,pmod(MOD:PhosRes,Ser,473))
-p(SFAM:"IRS Family",pmod(Ph)) directlyIncreases complex(p(SFAM:"PIK3R Class IA Family"),p(SFAM:"IRS Family"))
-p(SFAM:"MAPK JNK Family",pmod(Ph)) directlyIncreases act(p(SFAM:"MAPK JNK Family"), ma(GO:"kinase activity"))
-p(SFAM:"PDGF Family") increases act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity"))
-p(SFAM:"PDGF Family") increases p(MGI:Akt1,pmod(MOD:PhosRes,Ser,473))
-p(SFAM:"RAS Family",pmod(Farn)) directlyIncreases act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp))
-p(SFAM:"RAS Family",pmod(Farn)) directlyIncreases tloc(p(SFAM:"RAS Family"), fromLoc(MESHCS:"Intracellular Space"), toLoc(MESHCS:"Cell Membrane"))
-p(SFAM:"RAS Family",pmod(Farn,L)) directlyIncreases complex(p(SFAM:"RAS Family"),p(SFAM:"RAF Family"))
-p(SFAM:"VEGF Family") increases act(p(HGNC:CYBB), ma(DEFAULT:cat))
-p(SFAM:"VEGF Family") directlyIncreases act(p(HGNC:KDR), ma(DEFAULT:kin))
-p(SFAM:"VEGF Family") increases bp(GOBP:angiogenesis)
-p(SFAM:"VEGF Family") increases complex(p(HGNC:ARF6),p(HGNC:RAC1))
-p(SFAM:"VEGF Family") increases act(p(HGNC:RAC1), ma(DEFAULT:gtp))
-p(SFAM:"VEGF Family") increases p(HGNC:CAV1,pmod(Ph,Y,14))
-p(SFAM:"VEGF Family") directlyIncreases p(HGNC:KDR,pmod(Ph,Y,1054))
-path(SDIS:"Type II diabetes") negativeCorrelation act(p(HGNC:ATP5B), ma(DEFAULT:cat))
-path(SDIS:"Type II diabetes") negativeCorrelation act(p(HGNC:SLC2A4), ma(DEFAULT:tport))
-path(SDIS:"Type II diabetes") negativeCorrelation tloc(p(HGNC:SLC2A4), fromLoc(GOCC:"cytoplasmic, membrane-bounded vesicle"), toLoc(GOCC:"cell outer membrane))
-path(SDIS:Diabetes) negativeCorrelation act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(GO:"kinase activity"))
-r(fus(HGNC:TMPRSS2, "r.1_79", HGNC:ERG, "r.312_5034")) association path(SDIS:"prostate cancer")
-rxn(reactants(a(CHEBI:"acetyl-CoA")),products(a(SCHEM:Citrate))) subProcessOf bp(GOBP:"tricarboxylic acid cycle")
-rxn(reactants(a(CHEBI:glucose)),products(a(CHEBI:pyruvate))) subProcessOf bp(MESHPP:Glycolysis)
-tloc(p(HGNC:AIFM1), fromLoc(MESHCS:Mitochondria), toLoc(MESHCS:Cytoplasm)) increases bp(GOBP:"apoptotic DNA fragmentation")
-tloc(p(HGNC:CTNNB1), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) increases complex(p(HGNC:CTNNB1),p(HGNC:BCL9))
-tloc(p(HGNC:CYCS), fromLoc(MESHCS:Mitochondria), toLoc(MESHCS:Cytoplasm)) increases bp(GOBP:"apoptotic process")
-tloc(p(HGNC:HDAC4), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) directlyIncreases p(HGNC:HDAC4,pmod(Sumo,Lys,559))
-tloc(p(HGNC:PAWR), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) decreases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
-tloc(p(HGNC:SGK1),fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))  association bp(GOBP:"cell cycle")
-tloc(p(SFAM:"DVL Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Membrane")) increases complex(p(SFAM:"DVL Family"),p(SFAM:"DVL Family"))
-tloc(p(SFAM:"FOXO Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) increases act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity"))

data/bin/bel2_document_examples.bel

@@ -1,250 +0,0 @@
- complex(p(HGNC:CCND1), p(HGNC:CDK4))
- p(HGNC:CCND1) => act(p(HGNC:CDK4))
- p(HGNC:BCL2)-| bp(MESHPP:Apoptosis)
- p(HGNC:GATA1) => ( act(p(HGNC:ZBTB16)) => r(HGNC:MPL) )
- a(CHEBI:"oxygen atom")
- a(CHEBI:thapsigargin)
- complex(SCOMP:"AP-1 Complex")
- complex(p(HGNC:FOS), p(HGNC:JUN))
- composite(p(HGNC:IL6), complex(GOCC:"interleukin-23 complex")) increases bp(GOBP:"T-helper 17 cell differentiation")
- complex(p(HGNC:TP53), g(HGNC:CDKN1A))
- m(HGNC:MIR21)
- p(HGNC:AKT1)
- p(SFAM:"AKT Family")
- r(HGNC:AKT1)
- p(ns:protein_value, pmod(ns:type_value, <code>, <pos>))
- p(HGNC:AKT1, pmod(Ph, S, 473))
- p(HGNC:AKT1, pmod(Ph, Ser, 473))
- p(HGNC:AKT1, pmod(MOD:PhosRes, Ser, 473))
- p(HGNC:MAPK1, pmod(Ph, Thr, 185), pmod(Ph, Tyr, 187))
- p(HGNC:HRAS, pmod(Palm))
- p(HGNC:CFTR, var("="))
- p(HGNC:CFTR, var("?"))
- p(HGNC:CFTR, var("p.Gly576Ala"))
- p(REF:NP_000483.3, var("p.Gly576Ala"))
- p(HGNC:CFTR, var("p.Phe508del"))
- p(REF:NP_000483.3, var("p.Phe508del"))
- p(HGNC:CFTR, var("p.Thr1220Lysfs"))
- p(REF:NP_000483.3, var("p.Thr1220Lysfs"))
- g(SNP:rs113993960, var("delCTT"))
- g(REF:NC_000007.13, var("g.117199646_117199648delCTT"))
- g(HGNC:CFTR, var("c.1521_1523delCTT"))
- g(REF:NM_000492.3, var("c.1521_1523delCTT"))
- r(HGNC:CFTR, var("c.1521_1523delCTT"))
- r(REF:NM_000492.3, var("c.1521_1523delCTT"))
- r(HGNC:CFTR, var("r.1653_1655delcuu"))
- r(REF:NM_000492.3, var("r.1653_1655delcuu"))
- p(HGNC:YFG, frag(5_20))
- p(HGNC:YFG, frag(1_?))
- p(HGNC:YFG, frag(?_*))
- p(HGNC:YFG, frag(?))
- p(HGNC:YFG, frag(?, 55kD))
- p(HGNC:AKT1, loc(MESHCS:Cytoplasm))
- a(CHEBI:"calcium(2+)", loc(GOCC:"endoplasmic reticulum"))
- bp(GOBP:"cell cycle arrest")
- bp(GOBP:angiogenesis)
- pathology(MESHD:"Pulmonary Disease, Chronic Obstructive")
- pathology(MESHD:adenocarcinoma)
- act(p(HGNC:AKT1))
- act(p(HGNC:FOXO1), ma(DEFAULT:tscript))
- act(p(HGNC:FOXO1), ma(GO:"nucleic acid binding transcription factor activity"))
- act(p(HGNC:AKT1), ma(DEFAULT:kin))
- act(p(HGNC:AKT1), ma(GO:"kinase activity"))
- tloc(p(HGNC:EGFR), fromLoc(GOCC:"cell surface"), toLoc(GOCC:endosome))
- tloc(<abundance>, fromLoc(GOCC:intracellular), toLoc(GOCC:"extracellular space"))
- tloc(<abundance>, fromLoc(GOCC:intracellular), toLoc(GOCC:"cell surface"))
- deg(<abundance>) directlyDecreases <abundance>
- rxn(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide"), a(CHEBI: "oxygen"))
- fus(ns5':v5', "range5'", ns3':v3', "range3'")
- r(fus(HGNC:TMPRSS2, "r.1_79", HGNC:ERG, "r.312_5034"))
- r(fus(HGNC:TMPRSS2, "?", HGNC:ERG, "?"))
- act(p(HGNC:HMGCR), ma(DEFAULT:cat)) rateLimitingStepOf bp(GOBP:"cholesterol biosynthetic process")
- p(PFH:"Hedgehog Family") =| act(p(HGNC:PTCH1))
- act(p(HGNC:FOXO3),ma(DEFAULT:tscript)) =| r(HGNC:MIR21)
- p(HGNC:CLSPN) => (act(p(HGNC:ATR), ma(DEFAULT:kin)) => p(HGNC:CHEK1, pmod(P)))
- p(HGNC:GSK3B, pmod(P, S, 9)) =| act(p(HGNC:GSK3B), ma(DEFAULT:kin))
- g(HGNC:AKT1) orthologous g(MGI:AKT1)
- g(HGNC:AKT1) :> r(HGNC:AKT1)
- r(HGNC:AKT1) >> p(HGNC:AKT1)
- pathology(MESH:Psoriasis) isA pathology(MESH:"Skin Diseases")
- abundance(CHEBI:"nitrogen atom")
- abundance(CHEBI:"prostaglandin J2")
- a(CHEBI:"nitrogen atom")
- a(CHEBI:"prostaglandin J2")
- geneAbundance(HGNC:AKT1)
- rnaAbundance(HGNC:AKT1)
- proteinAbundance(HGNC:AKT1)
- g(HGNC:AKT1)
- r(HGNC:AKT1)
- p(HGNC:AKT1)
- r(EGID:207)
- r(SP:P31749)
- p(SFAM:"AKT Family")
- geneAbundance(MGI:Mir21)
- rnaAbundance(MGI:Mir21)
- microRNAAbundance(MGI:Mir21)
- g(MGI:Mir21)
- r(MGI:Mir21)
- m(MGI:Mir21)
- complexAbundance(GOCC:"IkappaB kinase complex")
- complexAbundance(proteinAbundance(HGNC:CHUK), proteinAbundance(HGNC:IKBKB), proteinAbundance(HGNC:IKBKG))
- complex(GOCC:"IkappaB kinase complex")
- complex(p(HGNC:CHUK), p(HGNC:IKBKB), p(HGNC:IKBKG))
- compositeAbundance(proteinAbundance(HGNC:TGFB1), proteinAbundance(HGNC:IL6))
- composite(p(HGNC:TGFB1), p(HGNC:IL6))
- activity(proteinAbundance(HGNC:TLR7))
- act(p(HGNC:TLR7))
- activity(proteinAbundance(RGD:Sod1), ma(DEFAULT:cat))
- activity(proteinAbundance(RGD:Sod1), molecularActivity(GOMF:"catalytic activity"))
- act(p(RGD:Sod1), ma(DEFAULT:cat))
- act(p(RGD:Sod1), ma(GOMF:"catalytic activity"))
- activity(proteinAbundance(MGI:Casp3), molecularActivity(DEFAULT:pep))
- activity(proteinAbundance(MGI:Casp3), molecularActivity(GOMF:"peptidase activity"))
- act(p(MGI:Casp3), ma(DEFAULT:pep))
- act(p(MGI:Casp3), ma(GOMF:"peptidase activity"))
- activity(proteinAbundance(SFAM:"RAS Family"), molecularActivity(DEFAULT:gtp))
- activity(proteinAbundance(SFAM:"RAS Family"), molecularActivity(GOMF:"GTP binding"))
- act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp))
- act(p(SFAM:"RAS Family"), ma(GOMF:"GTP binding"))
- activity(complexAbundance(SCOMP:"ENaC Complex"), molecularActivity(DEFAULT:tport))
- activity(complexAbundance(SCOMP:"ENaC Complex"), molecularActivity(GOMF:"transporter activity"))
- act(complex(NCH:"ENaC Complex"), ma(DEFAULT:tport))
- act(complex(NCH:"ENaC Complex"), ma(GOMF:"transporter activity"))
- activity(proteinAbundance(HGNC:CANX), molecularActivity(DEFAULT:chap))
- act(p(HGNC:CANX), ma(DEFAULT:chap))
- activity(proteinAbundance(MGI:Trp53), molecularActivity(DEFAULT:tscript))
- activity(proteinAbundance(MGI:Trp53), molecularActivity(GOMF:"nucleic acid binding transcription factor activity"))
- act(p(MGI:Trp53), ma(DEFAULT:tscript))
- act(p(MGI:Trp53), ma(GOMF:"nucleic acid binding transcription factor activity"))
- complexAbundance(proteinAbundance(HGNC:AKT1S1), proteinAbundance(HGNC:MTOR))
- complex(p(HGNC:AKT1S1), p(HGNC:MTOR))
- FKBP12/rapamycin-associated protein (FRAP), mammalian target of
- rapamycin (mTOR), associates with Stat3 and facilitates STAT activation."
- proteinAbundance(HGNC:BMP4) increases complexAbundance(proteinAbundance(HGNC:MTOR), proteinAbundance(HGNC:STAT3))
- p(HGNC:BMP4) -> complex(p(HGNC:MTOR), p(HGNC:STAT3))
- proteinAbundance(HGNC:IL17A) increases complexAbundance(proteinAbundance(HGNC:STAT3), geneAbundance(HGNC:CCL11))
- p(HGNC:IL17A) -> complex(p(HGNC:STAT3), g(HGNC:CCL11))
- complexAbundance(abundance(CHEBI:"1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate"), proteinAbundance(HGNC:AKT1))
- complex(a(CHEBI:"1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate"), p(HGNC:AKT1))
- biologicalProcess(GOBP:"cellular senescence")
- bp(GOBP:"cellular senescence")
- pathology(MESHD:"Muscle Hypotonia")
- path(MESHD:"Muscle Hypotonia")
- proteinAbundance(HGNC:HIF1A, proteinModification(Hy, Asn, 803))
- p(HGNC:HIF1A, pmod(Hy, N, 803))
- p(SFAM:"AKT Family", pmod(Ph))
- p(MGI:Rela, pmod(Ac, Lys, 315))
- p(HGNC:SP1, pmod(Glyco))
- p(RGD:STAT1, pmod(Me, Arg))
- p(HGNC:MYC, pmod(Ub, Lys))
- reaction(reactants(abundance(CHEBI:phosphoenolpyruvate), abundance(CHEBI:ADP)), products(abundance(CHEBI:pyruvate), abundance(CHEBI:ATP)))
- rxn(reactants(a(CHEBI:phophoenolpyruvate), a(CHEBI:ADP)), products(a(CHEBI:pyruvate), a(CHEBI:ATP)))
- translocation(proteinAbundance(HGNC:NFE2L2), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
- tloc(p(HGNC:NFE2L2), fromLoc(MESHCL:Cytoplasm), toLoc(MESHCL:"Cell Nucleus"))
- cellSecretion(proteinAbundance(MGI:Il6))
- sec(p(MGI:Il6))
- cellSurfaceExpression(proteinAbudance(RGD:Fas))
- surf(p(RGD:Fas))
- degradation(rnaAbundance(HGNC:MYC))
- deg(r(HGNC:MYC))
- proteinAbundance(HGNC:PIK3CA, variant("p.Glu545Lys"))
- p(HGNC:PIK3CA, var("p.Glu545Lys"))
- proteinAbundance(HGNC:ABCA1, variant("p.Arg1851*"))
- p(HGNC:ABCA1, var("p.Arg1851*"))
- proteinAbundance(fusion(HGNC:BCR, "p.1_426", HGNC:JAK2, "p.812_1132"))
- p(fus(HGNC:BCR, "p.1_426", HGNC:JAK2, "p.812_1132"))
- p(fus(HGNC:BCR, "?", HGNC:JAK2, "?"))
- proteinAbundance(HGNC:IL6) increases rnaAbundance(HGNC:ENO1)
- proteinAbundance(HGNC:IL6) increases rnaAbundance(HGNC:XBP1)
- p(HGNC:IL6) -> r(HGNC:ENO1)
- p(HGNC:IL6) -> r(HGNC:XBP1)
- abundance(CHEBI:corticosteroid) decreases biologicalProcess(MESHD:Inflammation)
- a(CHEBI:corticosteroid) -| path(MESHD:Inflammation)
- proteinAbundance(HGNC:AREG) increases activity(complexAbundance(GOCC:"NF-kappaB complex"), molecularActivity(DEFAULT:tscript))
- proteinAbundance(HGNC:EGF) causesNoChange activity(complexAbundance(GOCC:"NF-kappaB complex"), molecularActivity(DEFAULT:tscript))
- p(HGNC:AREG) -> act(complex(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
- p(HGNC:EGF) causesNoChange act(complex(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
- proteinAbundance(HGNC:FGF2, location(GOCC:cytoplasm)) positiveCorrelation pathology(MESHD:"Pulmonary Disease, Chronic Obstructive")
- proteinAbundance(MGI:Nr2f2) association biologicalProcess(GOBP:angiogenesis)
- p(MGI:NR2F2) -- bp(GOBP:angiogenesis)
- proteinAbundance(HGNC:AREG) directlyIncreases activity(proteinAbundance(HGNC:EGFR), molecularActivity(DEFAULT:kin))
- p(HGNC:AREG) => act(p(HGNC:EGFR), ma(DEFAULT:kin))
- activity(proteinAbundance(HGNC:CDK1), molecularActivity(DEFAULT:kin)) directlyIncreases proteinAbundance(HGNC:FOXO1, proteinModification(Ph, Ser, 249))
- act(p(HGNC:CDK1), ma(DEFAULT:kin)) => p(HGNC:FOXO1, pmod(Ph, S, 249))
- activity(proteinAbundance(HGNC:ALOX5), molecularActivity(DEFAULT:cat)) directlyIncreases reaction(reactants(abundance(CHEBI:"5(S)-HPETE")), products(abundance(CHEBI:"leukotriene A4"), abundance(CHEBI:water)))
- act(p(HGNC:ALOX5), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:"5(S)-HPETE")), products(a(CHEBI:"leukotriene A4"), a(CHEBI:water)))
- proteinAbundance(HGNC:GSK3A, proteinModification(Ph, Ser, 21)) directlyDecreases activity(proteinAbundance(HGNC:GSK3A))
- proteinAbundance(HGNC:GSK3B, proteinModification(Ph, Ser, 9)) directlyDecreases activity(proteinAbundance(HGNC:GSK3B))
- p(HGNC:GSK3A, pmod(Ph, S, 21)) =| act(p(HGNC:GSK3A))
- p(HGNC:GSK3B, pmod(Ph, S, 9)) =| act(p(HGNC:GSK3B))
- activity(proteinAbundance(HGNC:FOXO1), molecularActivity(DEFAULT:tscript)) directlyIncreases rnaAbundance(HGNC:CEBPB)
- act(p(HGNC:FOXO1), ma(DEFAULT:tscript)) => r(HGNC:CEBPB)
- proteinAbundance(HGNC:CLSPN) increases (activity(proteinAbundance(HGNC:ATR), molecularActivity(DEFAULT:kin)) directlyIncreases proteinAbundance(HGNC:CHEK1, proteinModification(Ph)))
- p(HGNC:CLSPN) -> (act(p(HGNC:ATR), ma(DEFAULT:kin)) => p(HGNC:CHEK1, pmod(Ph)))
- p(SFAM:"MAPK JNK Family") hasMembers list(p(HGNC:MAPK8), p(HGNC:MAPK9))
- p(SFAM:"MAPK JNK Family") hasMember p(HGNC:MAPK8)
- p(SFAM:"MAPK JNK Family") hasMember p(HGNC:MAPK9)
- complex(GOCC:"checkpoint clamp complex") hasComponents list(p(HGNC:RAD9A), p(HGNC:RAD1), p(HGNC:HUS1))
- complex(GOCC:"checkpoint clamp complex") hasComponent p(HGNC:RAD9A)
- complex(GOCC:"checkpoint clamp complex") hasComponent p(HGNC:RAD1)
- complex(GOCC:"checkpoint clamp complex") hasComponent p(HGNC:HUS1)
- a(SCHEM:"LY 294002") -| r(HGNC:TGFB2)
- act(p(HGNC:PIK3CA), ma(DEFAULT:kin)) -> r(HGNC:TGFB2)
- p(HGNC:FOXO1, var("p.Ser256Ala")) =| p(HGNC:FOXO1, pmod(Ph, Ser, 256))
- p(HGNC:FOXO1, var("p.Ser256Ala")) =| (p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Thr, 24)))
- p(HGNC:FOXO1, var("p.Ser256Ala")) =| (p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Ser, 319)))
- p(HGNC:FOXO1, pmod(Ph, Ser, 256)) =>(p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Thr, 24)))
- p(HGNC:FOXO1, pmod(Ph, Ser, 256)) =>(p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Ser, 319)))
- composite(p(MGI:Tgfb1), p(MGI:Il6)) -> bp(GOBP:"T-helper 17 cell differentiation")
- composite(p(MGI:Hgf), p(MGI:Met)) -> r(MGI:Itgav)
- kin(p(MGI:Met) ) -> r(MGI:Itgav)
- p(MGI:Hgf) -> r(MGI:Itgav)
- p(MGI:Nfe2l2) -> r(MGI:Gsta1)
- p(HGNC:PTEN) -| p(HGNC:CDKN1A)
- p(HGNC:SIAH2) => deg(p(HGNC:TPX2))
- p(MGI:Tert) -> bp(GOBP:"cell proliferation")
- act(p(MGI:Tert), ma(DEFAULT:cat)) causesNoChange bp(GOBP:"cell proliferation")
- p(HGNC:RIPK1) -> act(p(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
- act(p(HGNC:RIPK1), ma(DEFAULT:kin)) causesNoChange act(p(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
- act(p(MGI:Met), ma(DEFAULT:kin)) -> r(Mgi:Itgav)
- act(p(MGI:Met), ma(DEFAULT:kin)) -> r(Mgi:Itga3)
- act(p(MGI:Met), ma(DEFAULT:kin)) -> r(Mgi:Itgb1)
- p(MGI:Ctnnb1) -> r(MGI:Hhip)
- p(HGNC:EGFR, var("p.Leu858Arg")) negativeCorrelation p(HGNC:ERBB2, pmod(Ph,Tyr,1248))
- p(HGNC:EGFR, var("p.Leu858Arg")) -> r(HGNC:DUSP6)
- p(HGNC:PAWR) -| p(SFAM:"AKT Family", pmod(Ph, Ser, 473))
- p(HGNC:PAWR) -| p(SFAM:"AKT Family", pmod(Ph, Ser, 473))
- p(HGNC:PAWR) -| p(SFAM:"AKT Family", pmod(Ph, Ser, 473))
- p(HGNC:AKT1, pmod(Ph, Ser, 473))
- p(HGNC:AKT1, pmod(Ph, Ser))
- p(HGNC:AKT1, pmod(Ph))
- act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) => (act(p(HGNC:SKP2)) => deg(p(SFAM:"FOXO Family")))
- p(SFAM:"FOXO Family", pmod(Ph)) => (act(p(HGNC:SKP2)) => deg(p(SFAM:"FOXO Family")))
- p(HGNC:HIF1A, pmod(Hy, Pro, 402)) => complex(p(HGNC:HIF1A), p(HGNC:VHL))
- p(HGNC:HIF1A, pmod(Hy, Pro, 564)) => complex(p(HGNC:HIF1A), p(HGNC:VHL))
- complex(p(HGNC:HIF1A, pmod(Hy, Pro, 402)), p(HGNC:VHL))
- a(SCHEM:"smoke condensate, cigarette (gas phase)") -> complex(p(PFH:"Histone H3 Family",pmod(Me3, Lys, 27)), g(HGNC:DKK1))
- p(HGNC:MAPK3, pmod(Ph, Thr, 202)) => act(p(HGNC:MAPK3), ma(DEFAULT:kin))
- p(HGNC:MAPK3, pmod(Ph, Tyr, 204)) => act(p(HGNC:MAPK3), ma(DEFAULT:kin))
- p(HGNC:MAPK3, pmod(Ph, Thr, 202)), pmod(Ph, Tyr, 204)) => act(p(HGNC:MAPK3), ma(DEFAULT:kin))
- p(HGNC:CTNNB1, pmod(Ph, Ser, 45)) => p(HGNC:CTNNB1, pmod(Ph, Thr, 41))
- p(HGNC:CTNNB1, pmod(Ph, Ser, 45)) => (kin(p(SFAM:"GSK3 Family")) => p(HGNC:CTNNB1, pmod(Ph, Thr, 41)))
- act(p(HGNC:STAMBP)) =| p(HGNC:F2RL1, pmod(Ub))
- act(p(HGNC:CDC25C), ma(DEFAULT:phos)) =| p(HGNC:CDK1, pmod(Ph, Tyr, 15))
- act(p(HGNC:HSD11B1), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:NADPH), a(CHEBI:cortisone)), products(a(CHEBI:"NADP(+)"), a(CHEBI:cortisol)))
- act(p(HGNC:HSD11B1), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:"NADP(+)"), a(CHEBI:cortisol)), products(a(CHEBI:NADPH), a(CHEBI:cortisone)))
- act(p(HGNC:SOD1), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:superoxide)), products(a(CHEBI:"hydrogen peroxide")))
- act(p(HGNC:SOD1), ma(DEFAULT:cat)) =| a(CHEBI:superoxide)
- act(p(HGNC:SOD1), ma(DEFAULT:cat)) => a(CHEBI:"hydrogen peroxide")
- complex(p(MGI:EPOR), p(MGI:CSF2RB))
- complex(p(HGNC:KEAP1), a(CHEBI:"15-deoxy-Delta(12,14)-prostaglandin J2"))
- complex(p(HGNC:KEAP1), p(HGNC:RBX1), p(HGNC:CUL3))
- complex(p(GOCC:"AP1 complex"), g(HGNC:CCL23))
- act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) => p(HGNC:MDM2, pmod(Ph,Ser,166))
- act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) => p(HGNC:MDM2, pmod(Ph,Ser,186))
- act(p(PFH:"MAPK p38 Family"), ma(DEFAULT:kin)) => p(HGNC:SIAH2, pmod(Ph, Thr, 24))
- act(p(PFH:"MAPK p38 Family"), ma(DEFAULT:kin)) => p(HGNC:SIAH2, pmod(Ph, Ser, 29))
- complex(p(SFAM:"Hedgehog Family"), p(MGI:Hhip))
- complex(p(MGI:Ihh), p(MGI:Hhip))
- complex(p(MGI:Shh), p(MGI:Hhip))
- complex(p(MGI:Dhh), p(MGI:Hhip))