A JSON output data format for network/graph visualization #303

{
  network : {
    nodes : [
      {"data":{"class":"ball","id":"ABCB11","label":"ABCB11","queried":false,"parsedMetadata":
        [["Type","bp:Protein"],["Database IDs",[["uniprot knowledgebase","O95342"],
        ["hgnc symbol","ABCB11"]]]]}}, 
      {"data":{"class":"ball","id":"TNF","label":"TNF","queried":false,"parsedMetadata":[["Type","bp:Protein"],
        ["Database IDs",[["uniprot knowledgebase","P01375"],["hgnc symbol","TNF"]]]]}},
...
    ],
    edges : [
      {"data":{"id":"ABCB11\tcontrols-expression-of\tTNF",
        "label":"ABCB11 controls expression of TNF","source":"ABCB11",
        "target":"TNF","class":"Expression",
        "parsedMetadata":[["List",[["PubMed","28505368"]]],["Detailed Views",[["Pathway Commons","Control_9cf09917764babde4fd448610fa38927"],["Pathway Commons","TemplateReaction_79ba1b1dc9889c1e4f25bcbf2249cef7"]]]]},
        "classes":"Expression"},
      {"data":{"id":"ABCB6\tinteracts-with\tSMAD1",
        "label":"ABCB6 interacts with SMAD1","source":"ABCB6","target":"SMAD1","class":"Binding",
        "parsedMetadata":[["List",[["PubMed","15761153"]]],["Detailed Views",[["Pathway Commons","MolecularInteraction_6dbdc98a-5ce8-4184-92a7-95369e98467e___null__1517956_"]]]]},
        "classes":"Binding"},
...
    ]
}

{
 graph : { 
nodes : [
{"data":{"id":"http://pathwaycommons.org/pc2/Protein_ea518c37f72116263e0c265603eeec7f","class":"macromolecule","label":"SMAD6","parent":"cytosol","clonemarker":false,"stateVariables":[{"id":null,"class":"state variable","state":{"variable":"","value":"x[1 - 496]"}}],"unitsOfInformation":[],"bbox":{"x":24,"y":15,"w":48,"h":30},"parsedMetadata":[["Type","bp:Protein"],["Data Source","http://pathwaycommons.org/pc2/reactome"],["Display Name","SMAD6"],["Comment",["Reactome DB_ID: 3006350","REPLACED http://www.reactome.org/biopax/64/48887#Protein7405"]],["Names",["SMAD6_HUMAN","Mothers against decapentaplegic homolog 6","hSMAD6","Smad6","SMAD 6","SMAD6","MAD homolog 6","Mothers against DPP homolog 6","SMAD family member 6","MADH6"]],["Database IDs",[["reactome","R-HSA-3006350"],["hgnc symbol","SMAD6"],["uniprot knowledgebase","O43541"]]],["Standard Name","Mothers against decapentaplegic homolog 6"]],"geneSynonyms":[]}},
{"data":{"id":"http://identifiers.org/reactome/R-HSA-8877941_LEFTTORIGHT","class":"process","label":"","parent":"nucleoplasm","clonemarker":false,"stateVariables":[],"unitsOfInformation":[],"bbox":{"x":7.5,"y":7.5,"w":15,"h":15},"parsedMetadata":[["Type","bp:BiochemicalReaction"],["Data Source","http://pathwaycommons.org/pc2/reactome"],["Display Name","RUNX2 binds SMAD1 in the nucleus"],["Comment",["Edited: Orlic-Milacic, Marija, 2017-08-09","Reviewed: Ducy, Patricia, 2017-08-04","In response to BMP2 treatment, RUNX2 (presumably associated with CBFB) forms a complex with SMAD1 (Wang et al. 2006). Phosphorylation of SMAD1 in response to BMP signaling and formation of a heterotrimeric complex between phosphorylated SMAD1 and SMAD4 are prerequisites for SMAD1 retention in the nucleus (Qin et al. 2001, Xiao et al. 2001).<p>BMP2 signaling is implicated in promoting formation of a complex between RUNX2, SMAD1 and acetyltransferase EP300 (p300) and facilitating EP300-mediated acetylation of RUNX2, which activates RUNX2 transcriptional activity. This may involve ERK-mediated phosphorylation of RUNX2 and/or EP300 downstream of BMP2, but the exact mechanism has not been elucidated (Jun et al. 2010).","Authored: Orlic-Milacic, Marija, 2016-06-28"]],["Database IDs",[["pubmed","17215250"],["pubmed","11779505"],["pubmed","11509558"],["pubmed","20851880"],["reactome","R-HSA-8877941"]]]],"geneSynonyms":[]}},
... ],
edges : [
{"data":{"id":"OUT_http://identifiers.org/reactome/R-HSA-8938356_LEFTTORIGHT--TO--http://pathwaycommons.org/pc2/Complex_029c2be399f6c4e20fac1344b30cf615","class":"production","cardinality":0,"source":"http://identifiers.org/reactome/R-HSA-8938356_LEFTTORIGHT","target":"http://pathwaycommons.org/pc2/Complex_029c2be399f6c4e20fac1344b30cf615","bendPointPositions":[],"portSource":"http://identifiers.org/reactome/R-HSA-8938356_LEFTTORIGHT","portTarget":"http://pathwaycommons.org/pc2/Complex_029c2be399f6c4e20fac1344b30cf615"}},
{"data":{"id":"http://pathwaycommons.org/pc2/Protein_dfe49ca23c2925eebe90a01615d12782--TO--INP_http://identifiers.org/reactome/R-HSA-8938356_LEFTTORIGHT","class":"consumption","cardinality":0,"source":"http://pathwaycommons.org/pc2/Protein_dfe49ca23c2925eebe90a01615d12782","target":"http://identifiers.org/reactome/R-HSA-8938356_LEFTTORIGHT","bendPointPositions":[],"portSource":"http://pathwaycommons.org/pc2/Protein_dfe49ca23c2925eebe90a01615d12782","portTarget":"http://identifiers.org/reactome/R-HSA-8938356_LEFTTORIGHT"}}
... ]
 }
}