Identifying complexes: Xrefs

[jvwong]

Factoid includes two flavours of complexes

• complex which are compound nodes, identified by these components
• namedComplex which appear as simple nodes, identified by a FamPlex ID

Factoid labels both kinds as complex for this converter to process. In the second case, we'd like to identify a complex using its database ID directly (i.e. from FamPlex). Suggestion is to tag it directly with a UnificationXref.

See also:

• Supporting Complexes and Family members via Famplex
• Famplex: Named complex

Details

Sample document with namedComplex (NFKappaB):

Sample BioPAX template sent to converter (json-to-biopax) endpoint:

{
  "interactions":[
     {
        "type":"Other Interaction",
        "participants":[
           {
              "type":"protein",
              "name":"MDM2",
              "xref":{
                 "id":"4193",
                 "db":"NCBI Gene",
                 "dbPrefix":"ncbigene"
              },
              "organism":{
                 "id":"9606",
                 "db":"taxonomy"
              }
           },
           {
              "type":"complex",
              "name":"NFKappaB",
              "xref":{
                 "id":"NFkappaB",
                 "db":"FamPlex",
                 "dbPrefix":"fplx"
              },
              "organism":{
                 "id":"9606",
                 "db":"taxonomy"
              },
              "componentXrefs":[
                 {
                    "dbName":"FamPlex",
                    "dbPrefix":"fplx",
                    "id":"NFkappaB_1"
                 },
                 {
                    "dbName":"FamPlex",
                    "dbPrefix":"fplx",
                    "id":"NFkappaB_2"
                 }
              ]
           }
        ]
     }
  ],
  "pathwayName":"Structural basis for the action of the drug trametinib at KSR-bound MEK.",
  "pathwayId":"b43818b1-d13f-4f2b-9d62-1df20393ef3c",
  "publication":{
     "id":"32927473",
     "db":"pubmed"
  }
}