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FORMAT: 1A

iMuSE Server API

Note that this API does NOT follow the traditional RESTful HTTP verb conventions. All requests are made via POST.

Table of Contents:

Data Listing [/data-listing]

  • Response 200 (application/json)

    • Body

        {
  	"projects": {
  		"ICGC-BRCA-EU": {
  			"name": "Breast ER+ and HER2- Cancer - EU/UK",
  			"num_donors": 569,
  			"source": "ICGC",
  			"has_clinical": true,
  			"has_extended": true,
  			"has_counts": true
  		},
  		...
  	},
  	"sigs": {
  		"SBS": [
  			{
  				"name": "COSMIC 1",
  				"description": "Signature 1 is the result...",
  				"index": 10,
  				"publication": "Alexandrov L.B. et al., Nature (2013)"
  			},
  			...
  		],
  		"DBS": [
  			...
  		],
  		"INDEL": [
  			...
  		]
  	},
  	"sig_per_cancer_type": [
  		{
  			"group": "COSMIC",
  			"id": "COSMIC",
  			"cancer-types": [
  				{
  					"name": "Adrenocortical Carcinoma",
  					"id": "COSMIC-ACC",
  					"signatures": [
  						"COSMIC 1",
  						...
  					]
  				},
  				...
  			]
  		},
  		...
  	]
  }

Signature [/signature]

  • Request (text/plain)

    • Body

        {
  	"name": "COSMIC 1",
  	"mut_type": "SBS"
  }

  • Response 200 (application/json)

    • Body

        [
  	{
  		"sample_id": "SA543682",
  		"proj_id": "ICGC-BRCA-EU",
  		"exposures": {
  			"SBS": {
  				"COSMIC 1": 515.9603424981033,
  				"COSMIC 2": 1.5975135739615894e-14,
  				...
  			},
  			"DBS": {
  				...
  			},
  			"INDEL": {
  				...
  			}
  		},
  		"clinical": {
  			"Patient": "DO218489",
  			"Tobacco User": "nan",
  			"Diagnosis Age": 45,
  			"Sex": "female",
  			...
  		}
  	},
  	...
  ]

Exposures [/exposures]

  • Request (text/plain)

    • Body

        {
  	"projects": [
  		"ICGC-BRCA-EU",
  		...
  	],
  	"signatures": {
  		"SBS": [
  			"COSMIC 1",
  			...
  		],
  		"DBS": [
  			...
  		],
  		"INDEL": [
  			...
  		]
  	}
  }

  • Response 200 (application/json)

    • Body

        [
  	{
  		"sample_id": "SA543682",
  		"proj_id": "ICGC-BRCA-EU",
  		"exposures": {
  			"SBS": {
  				"COSMIC 1": 515.9603424981033,
  				"COSMIC 2": 1.5975135739615894e-14,
  				...
  			},
  			"DBS": {
  				...
  			},
  			"INDEL": {
  				...
  			}
  		},
  		"clinical": {
  			"Patient": "DO218489",
  			"Tobacco User": "nan",
  			"Diagnosis Age": 45,
  			"Sex": "female",
  			...
  		}
  	},
  	...
  ]

Exposures - Single Sample [/exposures-single-sample]

  • Request (text/plain)

    • Body

        {
  	"sample_id": "SA543682", 
  	"proj_id": "ICGC-BRCA-EU", 
  	"signatures": {
  		"SBS": [
  			"COSMIC 1",
  			...
  		],
  		"DBS": [
  			...
  		],
  		"INDEL": [
  			...
  		]
  	}
  }

  • Response 200 (application/json)

    • Body

        [
  	{
  		"sample_id": "SA543682",
  		"proj_id": "ICGC-BRCA-EU",
  		"exposures": {
  			"SBS": {
  				"COSMIC 7": 14.533149065470633,
  				...
  			},
  			"DBS": {
  				...
  			},
  			"INDEL": {
  				...
  			}
  		},
  		"clinical": {
  			"Patient": "DO218489",
  			"Tobacco User": "nan",
  			"Diagnosis Age": 45,
  			"Sex": "female",
  			...
  		}
  	}
  ]

Kataegis [/kataegis]

  • Request (text/plain)

    • Body

        {
  	"projects": [
  		"ICGC-BRCA-EU",
  		...
  	]
  }

  • Response 200 (application/json)

    • Body

        {
  	"SA543567": {
  		"kataegis": {
  			"8": [
  				43624586,
  				68097779
  			],
  			"10": [
  				79959348,
  				79959543
  			],
  			"12": [
  				31335571
  			],
  			"15": [
  				97354064
  			],
  			"16": [
  				2398365
  			],
  			"17": [
  				51822158,
  				70629730,
  				70629755
  			],
  			"20": [
  				20690422,
  				20690503,
  				20690512,
  				20690643
  			]
  		},
  		"proj_id": "ICGC-BRCA-EU"
  	},
  	...
  }

Rainfall [/kataegis-rainfall]

  • Request (text/plain)

    • Body

        {
  	"proj_id": "ICGC-BRCA-EU",
  	"sample_id": "SA543567"
  }

  • Response 200 (text/csv)

    • Body

        chr,pos,cat,mut_dist,kataegis
  1,1670458,A[C>A]A,1084547,0
  1,1930665,T[T>C]C,260207,0
  1,2057510,A[C>T]C,126845,0
  1,2110902,T[C>T]A,53392,0
  1,4136526,A[C>T]A,2025624,0
  1,4387515,A[T>G]A,250989,0
  1,4652247,T[C>T]G,264732,0

Signature Genome Bins - Single Sample [/signature-genome-bins-single-sample]

  • Request (text/plain)

    • Body

        {
  	"proj_id": "ICGC-BRCA-EU",
  	"sample_id": "SA543682",
  	"signatures": {
  		"SBS": [
  			"COSMIC 1",
  			...
  		],
  		"DBS": [
  			...
  		],
  		"INDEL": [
  			...
  		]
  	}, 
  	"regionWidth": 10000000
  }

  • Response 200 (application/json)

    • Body

        {
  	"1": {
  		"SBS": {
  			"0": {
  				"COSMIC 1": 3,
  				...
  			},
  			"10000000": {
  				"COSMIC 1": 0,
  				...
  			},
  			"20000000": {
  				"COSMIC 1": 1,
  				...
  			},
  			...
  		},
  		"DBS": {
  			...
  		},
  		"INDEL": {
  			...
  		}
  	},
  	...
  	"22": {
  		...
  	},
  	"X": {
  		...
  	},
  	...
  }

Samples with Signatures [/samples-with-signatures]

  • Request (text/plain)

    • Body

        {
  	"projects":["ICGC-BRCA-EU"],
  	"signatures": {
  		"SBS": [
  			"COSMIC 1",
  			...
  		],
  		"DBS": [
  			...
  		],
  		"INDEL": [
  			...
  		]
  	}
  }

  • Response 200 (application/json)

    • Body

        {
  	"signatures": {
  		"SBS": {
  			"COSMIC 1": {
  				"ICGC-BRCA-EU": 561
  			},
  			...
  		},
  		"DBS": {
  			...
  		},
  		"INDEL": {
  			...
  		}
  	},
  	"projects": {
  		"ICGC-BRCA-EU": 1139,
  		...
  	}
  }

Hierarchical Clustering [/clustering]

  • Request (text/plain)

    • Body

        {
  	"projects": [
  		"ICGC-BRCA-EU",
  		...
  	],
  	"signatures": {
  		"SBS":[
  			"COSMIC 1",
  			...
  		],
  		"DBS": [
  			...
  		],
  		"INDEL": [
  			...
  		]
  	}
  }

  • Response 200 (application/json)

    • Body

        {
  	"children": [
  		{
  			"children": [
  				{
  					"children": [
  						{
  							"children": [
  								{
  									"children": [
  										{
  											"children": [
  												{
  													"children": [
  														{
  															"children": [],
  															"name": "SA569469"
  														},
  														{
  															"children": [],
  															"name": "SA570293"
  														}
  													],
  													"name": "SA569469-SA570293"
  												},
  												{
  													"children": [
  														{
  															"children": [
  																{
  																	"children": [
  																		{
  																			"children": [],
  																			"name": "SA569588"
  																		},
  																		{
  																			"children": [],
  																			"name": "SA570579"
  																		}
  																	],
  																	"name": "SA569588-SA570579"
  																},
  																...
  														},
  														...
  												},
  												...
  										},
  										...
  								},
  								...
  						},
  						...
  				},
  				...
  		},
  		...
  }