diff --git a/notebooks/cbio_json.ipynb b/notebooks/cbio_json.ipynb index 5198a0be..aafbe4f9 100644 --- a/notebooks/cbio_json.ipynb +++ b/notebooks/cbio_json.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -741,7 +741,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 3, "metadata": {}, "outputs": [ { @@ -767,668 +767,10 @@ " 'patientAttribute': False,\n", " 'priority': '1',\n", " 'clinicalAttributeId': 'CANCER_TYPE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Cancer Type Detailed',\n", - " 'description': 'Cancer Type Detailed',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'CANCER_TYPE_DETAILED',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'EXPRESSION',\n", - " 'description': 'EXPRESSION',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '2',\n", - " 'clinicalAttributeId': 'EXPRESSION',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Fraction Genome Altered',\n", - " 'description': 'Fraction Genome Altered',\n", - " 'datatype': 'NUMBER',\n", - " 'patientAttribute': False,\n", - " 'priority': '20',\n", - " 'clinicalAttributeId': 'FRACTION_GENOME_ALTERED',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'HISTOPATHOLOGY',\n", - " 'description': 'HISTOPATHOLOGY',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '3',\n", - " 'clinicalAttributeId': 'HISTOPATHOLOGY',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Inferred Ethnicity',\n", - " 'description': 'Inferred Ethnicity',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': True,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'INFERRED_ETHNICITY',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Mutation Count',\n", - " 'description': 'Mutation Count',\n", - " 'datatype': 'NUMBER',\n", - " 'patientAttribute': False,\n", - " 'priority': '30',\n", - " 'clinicalAttributeId': 'MUTATION_COUNT',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Note',\n", - " 'description': 'Note.',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '2',\n", - " 'clinicalAttributeId': 'NOTE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Oncotree Code',\n", - " 'description': 'Oncotree Code',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'ONCOTREE_CODE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'PHASE',\n", - " 'description': 'PHASE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '4',\n", - " 'clinicalAttributeId': 'PHASE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Reported Ethnicity',\n", - " 'description': 'Reported Ethnicity',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': True,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'REPORTED_ETHNICITY',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Number of Samples Per Patient',\n", - " 'description': 'Number of Samples Per Patient',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': True,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'SAMPLE_COUNT',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Site of Sample',\n", - " 'description': 'Sample Site',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '4',\n", - " 'clinicalAttributeId': 'SAMPLE_SITE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Sex',\n", - " 'description': 'Sex',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': True,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'SEX',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'SPECIMEN_SITE',\n", - " 'description': 'SPECIMEN_SITE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '4',\n", - " 'clinicalAttributeId': 'SITE_OF_SPECIMEN',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'TMB (nonsynonymous)',\n", - " 'description': 'TMB (nonsynonymous)',\n", - " 'datatype': 'NUMBER',\n", - " 'patientAttribute': False,\n", - " 'priority': '1',\n", - " 'clinicalAttributeId': 'TMB_NONSYNONYMOUS',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment 17-DMAG',\n", - " 'description': 'Treatment 17-DMAG',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_17-DMAG',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment 19D12',\n", - " 'description': 'Treatment 19D12',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_19D12',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment ABRAXANE',\n", - " 'description': 'Treatment ABRAXANE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_ABRAXANE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment ABT-199',\n", - " 'description': 'Treatment ABT-199',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_ABT-199',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment ABT-263',\n", - " 'description': 'Treatment ABT-263',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_ABT-263',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment ACTINOMYCIN D',\n", - " 'description': 'Treatment ACTINOMYCIN D',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_ACTINOMYCIN D',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment APLIDIN',\n", - " 'description': 'Treatment APLIDIN',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_APLIDIN',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment AZD-2171',\n", - " 'description': 'Treatment AZD-2171',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_AZD-2171',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment AZD-6244',\n", - " 'description': 'Treatment AZD-6244',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_AZD-6244',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment AZD1480',\n", - " 'description': 'Treatment AZD1480',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_AZD1480',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment AZD8055',\n", - " 'description': 'Treatment AZD8055',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_AZD8055',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment BAL101553',\n", - " 'description': 'Treatment BAL101553',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_BAL101553',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment BI6727 (VOLASERTIB)',\n", - " 'description': 'Treatment BI6727 (VOLASERTIB)',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_BI6727 (VOLASERTIB)',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment BMN-673',\n", - " 'description': 'Treatment BMN-673',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_BMN-673',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment BMS-354825',\n", - " 'description': 'Treatment BMS-354825',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_BMS-354825',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment BMS-754807',\n", - " 'description': 'Treatment BMS-754807',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_BMS-754807',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment BORTEZOMIB',\n", - " 'description': 'Treatment BORTEZOMIB',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_BORTEZOMIB',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CABOZANTINIB (XL-148)',\n", - " 'description': 'Treatment CABOZANTINIB (XL-148)',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CABOZANTINIB (XL-148)',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CBL0137',\n", - " 'description': 'Treatment CBL0137',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CBL0137',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CDX-011 (GLEMBATUMUMAB)',\n", - " 'description': 'Treatment CDX-011 (GLEMBATUMUMAB)',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CDX-011 (GLEMBATUMUMAB)',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CGC(PG)-11047',\n", - " 'description': 'Treatment CGC(PG)-11047',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CGC(PG)-11047',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CISPLATIN',\n", - " 'description': 'Treatment CISPLATIN',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CISPLATIN',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CLORETAZINE',\n", - " 'description': 'Treatment CLORETAZINE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CLORETAZINE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CPX351',\n", - " 'description': 'Treatment CPX351',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CPX351',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CX-5461 (POL1)',\n", - " 'description': 'Treatment CX-5461 (POL1)',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CX-5461 (POL1)',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CYCLOPHOSPHAMIDE',\n", - " 'description': 'Treatment CYCLOPHOSPHAMIDE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CYCLOPHOSPHAMIDE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment CYTARABINE',\n", - " 'description': 'Treatment CYTARABINE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_CYTARABINE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment E7438/EPZ6438',\n", - " 'description': 'Treatment E7438/EPZ6438',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_E7438/EPZ6438',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment EC1456',\n", - " 'description': 'Treatment EC1456',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_EC1456',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment ERIBULIN',\n", - " 'description': 'Treatment ERIBULIN',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_ERIBULIN',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment FENRETINIDE',\n", - " 'description': 'Treatment FENRETINIDE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_FENRETINIDE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment GENZ-644282',\n", - " 'description': 'Treatment GENZ-644282',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_GENZ-644282',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment GS-9820',\n", - " 'description': 'Treatment GS-9820',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_GS-9820',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment GSK690693',\n", - " 'description': 'Treatment GSK690693',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_GSK690693',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment GSK923295A',\n", - " 'description': 'Treatment GSK923295A',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_GSK923295A',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment HGS-ETR1',\n", - " 'description': 'Treatment HGS-ETR1',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_HGS-ETR1',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment IMC-A12',\n", - " 'description': 'Treatment IMC-A12',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_IMC-A12',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment INK128-1110-028',\n", - " 'description': 'Treatment INK128-1110-028',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_INK128-1110-028',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment JNJ26481585',\n", - " 'description': 'Treatment JNJ26481585',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_JNJ26481585',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment JNJ26854165',\n", - " 'description': 'Treatment JNJ26854165',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_JNJ26854165',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment KPT-330',\n", - " 'description': 'Treatment KPT-330',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_KPT-330',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment LAPATINIB',\n", - " 'description': 'Treatment LAPATINIB',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_LAPATINIB',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment LENOLIDAMIDE',\n", - " 'description': 'Treatment LENOLIDAMIDE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_LENOLIDAMIDE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment LY 2606368',\n", - " 'description': 'Treatment LY 2606368',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_LY 2606368',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment MK-2206',\n", - " 'description': 'Treatment MK-2206',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_MK-2206',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment MK-8242',\n", - " 'description': 'Treatment MK-8242',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_MK-8242',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment MLN4924',\n", - " 'description': 'Treatment MLN4924',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_MLN4924',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment MLN8237',\n", - " 'description': 'Treatment MLN8237',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_MLN8237',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment MM-141',\n", - " 'description': 'Treatment MM-141',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_MM-141',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment NSC060043',\n", - " 'description': 'Treatment NSC060043',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_NSC060043',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment NSC750854',\n", - " 'description': 'Treatment NSC750854',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_NSC750854',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment PCI-32765',\n", - " 'description': 'Treatment PCI-32765',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_PCI-32765',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment PF-03084014',\n", - " 'description': 'Treatment PF-03084014',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_PF-03084014',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment PIXANTRONE',\n", - " 'description': 'Treatment PIXANTRONE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_PIXANTRONE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment PR-104',\n", - " 'description': 'Treatment PR-104',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_PR-104',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment RAPAMYCIN',\n", - " 'description': 'Treatment RAPAMYCIN',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_RAPAMYCIN',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment RG7112',\n", - " 'description': 'Treatment RG7112',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_RG7112',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment RO4929097',\n", - " 'description': 'Treatment RO4929097',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_RO4929097',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment RUXOLITINIB',\n", - " 'description': 'Treatment RUXOLITINIB',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_RUXOLITINIB',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SAHA',\n", - " 'description': 'Treatment SAHA',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SAHA',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SAR3419',\n", - " 'description': 'Treatment SAR3419',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SAR3419',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SB-715992',\n", - " 'description': 'Treatment SB-715992',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SB-715992',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SCH 727965',\n", - " 'description': 'Treatment SCH 727965',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SCH 727965',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SGI-1776',\n", - " 'description': 'Treatment SGI-1776',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SGI-1776',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SGN-CD19A',\n", - " 'description': 'Treatment SGN-CD19A',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SGN-CD19A',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SORAFENIB',\n", - " 'description': 'Treatment SORAFENIB',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SORAFENIB',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment STA9090 (GANETESPIB)',\n", - " 'description': 'Treatment STA9090 (GANETESPIB)',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_STA9090 (GANETESPIB)',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment STF-118804',\n", - " 'description': 'Treatment STF-118804',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_STF-118804',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SU11248',\n", - " 'description': 'Treatment SU11248',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SU11248',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment SVV-001',\n", - " 'description': 'Treatment SVV-001',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_SVV-001',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment TAK-701',\n", - " 'description': 'Treatment TAK-701',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_TAK-701',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment TB-403',\n", - " 'description': 'Treatment TB-403',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_TB-403',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment TL32711',\n", - " 'description': 'Treatment TL32711',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_TL32711',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment TOPOTECAN',\n", - " 'description': 'Treatment TOPOTECAN',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_TOPOTECAN',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment TRISENOX(ATO)',\n", - " 'description': 'Treatment TRISENOX(ATO)',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_TRISENOX(ATO)',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment VINCRISTINE',\n", - " 'description': 'Treatment VINCRISTINE',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_VINCRISTINE',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment VS-4718',\n", - " 'description': 'Treatment VS-4718',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_VS-4718',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment XL147',\n", - " 'description': 'Treatment XL147',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_XL147',\n", - " 'studyId': 'pptc_2019'},\n", - " {'displayName': 'Treatment XL765',\n", - " 'description': 'Treatment XL765',\n", - " 'datatype': 'STRING',\n", - " 'patientAttribute': False,\n", - " 'priority': '0',\n", - " 'clinicalAttributeId': 'TX_XL765',\n", " 'studyId': 'pptc_2019'}]" ] }, - "execution_count": 15, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -1436,7 +778,7 @@ "source": [ "study_name = 'pptc_2019'\n", "r = requests.get(f'https://www.cbioportal.org/api/studies/{study_name}/clinical-attributes?projection=DETAILED&pageSize=10000000&pageNumber=0&direction=ASC')\n", - "r.json()" + "r.json()[0:3]" ] }, {