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Gets all cases
get ?query={allCases(offset: 0 limit: 10) {case_id case_submitter_id project_id project_submitter_id disease_type primary_site externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location }}}
Returns case details.
Fields:- case_id
- case_submitter_id
- project_id
- project_submitter_id
- disease_type
- primary_site
- externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location }
Response Sample
{ "data": { "allCases": [ { "case_id": "327f8188-0a5d-11eb-bc0e-0aad30af8a83", "case_submitter_id": "05BR016", "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "project_submitter_id": "CPTAC-2", "disease_type": "Breast Invasive Carcinoma", "primary_site": "Breast", "externalReferences": [ { "external_reference_id": "152f9e71-a437-4a4b-8c58-3ffcda41904b", "reference_resource_shortname": "GDC", "reference_resource_name": "Genomic Data Commons", "reference_entity_location": "https://portal.gdc.cancer.gov/cases/152f9e71-a437-4a4b-8c58-3ffcda41904b" } ] } ] } }
Response Schema
{} allCasesdataallCasesDef(optional){} allCasesDefallCasesarray[allCasesDescription](optional){} allCasesDescriptioncase_idstring(optional)case_submitter_idstring(optional)project_idstring(optional)project_submitter_idstring(optional)disease_typestring(optional)primary_sitestring(optional)externalReferencesarray[ExternalReferencesAllCases](optional){} ExternalReferencesAllCasesexternal_reference_idstring(optional)reference_resource_shortnamestring(optional)reference_resource_namestring(optional)reference_entity_locationstring(optional)
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Get info of experiment types
get ?query={allExperimentTypes (experiment_type: "{experiment_type}") {experiment_type tissue_or_organ_of_origin disease_type}}
Input Parameters (multiple parameters can be passed in one call):
- experiment_type (example: Label Free)
- tissue_or_organ_of_origin (example: Cheek mucosa)
- disease_type (example: Clear Cell Renal Cell Carcinoma)
Fields:- experiment_type: Name of experiment type
- tissue_or_organ_of_origin: Text term that describes the anatomic site of the tumor or disease
- disease_type
Response Sample
{ "data": { "allExperimentTypes": [ { "experiment_type": "Label Free", "tissue_or_organ_of_origin": "Kidney, NOS", "disease_type": "Clear Cell Renal Cell Carcinoma" } ] } }
Response Schema
{} allExperimentsdataallExperimentsDef(optional){} allExperimentsDefallExperimentTypesarray[Experiment](optional){} Experimentexperiment_typestring(optional)tissue_or_organ_of_originstring(optional)disease_typestring(optional)
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Find case(s)
get ?query={case (case_submitter_id: "{case_submitter_id}") { case_id case_submitter_id project_submitter_id days_to_lost_to_followup disease_type index_date lost_to_followup primary_site consent_type days_to_consent externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location } demographics{ demographic_id ethnicity gender demographic_submitter_id race cause_of_death days_to_birth days_to_death vital_status year_of_birth year_of_death age_at_index premature_at_birth weeks_gestation_at_birth age_is_obfuscated cause_of_death_source occupation_duration_years country_of_residence_at_enrollment } samples { sample_id sample_submitter_id sample_type sample_type_id gdc_sample_id gdc_project_id biospecimen_anatomic_site composition current_weight days_to_collection days_to_sample_procurement diagnosis_pathologically_confirmed freezing_method initial_weight intermediate_dimension longest_dimension method_of_sample_procurement pathology_report_uuid preservation_method sample_type_id shortest_dimension time_between_clamping_and_freezing time_between_excision_and_freezing tissue_type tumor_code tumor_code_id tumor_descriptor biospecimen_laterality catalog_reference distance_normal_to_tumor distributor_reference growth_rate passage_count sample_ordinal tissue_collection_type diagnoses{ diagnosis_id diagnosis_submitter_id annotation} aliquots { aliquot_id aliquot_submitter_id analyte_type aliquot_run_metadata {aliquot_run_metadata_id label experiment_number fraction replicate_number date alias analyte} } } diagnoses{ diagnosis_id tissue_or_organ_of_origin age_at_diagnosis primary_diagnosis tumor_grade tumor_stage diagnosis_submitter_id classification_of_tumor days_to_last_follow_up days_to_last_known_disease_status days_to_recurrence last_known_disease_status morphology progression_or_recurrence site_of_resection_or_biopsy prior_malignancy ajcc_clinical_m ajcc_clinical_n ajcc_clinical_stage ajcc_clinical_t ajcc_pathologic_m ajcc_pathologic_n ajcc_pathologic_stage ajcc_pathologic_t ann_arbor_b_symptoms ann_arbor_clinical_stage ann_arbor_extranodal_involvement ann_arbor_pathologic_stage best_overall_response burkitt_lymphoma_clinical_variant circumferential_resection_margin colon_polyps_history days_to_best_overall_response days_to_diagnosis days_to_hiv_diagnosis days_to_new_event figo_stage hiv_positive hpv_positive_type hpv_status iss_stage laterality ldh_level_at_diagnosis ldh_normal_range_upper lymph_nodes_positive lymphatic_invasion_present method_of_diagnosis new_event_anatomic_site new_event_type overall_survival perineural_invasion_present prior_treatment progression_free_survival progression_free_survival_event residual_disease vascular_invasion_present year_of_diagnosis icd_10_code synchronous_malignancy tumor_largest_dimension_diameter anaplasia_present anaplasia_present_type child_pugh_classification cog_liver_stage cog_neuroblastoma_risk_group cog_renal_stage cog_rhabdomyosarcoma_risk_group enneking_msts_grade enneking_msts_metastasis enneking_msts_stage enneking_msts_tumor_site esophageal_columnar_dysplasia_degree esophageal_columnar_metaplasia_present first_symptom_prior_to_diagnosis gastric_esophageal_junction_involvement goblet_cells_columnar_mucosa_present gross_tumor_weight inpc_grade inpc_histologic_group inrg_stage inss_stage irs_group irs_stage ishak_fibrosis_score lymph_nodes_tested medulloblastoma_molecular_classification metastasis_at_diagnosis metastasis_at_diagnosis_site mitosis_karyorrhexis_index peripancreatic_lymph_nodes_positive peripancreatic_lymph_nodes_tested supratentorial_localization tumor_confined_to_organ_of_origin tumor_focality tumor_regression_grade vascular_invasion_type wilms_tumor_histologic_subtype breslow_thickness gleason_grade_group igcccg_stage international_prognostic_index largest_extrapelvic_peritoneal_focus masaoka_stage non_nodal_regional_disease non_nodal_tumor_deposits ovarian_specimen_status ovarian_surface_involvement percent_tumor_invasion peritoneal_fluid_cytological_status primary_gleason_grade secondary_gleason_grade weiss_assessment_score adrenal_hormone ann_arbor_b_symptoms_described diagnosis_is_primary_disease eln_risk_classification figo_staging_edition_year gleason_grade_tertiary gleason_patterns_percent margin_distance margins_involved_site pregnant_at_diagnosis satellite_nodule_present sites_of_involvement tumor_depth who_cns_grade who_nte_grade samples { sample_id sample_submitter_id annotation}} exposures { exposure_id exposure_submitter_id alcohol_days_per_week alcohol_drinks_per_day alcohol_history alcohol_intensity asbestos_exposure cigarettes_per_day coal_dust_exposure environmental_tobacco_smoke_exposure pack_years_smoked radon_exposure respirable_crystalline_silica_exposure smoking_frequency time_between_waking_and_first_smoke tobacco_smoking_onset_year tobacco_smoking_quit_year tobacco_smoking_status type_of_smoke_exposure type_of_tobacco_used years_smoked age_at_onset, alcohol_type, exposure_duration, exposure_duration_years, exposure_type, marijuana_use_per_week, parent_with_radiation_exposure, secondhand_smoke_as_child, smokeless_tobacco_quit_age, tobacco_use_per_day} follow_ups {follow_up_id, follow_up_submitter_id, adverse_event, barretts_esophagus_goblet_cells_present, bmi, cause_of_response, comorbidity, comorbidity_method_of_diagnosis, days_to_adverse_event, days_to_comorbidity, days_to_follow_up, days_to_progression, days_to_progression_free, days_to_recurrence, diabetes_treatment_type, disease_response, dlco_ref_predictive_percent, ecog_performance_status, fev1_ref_post_bronch_percent, fev1_ref_pre_bronch_percent, fev1_fvc_pre_bronch_percent, fev1_fvc_post_bronch_percent, height, hepatitis_sustained_virological_response, hpv_positive_type, karnofsky_performance_status, menopause_status, pancreatitis_onset_year, progression_or_recurrence, progression_or_recurrence_anatomic_site, progression_or_recurrence_type, reflux_treatment_type, risk_factor, risk_factor_treatment, viral_hepatitis_serologies, weight, adverse_event_grade, aids_risk_factors, body_surface_area, cd4_count, cdc_hiv_risk_factors, days_to_imaging, evidence_of_recurrence_type, eye_color, haart_treatment_indicator, history_of_tumor, history_of_tumor_type, hiv_viral_load, hormonal_contraceptive_type, hormonal_contraceptive_use, hormone_replacement_therapy_type, hysterectomy_margins_involved, hysterectomy_type, imaging_result, imaging_type, immunosuppressive_treatment_type, nadir_cd4_count, pregnancy_outcome, procedures_performed, recist_targeted_regions_number, recist_targeted_regions_sum, scan_tracer_used, undescended_testis_corrected, undescended_testis_corrected_age, undescended_testis_corrected_laterality, undescended_testis_corrected_method, undescended_testis_history, undescended_testis_history_laterality} treatments {treatment_id, treatment_submitter_id, days_to_treatment_end, days_to_treatment_start, initial_disease_status, regimen_or_line_of_therapy, therapeutic_agents, treatment_anatomic_site, treatment_effect, treatment_intent_type, treatment_or_therapy, treatment_outcome, treatment_type, chemo_concurrent_to_radiation, number_of_cycles, reason_treatment_ended, route_of_administration, treatment_arm, treatment_dose, treatment_dose_units, treatment_effect_indicator, treatment_frequency}}}
Input Parameters (multiple parameters can be passed in one call):
- case_submitter_id (example: C3N-00386)
- case_id (example: a023e964-118a-11e9-afb9-0a9c39d33490)
- pdc_study_id (example: PDC000431)
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
Response Sample
{ "data": { "case": { "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490", "case_submitter_id": "C3N-00386", "days_to_lost_to_followup": 0, "disease_type": "Uterine Corpus Endometrial Carcinoma", "index_date": "Diagnosis", "lost_to_followup": "string", "primary_site": "Uterus, NOS", "consent_type": "Consent Exemption", "days_to_consent": 10, "externalReferences": [ { "external_reference_id": "c94de5fb-4fcf-46f0-a4f1-41a88f557770", "reference_resource_shortname": "GDC", "reference_resource_name": "Genomic Data Commons", "reference_entity_location": "https://portal.gdc.cancer.gov/cases/c94de5fb-4fcf-46f0-a4f1-41a88f557770" } ], "demographics": [ { "demographic_id": "848b480c-0f56-11e9-a064-0a9c39d33490", "ethnicity": "Not Reported", "gender": "Female", "demographic_submitter_id": "C3N-00386-DEMO", "race": "Not Reported", "cause_of_death": "Not Reported", "days_to_birth": "-16190", "days_to_death": "0", "vital_status": "Alive", "year_of_birth": "1972", "year_of_death": "0", "age_at_index": "50", "premature_at_birth": "Yes", "weeks_gestation_at_birth": "6", "age_is_obfuscated": "true", "cause_of_death_source": "Autopsy", "occupation_duration_years": "30", "country_of_residence_at_enrollment": "Afghanistan" } ], "exposures": [ { "exposure_id": "848b480c-0f56-11e9-a064-0a9c39d33490", "exposure_submitter_id": "C3N-00386-EX", "alcohol_days_per_week": "3", "alcohol_drinks_per_day": "2", "alcohol_history": "Yes", "alcohol_intensity": "Lifelong Non-Drinker", "asbestos_exposure": "Not Reported", "cigarettes_per_day": "5", "coal_dust_exposure": "Not Reported", "environmental_tobacco_smoke_exposure": "Not Reported", "pack_years_smoked": "52", "radon_exposure": "Not Reported", "respirable_crystalline_silica_exposure": "Not Reported", "smoking_frequency": "Not Reported", "time_between_waking_and_first_smoke": "Not Reported", "tobacco_smoking_onset_year": "1972", "tobacco_smoking_quit_year": "1992", "tobacco_smoking_status": "Not Reported", "type_of_smoke_exposure": "Smoke exposure, NOS", "type_of_tobacco_used": "pipe", "years_smoked": "20", "age_at_onset": "45", "alcohol_type": "Liquor", "exposure_duration": "Six Weeks or More", "exposure_duration_years": "15", "exposure_type": "Marijuana", "marijuana_use_per_week": "3.5", "parent_with_radiation_exposure": "Not Reported", "secondhand_smoke_as_child": "Unknown", "smokeless_tobacco_quit_age": "48", "tobacco_use_per_day": "7.5" } ], "follow_ups": [ { "follow_up_id": "d12a10c4-1075-11ec-b712-0a4e2186f121", "follow_up_submitter_id": "C3N-03662-FL", "adverse_event": "Abdominal Distension", "barretts_esophagus_goblet_cells_present": "Yes", "bmi": "1.75", "cause_of_response": "Not Reported", "comorbidity": "Adenocarcinoma", "comorbidity_method_of_diagnosis": "Histology", "days_to_adverse_event": "10", "days_to_comorbidity": "15", "days_to_follow_up": "14", "days_to_progression": "14", "days_to_progression_free": "14", "days_to_recurrence": "14", "diabetes_treatment_type": "Biguanide", "disease_response": "AJ-Adjuvant Therapy", "dlco_ref_predictive_percent": "25.0", "ecog_performance_status": "0", "fev1_ref_post_bronch_percent": "10", "fev1_ref_pre_bronch_percent": "10", "fev1_fvc_pre_bronch_percent": "10", "fev1_fvc_post_bronch_percent": "10", "height": "1.75", "hepatitis_sustained_virological_response": "Unknown", "hpv_positive_type": "16", "karnofsky_performance_status": "50", "menopause_status": "Postmenopausal", "pancreatitis_onset_year": "45", "progression_or_recurrence": "Yes", "progression_or_recurrence_anatomic_site": "Abdomen, NOS", "progression_or_recurrence_type": "Biochemical", "reflux_treatment_type": "Antacids", "risk_factor": "Alcoholic Liver Disease", "risk_factor_treatment": "Yes", "viral_hepatitis_serologies": "HBV DNA", "weight": "178.5", "adverse_event_grade": "Grade 1", "aids_risk_factors": "Coccidioidomycosis", "body_surface_area": "15", "cd4_count": "2.5", "cdc_hiv_risk_factors": "Hemophiliac", "days_to_imaging": "14", "evidence_of_recurrence_type": "Physical Examination", "eye_color": "Hazel", "haart_treatment_indicator": "No", "history_of_tumor": "No", "history_of_tumor_type": "Phenochromocytoma", "hiv_viral_load": "2.0", "hormonal_contraceptive_type": "Progestin", "hormonal_contraceptive_use": "Never Used", "hormone_replacement_therapy_type": "Estrogen only", "hysterectomy_margins_involved": "Bladder", "hysterectomy_type": "Simple Hysterectomy", "imaging_result": "Positive", "imaging_type": "MRI", "immunosuppressive_treatment_type": "Azathioprine", "nadir_cd4_count": "1.5", "pregnancy_outcome": "Live Birth", "procedures_performed": "Colonoscopy", "recist_targeted_regions_number": "2", "recist_targeted_regions_sum": "2.5", "scan_tracer_used": "Acetate", "undescended_testis_corrected": "Yes", "undescended_testis_corrected_age": "35", "undescended_testis_corrected_laterality": "Bilateral", "undescended_testis_corrected_method": "Hormones", "undescended_testis_history": "Yes", "undescended_testis_history_laterality": "Left" } ], "treatments": [ { "treatment_id": "a2518568-1adc-43fe-852f-049ad21ec2df", "treatment_submitter_id": "AP-27JZ-TR", "days_to_treatment_end": " ", "days_to_treatment_start": " ", "initial_disease_status": " ", "regimen_or_line_of_therapy": " ", "therapeutic_agents": " ", "treatment_anatomic_site": " ", "treatment_effect": " ", "treatment_intent_type": "Adjuvant", "treatment_or_therapy": " ", "treatment_outcome": " ", "treatment_type": "Radiation Therapy, NOS", "chemo_concurrent_to_radiation": " ", "number_of_cycles": " ", "reason_treatment_ended": " ", "route_of_administration": " ", "treatment_arm": " ", "treatment_dose": " ", "treatment_dose_units": " ", "treatment_effect_indicator": " ", "treatment_frequency": " " } ], "samples": [ { "sample_id": "99a4bcef-1259-11e9-afb9-0a9c39d33490", "sample_submitter_id": "C3N-00386-02", "sample_type": "Primary Tumor", "sample_type_id": "null", "gdc_sample_id": "null", "gdc_project_id": "null", "biospecimen_anatomic_site": "Not Reported", "composition": "Solid Tissue", "current_weight": "0", "days_to_collection": "0", "days_to_sample_procurement": "0", "diagnosis_pathologically_confirmed": "Not Reported", "freezing_method": "LN2", "initial_weight": "400", "intermediate_dimension": "null", "longest_dimension": "null", "method_of_sample_procurement": "Not Reported", "pathology_report_uuid": "null", "preservation_method": "Snap Frozen", "shortest_dimension": "null", "time_between_clamping_and_freezing": "0", "time_between_excision_and_freezing": "11", "tissue_type": "Tumor", "tumor_code": "null", "tumor_code_id": "null", "tumor_descriptor": "Not Reported", "biospecimen_laterality": "Bilateral", "catalog_reference": "Not Reported", "distance_normal_to_tumor": "Adjacent (< or = 2cm)", "distributor_reference": "Not Reported", "growth_rate": "1", "passage_count": "2", "sample_ordinal": "3", "tissue_collection_type": "Prospective", "diagnoses": [ { "diagnosis_id": "f748299b-0f5a-11e9-a064-0a9c39d33490", "diagnosis_submitter_id": "C3N-00386-DIAG", "annotation": "The sample 7316-2901 is associated with this clinical record." } ], "aliquots": [ { "aliquot_id": "141959ca-6424-11e8-bcf1-0a2705229b82", "aliquot_submitter_id": "3f957017-d081-45f4-b458-ec3f8d_D2", "analyte_type": "Protein", "aliquot_run_metadata": [ { "aliquot_run_metadata_id": "1661cee5-5731-11e8-b664-00a098d917f8", "label": "itraq_116", "experiment_number": "13", "fraction": "24-Jan", "replicate_number": "1", "date": "2013-02-28", "alias": "B1S6", "analyte": "Proteome" } ] } ] } ], "diagnoses": [ { "diagnosis_id": "f748299b-0f5a-11e9-a064-0a9c39d33490", "tissue_or_organ_of_origin": "Corpus uteri", "age_at_diagnosis": "16190", "primary_diagnosis": "Endometrioid adenocarcinoma, NOS", "tumor_grade": "G1", "tumor_stage": "Stage I", "diagnosis_submitter_id": "C3N-00386-DIAG", "classification_of_tumor": "Not Reported", "days_to_last_follow_up": "673", "days_to_last_known_disease_status": "673", "days_to_recurrence": "0", "last_known_disease_status": "Tumor free", "morphology": "8380/3", "progression_or_recurrence": "no", "site_of_resection_or_biopsy": "Corpus uteri", "prior_malignancy": "Not Reported", "ajcc_clinical_m": "Not Reported", "ajcc_clinical_n": "Not Reported", "ajcc_clinical_stage": "Not Reported", "ajcc_clinical_t": "Not Reported", "ajcc_pathologic_m": "Not Reported", "ajcc_pathologic_n": "Not Reported", "ajcc_pathologic_stage": "Not Reported", "ajcc_pathologic_t": "Not Reported", "ann_arbor_b_symptoms": "Not Reported", "ann_arbor_clinical_stage": "Not Reported", "ann_arbor_extranodal_involvement": "Not Reported", "ann_arbor_pathologic_stage": "Not Reported", "best_overall_response": "null", "burkitt_lymphoma_clinical_variant": "Not Reported", "circumferential_resection_margin": "null", "colon_polyps_history": "null", "days_to_best_overall_response": "null", "days_to_diagnosis": "null", "days_to_hiv_diagnosis": "null", "days_to_new_event": "null", "figo_stage": "Not Reported", "hiv_positive": "null", "hpv_positive_type": "null", "hpv_status": "null", "iss_stage": "Not Reported", "laterality": "Not Reported", "ldh_level_at_diagnosis": "null", "ldh_normal_range_upper": "null", "lymph_nodes_positive": "null", "lymphatic_invasion_present": "Not Reported", "method_of_diagnosis": "Not Reported", "new_event_anatomic_site": "null", "new_event_type": "null", "overall_survival": "null", "perineural_invasion_present": "Not Reported", "prior_treatment": "Not Reported", "progression_free_survival": "null", "progression_free_survival_event": "null", "residual_disease": "Not Reported", "vascular_invasion_present": "Not Reported", "year_of_diagnosis": "null", "icd_10_code": "null", "synchronous_malignancy": "null", "tumor_largest_dimension_diameter": "null", "anaplasia_present": "Yes", "anaplasia_present_type": "Diffuse", "child_pugh_classification": "A", "cog_liver_stage": "Stage I", "cog_neuroblastoma_risk_group": "High Risk", "cog_renal_stage": "Stage I", "cog_rhabdomyosarcoma_risk_group": "Low Risk", "enneking_msts_grade": "Low Grade (G1)", "enneking_msts_metastasis": "Regional or Distant Metastasis (M1)", "enneking_msts_stage": "Stage IA", "enneking_msts_tumor_site": "Extracompartmental (T2)", "esophageal_columnar_dysplasia_degree": "Indefinite for Dysplasia", "esophageal_columnar_metaplasia_present": "No", "first_symptom_prior_to_diagnosis": "Headaches", "gastric_esophageal_junction_involvement": "Yes", "goblet_cells_columnar_mucosa_present": "No", "gross_tumor_weight": "1", "inpc_grade": "Differentiating", "inpc_histologic_group": "Favorable", "inrg_stage": "L1", "inss_stage": "Stage 1", "irs_group": "Group I", "irs_stage": "1", "ishak_fibrosis_score": "1,2 - Portal Fibrosis", "lymph_nodes_tested": "1", "medulloblastoma_molecular_classification": "SHH-Activated", "metastasis_at_diagnosis": "Distant Metastasis", "metastasis_at_diagnosis_site": "Abdomen", "mitosis_karyorrhexis_index": "Low", "peripancreatic_lymph_nodes_positive": "0", "peripancreatic_lymph_nodes_tested": "1", "supratentorial_localization": "Cerebral Cortex", "tumor_confined_to_organ_of_origin": "Yes", "tumor_focality": "Unifocal", "tumor_regression_grade": "1", "vascular_invasion_type": "Extramural", "wilms_tumor_histologic_subtype": "Favorable", "breslow_thickness": "1", "gleason_grade_group": "Group 1", "igcccg_stage": "Good Prognosis", "international_prognostic_index": "Low Risk", "largest_extrapelvic_peritoneal_focus": "Macroscopic (2cm or less)", "masaoka_stage": "Stage I", "non_nodal_regional_disease": "Present", "non_nodal_tumor_deposits": "Yes", "ovarian_specimen_status": "Ovarian Capsule Intact", "ovarian_surface_involvement": "Present", "percent_tumor_invasion": "1", "peritoneal_fluid_cytological_status": "Atypical", "primary_gleason_grade": "Pattern 1", "secondary_gleason_grade": "Pattern 1", "weiss_assessment_score": "1", "adrenal_hormone": "No", "ann_arbor_b_symptoms_described": "Fever", "diagnosis_is_primary_disease": "false", "eln_risk_classification": "Favorable", "figo_staging_edition_year": "2009", "gleason_grade_tertiary": "Pattern 4", "gleason_patterns_percent": "1", "margin_distance": "1.5", "margins_involved_site": "Gerota Fascia", "pregnant_at_diagnosis": "Yes", "satellite_nodule_present": "Absent", "sites_of_involvement": "Unknown", "tumor_depth": "1.2", "who_cns_grade": "Grade I", "who_nte_grade": "G1", "samples": [ { "sample_id": "99a4bcef-1259-11e9-afb9-0a9c39d33490", "sample_submitter_id": "C3N-00386-02", "annotation": "The sample 7316-2901 is associated with this clinical record." } ] } ] } } }
Response Schema
{} findCasedatafindCaseDef(optional){} findCaseDefcasecaseFullDesc(optional){} caseFullDesccase_idstring(optional)case_submitter_idstring(optional)days_to_lost_to_followupinteger(optional)disease_typestring(optional)index_datestring(optional)lost_to_followupstring(optional)primary_sitestring(optional)consent_typestring(optional)days_to_consentinteger(optional)externalReferencesarray[ExternalReferences](optional)demographicsarray[Demographic](optional)exposuresarray[Exposure](optional)follow_upsarray[FollowUp](optional)treatmentsarray[Treatment](optional)samplesarray[Sample](optional)diagnosesarray[Diagnosis](optional){} ExternalReferencesexternal_reference_idstring(optional)reference_resource_shortnamestring(optional)reference_resource_namestring(optional)reference_entity_locationstring(optional){} Demographicdemographic_idstring(optional)ethnicitystring(optional)genderstring(optional)demographic_submitter_idstring(optional)racestring(optional)cause_of_deathstring(optional)days_to_birthinteger(optional)days_to_deathinteger(optional)vital_statusstring(optional)year_of_birthinteger(optional)year_of_deathinteger(optional)age_at_indexinteger(optional)premature_at_birthstring(optional)weeks_gestation_at_birthinteger(optional)age_is_obfuscatedboolean(optional)cause_of_death_sourcestring(optional)occupation_duration_yearsinteger(optional)country_of_residence_at_enrollmentstring(optional){} Exposureexposure_idstring(optional)exposure_submitter_idstring(optional)alcohol_days_per_weekinteger(optional)alcohol_drinks_per_dayinteger(optional)alcohol_historystring(optional)alcohol_intensitystring(optional)asbestos_exposurestring(optional)cigarettes_per_dayinteger(optional)coal_dust_exposurestring(optional)environmental_tobacco_smoke_exposurestring(optional)pack_years_smokedinteger(optional)radon_exposurestring(optional)respirable_crystalline_silica_exposurestring(optional)smoking_frequencystring(optional)time_between_waking_and_first_smokestring(optional)tobacco_smoking_onset_yearinteger(optional)tobacco_smoking_quit_yearinteger(optional)tobacco_smoking_statusstring(optional)type_of_smoke_exposurestring(optional)type_of_tobacco_usedstring(optional)years_smokedinteger(optional)age_at_onsetinteger(optional)alcohol_typestring(optional)exposure_durationstring(optional)exposure_duration_yearsinteger(optional)exposure_typestring(optional)marijuana_use_per_weeknumber(optional)parent_with_radiation_exposurestring(optional)secondhand_smoke_as_childstring(optional)smokeless_tobacco_quit_ageinteger(optional)tobacco_use_per_daynumber(optional){} FollowUpfollow_up_idstring(optional)follow_up_submitter_idstring(optional)adverse_eventstring(optional)barretts_esophagus_goblet_cells_presentstring(optional)bmifloat(optional)cause_of_responsestring(optional)comorbiditystring(optional)comorbidity_method_of_diagnosisstring(optional)days_to_adverse_eventinteger(optional)days_to_comorbidityinteger(optional)days_to_follow_upinteger(optional)days_to_progressioninteger(optional)days_to_progression_freeinteger(optional)days_to_recurrenceinteger(optional)diabetes_treatment_typestring(optional)disease_responsestring(optional)dlco_ref_predictive_percentfloat(optional)ecog_performance_statusstring(optional)fev1_ref_post_bronch_percentfloat(optional)fev1_ref_pre_bronch_percentfloat(optional)fev1_fvc_pre_bronch_percentfloat(optional)fev1_fvc_post_bronch_percentfloat(optional)heightfloat(optional)hepatitis_sustained_virological_responsestring(optional)hpv_positive_typestring(optional)karnofsky_performance_statusstring(optional)menopause_statusstring(optional)pancreatitis_onset_yearinteger(optional)progression_or_recurrencestring(optional)progression_or_recurrence_anatomic_sitestring(optional)progression_or_recurrence_typestring(optional)reflux_treatment_typestring(optional)risk_factorstring(optional)risk_factor_treatmentstring(optional)viral_hepatitis_serologiesstring(optional)weightfloat(optional)adverse_event_gradestring(optional)aids_risk_factorsstring(optional)body_surface_areafloat(optional)cd4_countfloat(optional)cdc_hiv_risk_factorsstring(optional)days_to_imaginginteger(optional)evidence_of_recurrence_typestring(optional)eye_colorstring(optional)haart_treatment_indicatorstring(optional)history_of_tumorstring(optional)history_of_tumor_typestring(optional)hiv_viral_loadfloat(optional)hormonal_contraceptive_typestring(optional)hormonal_contraceptive_usestring(optional)hormone_replacement_therapy_typestring(optional)hysterectomy_margins_involvedstring(optional)hysterectomy_typestring(optional)imaging_resultstring(optional)imaging_typestring(optional)immunosuppressive_treatment_typestring(optional)nadir_cd4_countfloat(optional)pregnancy_outcomestring(optional)procedures_performedstring(optional)recist_targeted_regions_numberinteger(optional)recist_targeted_regions_sumfloat(optional)scan_tracer_usedstring(optional)undescended_testis_correctedstring(optional)undescended_testis_corrected_ageinteger(optional)undescended_testis_corrected_lateralitystring(optional)undescended_testis_corrected_methodstring(optional)undescended_testis_historystring(optional)undescended_testis_history_lateralitystring(optional){} Treatmenttreatment_idstring(optional)treatment_submitter_idstring(optional)days_to_treatment_endinteger(optional)days_to_treatment_startinteger(optional)initial_disease_statusstring(optional)regimen_or_line_of_therapystring(optional)therapeutic_agentsstring(optional)treatment_anatomic_sitestring(optional)treatment_effectstring(optional)treatment_intent_typestring(optional)treatment_or_therapystring(optional)treatment_outcomestring(optional)treatment_typestring(optional)chemo_concurrent_to_radiationstring(optional)number_of_cyclesinteger(optional)reason_treatment_endedstring(optional)route_of_administrationstring(optional)treatment_armstring(optional)treatment_doseinteger(optional)treatment_dose_unitsstring(optional)treatment_effect_indicatorstring(optional)treatment_frequencystring(optional){} Samplesample_idstring(optional)sample_submitter_idstring(optional)sample_typestring(optional)sample_type_idstring(optional)gdc_sample_idstring(optional)gdc_project_idstring(optional)biospecimen_anatomic_sitestring(optional)compositionstring(optional)current_weightstring(optional)days_to_collectionstring(optional)days_to_sample_procurementstring(optional)diagnosis_pathologically_confirmedstring(optional)freezing_methodstring(optional)initial_weightstring(optional)intermediate_dimensionstring(optional)longest_dimensionstring(optional)method_of_sample_procurementstring(optional)pathology_report_uuidstring(optional)preservation_methodstring(optional)shortest_dimensionstring(optional)time_between_clamping_and_freezingstring(optional)time_between_excision_and_freezingstring(optional)tissue_typestring(optional)tumor_codestring(optional)tumor_code_idstring(optional)tumor_descriptorstring(optional)biospecimen_lateralitystring(optional)catalog_referencestring(optional)distance_normal_to_tumorstring(optional)distributor_referencestring(optional)growth_rateinteger(optional)passage_countinteger(optional)sample_ordinalinteger(optional)tissue_collection_typestring(optional)diagnosesarray[DiagnosisRef](optional)aliquotsarray[Aliquot](optional){} Diagnosisdiagnosis_idstring(optional)tissue_or_organ_of_originnumber(optional)age_at_diagnosisstring(optional)primary_diagnosisstring(optional)tumor_gradestring(optional)tumor_stagestring(optional)diagnosis_submitter_idstring(optional)classification_of_tumorstring(optional)days_to_last_follow_upstring(optional)days_to_last_known_disease_statusstring(optional)days_to_recurrencestring(optional)last_known_disease_statusstring(optional)morphologystring(optional)progression_or_recurrencestring(optional)site_of_resection_or_biopsystring(optional)prior_malignancystring(optional)ajcc_clinical_mstring(optional)ajcc_clinical_nstring(optional)ajcc_clinical_stagestring(optional)ajcc_clinical_tstring(optional)ajcc_pathologic_mstring(optional)ajcc_pathologic_nstring(optional)ajcc_pathologic_stagestring(optional)ajcc_pathologic_tstring(optional)ann_arbor_b_symptomsstring(optional)ann_arbor_clinical_stagestring(optional)ann_arbor_extranodal_involvementstring(optional)ann_arbor_pathologic_stagestring(optional)best_overall_responsestring(optional)burkitt_lymphoma_clinical_variantstring(optional)circumferential_resection_marginstring(optional)colon_polyps_historystring(optional)days_to_best_overall_responsestring(optional)days_to_diagnosisstring(optional)days_to_hiv_diagnosisstring(optional)days_to_new_eventstring(optional)figo_stagestring(optional)hiv_positivestring(optional)hpv_positive_typestring(optional)hpv_statusstring(optional)iss_stagestring(optional)lateralitystring(optional)ldh_level_at_diagnosisstring(optional)ldh_normal_range_upperstring(optional)lymph_nodes_positivestring(optional)lymphatic_invasion_presentstring(optional)method_of_diagnosisstring(optional)new_event_anatomic_sitestring(optional)new_event_typestring(optional)overall_survivalstring(optional)perineural_invasion_presentstring(optional)prior_treatmentstring(optional)progression_free_survivalstring(optional)progression_free_survival_eventstring(optional)residual_diseasestring(optional)vascular_invasion_presentstring(optional)year_of_diagnosisstring(optional)icd_10_codestring(optional)synchronous_malignancystring(optional)tumor_largest_dimension_diameterstring(optional)anaplasia_presentstring(optional)anaplasia_present_typestring(optional)child_pugh_classificationstring(optional)cog_liver_stagestring(optional)cog_neuroblastoma_risk_groupstring(optional)cog_renal_stagestring(optional)cog_rhabdomyosarcoma_risk_groupstring(optional)enneking_msts_gradestring(optional)enneking_msts_metastasisstring(optional)enneking_msts_stagestring(optional)enneking_msts_tumor_sitestring(optional)esophageal_columnar_dysplasia_degreestring(optional)esophageal_columnar_metaplasia_presentstring(optional)first_symptom_prior_to_diagnosisstring(optional)gastric_esophageal_junction_involvementstring(optional)goblet_cells_columnar_mucosa_presentstring(optional)gross_tumor_weightinteger(optional)inpc_gradestring(optional)inpc_histologic_groupstring(optional)inrg_stagestring(optional)inss_stagestring(optional)irs_groupstring(optional)irs_stagestring(optional)ishak_fibrosis_scorestring(optional)lymph_nodes_testedinteger(optional)medulloblastoma_molecular_classificationstring(optional)metastasis_at_diagnosisstring(optional)metastasis_at_diagnosis_sitestring(optional)mitosis_karyorrhexis_indexstring(optional)peripancreatic_lymph_nodes_positivestring(optional)peripancreatic_lymph_nodes_testedinteger(optional)supratentorial_localizationstring(optional)tumor_confined_to_organ_of_originstring(optional)tumor_focalitystring(optional)tumor_regression_gradestring(optional)vascular_invasion_typestring(optional)wilms_tumor_histologic_subtypestring(optional)breslow_thicknessinteger(optional)gleason_grade_groupstring(optional)igcccg_stagestring(optional)international_prognostic_indexstring(optional)largest_extrapelvic_peritoneal_focusstring(optional)masaoka_stagestring(optional)non_nodal_regional_diseasestring(optional)non_nodal_tumor_depositsstring(optional)ovarian_specimen_statusstring(optional)ovarian_surface_involvementstring(optional)percent_tumor_invasioninteger(optional)peritoneal_fluid_cytological_statusstring(optional)primary_gleason_gradestring(optional)secondary_gleason_gradestring(optional)weiss_assessment_scorestring(optional)adrenal_hormonestring(optional)ann_arbor_b_symptoms_describedstring(optional)diagnosis_is_primary_diseasestring(optional)eln_risk_classificationstring(optional)figo_staging_edition_yearstring(optional)gleason_grade_tertiarystring(optional)gleason_patterns_percentinteger(optional)margin_distancenumber(optional)margins_involved_sitestring(optional)pregnant_at_diagnosisstring(optional)satellite_nodule_presentstring(optional)sites_of_involvementstring(optional)tumor_depthnumber(optional)who_cns_gradestring(optional)who_nte_gradestring(optional)samplesarray[SampleRef](optional){} DiagnosisRefdiagnosis_idstring(optional)diagnosis_submitter_idstring(optional)annotationstring(optional){} Aliquotaliquot_idstringaliquot_submitter_idstringanalyte_typestring(optional)aliquot_run_metadataarray[aliquotRunMetaDataForPaginated](optional){} SampleRefsample_idstring(optional)sample_submitter_idstring(optional)annotationstring(optional){} aliquotRunMetaDataForPaginatedaliquot_run_metadata_idstring(optional)labelstring(optional)experiment_numberstring(optional)fractionstring(optional)replicate_numberstring(optional)datestring(optional)aliasstring(optional)analytestring(optional)
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Get paginated case records
get ?query={getPaginatedCases(offset: {offset} limit: {limit}) {total cases {case_submitter_id project_id project_submitter_id disease_type} pagination {count sort from page total pages size}}}
Returns a list of cases and a pagination record
Fields:- total
- cases
- pagination
Response Sample
{ "data": { "getPaginatedCases": { "total": 977, "cases": [ { "case_submitter_id": "05BR016", "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "project_submitter_id": "CPTAC-2", "disease_type": "Breast Invasive Carcinoma" } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} getPaginatedCasesdatagetPaginatedCasesDef(optional){} getPaginatedCasesDefgetPaginatedCasesgetPaginatedCasesDesc(optional){} getPaginatedCasesDesctotalnumber(optional)casesarray[allCasesDesc](optional)paginationPagination(optional){} allCasesDesccase_submitter_idstring(optional)project_idstring(optional)project_submitter_idstring(optional)disease_typestring(optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger
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Get Cases/Demographics Per Study
get ?query={paginatedCaseDemographicsPerStudy (study_id: "{study_id}" offset: {offset} limit: {limit}) { total caseDemographicsPerStudy { case_id case_submitter_id disease_type primary_site demographics { demographic_id ethnicity gender demographic_submitter_id race cause_of_death days_to_birth days_to_death vital_status year_of_birth year_of_death age_at_index premature_at_birth weeks_gestation_at_birth age_is_obfuscated cause_of_death_source occupation_duration_years country_of_residence_at_enrollment} } pagination { count sort from page total pages size } }}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
It may take a long time to execute because of the huge volume of data.
Fields:- total
- caseDemographicsPerStudy
- pagination
Response Sample
{ "data": { "paginatedCaseDemographicsPerStudy": { "total": 93, "caseDemographicsPerStudy": [ { "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490", "case_submitter_id": "C3N-00386", "disease_type": "Uterine Corpus Endometrial Carcinoma", "primary_site": "Uterus, NOS", "demographics": [ { "demographic_id": "848b480c-0f56-11e9-a064-0a9c39d33490", "ethnicity": "Not Reported", "gender": "Female", "demographic_submitter_id": "C3N-00386-DEMO", "race": "Not Reported", "cause_of_death": "Not Reported", "days_to_birth": "-16190", "days_to_death": "0", "vital_status": "Alive", "year_of_birth": "1972", "year_of_death": "0", "age_at_index": "50", "premature_at_birth": "Yes", "weeks_gestation_at_birth": "6", "age_is_obfuscated": "true", "cause_of_death_source": "Autopsy", "occupation_duration_years": "30", "country_of_residence_at_enrollment": "Afghanistan" } ] } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedCaseDemographicsPerStudydatapaginatedCaseDemographicsPerStudyDef(optional){} paginatedCaseDemographicsPerStudyDefpaginatedCaseDemographicsPerStudypaginatedCaseDemographicsPerStudyDesc(optional){} paginatedCaseDemographicsPerStudyDesctotalnumber(optional)caseDemographicsPerStudyarray[paginatedCaseDemographics](optional)paginationPagination(optional){} paginatedCaseDemographicscase_idstring(optional)case_submitter_idstring(optional)disease_typestring(optional)primary_sitestring(optional)demographicsarray[Demographic](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} Demographicdemographic_idstring(optional)ethnicitystring(optional)genderstring(optional)demographic_submitter_idstring(optional)racestring(optional)cause_of_deathstring(optional)days_to_birthinteger(optional)days_to_deathinteger(optional)vital_statusstring(optional)year_of_birthinteger(optional)year_of_deathinteger(optional)age_at_indexinteger(optional)premature_at_birthstring(optional)weeks_gestation_at_birthinteger(optional)age_is_obfuscatedboolean(optional)cause_of_death_sourcestring(optional)occupation_duration_yearsinteger(optional)country_of_residence_at_enrollmentstring(optional)
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Get Cases/Exposures Per Study
get ?query={paginatedCaseExposuresPerStudy (study_submitter_id: "{study_submitter_id}" offset: {offset} limit: {limit}) { total caseExposuresPerStudy { case_id case_submitter_id disease_type primary_site exposures { exposure_id exposure_submitter_id alcohol_days_per_week alcohol_drinks_per_day alcohol_history alcohol_intensity asbestos_exposure cigarettes_per_day coal_dust_exposure environmental_tobacco_smoke_exposure pack_years_smoked radon_exposure respirable_crystalline_silica_exposure smoking_frequency time_between_waking_and_first_smoke tobacco_smoking_onset_year tobacco_smoking_quit_year tobacco_smoking_status type_of_smoke_exposure type_of_tobacco_used years_smoked age_at_onset, alcohol_type exposure_duration exposure_duration_years exposure_type marijuana_use_per_week parent_with_radiation_exposure secondhand_smoke_as_child smokeless_tobacco_quit_age tobacco_use_per_day } } pagination { count sort from page total pages size } }}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
It may take a long time to execute because of the huge volume of data.
Fields:- total
- caseExposuresPerStudy
- pagination
Response Sample
{ "data": { "paginatedCaseExposuresPerStudy": { "total": 93, "caseExposuresPerStudy": [ { "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490", "case_submitter_id": "C3N-00386", "disease_type": "Uterine Corpus Endometrial Carcinoma", "primary_site": "Uterus, NOS", "exposures": [ { "exposure_id": "848b480c-0f56-11e9-a064-0a9c39d33490", "exposure_submitter_id": "C3N-00386-EX", "alcohol_days_per_week": "3", "alcohol_drinks_per_day": "2", "alcohol_history": "Yes", "alcohol_intensity": "Lifelong Non-Drinker", "asbestos_exposure": "Not Reported", "cigarettes_per_day": "5", "coal_dust_exposure": "Not Reported", "environmental_tobacco_smoke_exposure": "Not Reported", "pack_years_smoked": "52", "radon_exposure": "Not Reported", "respirable_crystalline_silica_exposure": "Not Reported", "smoking_frequency": "Not Reported", "time_between_waking_and_first_smoke": "Not Reported", "tobacco_smoking_onset_year": "1972", "tobacco_smoking_quit_year": "1992", "tobacco_smoking_status": "Not Reported", "type_of_smoke_exposure": "Smoke exposure, NOS", "type_of_tobacco_used": "pipe", "years_smoked": "20", "age_at_onset": "45", "alcohol_type": "Liquor", "exposure_duration": "Six Weeks or More", "exposure_duration_years": "15", "exposure_type": "Marijuana", "marijuana_use_per_week": "3.5", "parent_with_radiation_exposure": "Not Reported", "secondhand_smoke_as_child": "Unknown", "smokeless_tobacco_quit_age": "48", "tobacco_use_per_day": "7.5" } ] } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedCaseExposuresPerStudydatapaginatedCaseExposuresPerStudyDef(optional){} paginatedCaseExposuresPerStudyDefpaginatedCaseExposuresPerStudypaginatedCaseExposuresPerStudyDesc(optional){} paginatedCaseExposuresPerStudyDesctotalnumber(optional)caseExposuresPerStudyarray[paginatedCaseExposures](optional)paginationPagination(optional){} paginatedCaseExposurescase_idstring(optional)case_submitter_idstring(optional)disease_typestring(optional)primary_sitestring(optional)exposuresarray[Exposure](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} Exposureexposure_idstring(optional)exposure_submitter_idstring(optional)alcohol_days_per_weekinteger(optional)alcohol_drinks_per_dayinteger(optional)alcohol_historystring(optional)alcohol_intensitystring(optional)asbestos_exposurestring(optional)cigarettes_per_dayinteger(optional)coal_dust_exposurestring(optional)environmental_tobacco_smoke_exposurestring(optional)pack_years_smokedinteger(optional)radon_exposurestring(optional)respirable_crystalline_silica_exposurestring(optional)smoking_frequencystring(optional)time_between_waking_and_first_smokestring(optional)tobacco_smoking_onset_yearinteger(optional)tobacco_smoking_quit_yearinteger(optional)tobacco_smoking_statusstring(optional)type_of_smoke_exposurestring(optional)type_of_tobacco_usedstring(optional)years_smokedinteger(optional)age_at_onsetinteger(optional)alcohol_typestring(optional)exposure_durationstring(optional)exposure_duration_yearsinteger(optional)exposure_typestring(optional)marijuana_use_per_weeknumber(optional)parent_with_radiation_exposurestring(optional)secondhand_smoke_as_childstring(optional)smokeless_tobacco_quit_ageinteger(optional)tobacco_use_per_daynumber(optional)
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Get Cases/FollowUps Per Study
get ?query={paginatedCaseFollowUpsPerStudy (pdc_study_id: "{pdc_study_id}" offset: {offset} limit: {limit}) { total caseFollowUpsPerStudy { case_id case_submitter_id disease_type primary_site follow_ups { follow_up_id follow_up_submitter_id adverse_event barretts_esophagus_goblet_cells_present bmi cause_of_response comorbidity comorbidity_method_of_diagnosis days_to_adverse_event days_to_comorbidity days_to_follow_up days_to_progression days_to_progression_free days_to_recurrence diabetes_treatment_type disease_response dlco_ref_predictive_percent ecog_performance_status fev1_ref_post_bronch_percent fev1_ref_pre_bronch_percent fev1_fvc_pre_bronch_percent fev1_fvc_post_bronch_percent height hepatitis_sustained_virological_response hpv_positive_type karnofsky_performance_status menopause_status pancreatitis_onset_year progression_or_recurrence progression_or_recurrence_anatomic_site progression_or_recurrence_type reflux_treatment_type risk_factor risk_factor_treatment viral_hepatitis_serologies weight adverse_event_grade aids_risk_factors body_surface_area cd4_count cdc_hiv_risk_factors days_to_imaging evidence_of_recurrence_type eye_color haart_treatment_indicator history_of_tumor history_of_tumor_type hiv_viral_load hormonal_contraceptive_type hormonal_contraceptive_use hormone_replacement_therapy_type hysterectomy_margins_involved hysterectomy_type imaging_result imaging_type immunosuppressive_treatment_type nadir_cd4_count pregnancy_outcome procedures_performed recist_targeted_regions_number recist_targeted_regions_sum scan_tracer_used undescended_testis_corrected undescended_testis_corrected_age undescended_testis_corrected_laterality undescended_testis_corrected_method undescended_testis_history undescended_testis_history_laterality } } pagination { count sort from page total pages size } }}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
It may take a long time to execute because of the huge volume of data.
Fields:- total
- caseFollowUpsPerStudy
- pagination
Response Sample
{ "data": { "paginatedCaseFollowUpsPerStudy": { "total": 93, "caseFollowUpsPerStudy": [ { "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490", "case_submitter_id": "C3N-00386", "disease_type": "Uterine Corpus Endometrial Carcinoma", "primary_site": "Uterus, NOS", "follow_ups": [ { "follow_up_id": "d12a10c4-1075-11ec-b712-0a4e2186f121", "follow_up_submitter_id": "C3N-03662-FL", "adverse_event": "Abdominal Distension", "barretts_esophagus_goblet_cells_present": "Yes", "bmi": "1.75", "cause_of_response": "Not Reported", "comorbidity": "Adenocarcinoma", "comorbidity_method_of_diagnosis": "Histology", "days_to_adverse_event": "10", "days_to_comorbidity": "15", "days_to_follow_up": "14", "days_to_progression": "14", "days_to_progression_free": "14", "days_to_recurrence": "14", "diabetes_treatment_type": "Biguanide", "disease_response": "AJ-Adjuvant Therapy", "dlco_ref_predictive_percent": "25.0", "ecog_performance_status": "0", "fev1_ref_post_bronch_percent": "10", "fev1_ref_pre_bronch_percent": "10", "fev1_fvc_pre_bronch_percent": "10", "fev1_fvc_post_bronch_percent": "10", "height": "1.75", "hepatitis_sustained_virological_response": "Unknown", "hpv_positive_type": "16", "karnofsky_performance_status": "50", "menopause_status": "Postmenopausal", "pancreatitis_onset_year": "45", "progression_or_recurrence": "Yes", "progression_or_recurrence_anatomic_site": "Abdomen, NOS", "progression_or_recurrence_type": "Biochemical", "reflux_treatment_type": "Antacids", "risk_factor": "Alcoholic Liver Disease", "risk_factor_treatment": "Yes", "viral_hepatitis_serologies": "HBV DNA", "weight": "178.5", "adverse_event_grade": "Grade 1", "aids_risk_factors": "Coccidioidomycosis", "body_surface_area": "15", "cd4_count": "2.5", "cdc_hiv_risk_factors": "Hemophiliac", "days_to_imaging": "14", "evidence_of_recurrence_type": "Physical Examination", "eye_color": "Hazel", "haart_treatment_indicator": "No", "history_of_tumor": "No", "history_of_tumor_type": "Phenochromocytoma", "hiv_viral_load": "2.0", "hormonal_contraceptive_type": "Progestin", "hormonal_contraceptive_use": "Never Used", "hormone_replacement_therapy_type": "Estrogen only", "hysterectomy_margins_involved": "Bladder", "hysterectomy_type": "Simple Hysterectomy", "imaging_result": "Positive", "imaging_type": "MRI", "immunosuppressive_treatment_type": "Azathioprine", "nadir_cd4_count": "1.5", "pregnancy_outcome": "Live Birth", "procedures_performed": "Colonoscopy", "recist_targeted_regions_number": "2", "recist_targeted_regions_sum": "2.5", "scan_tracer_used": "Acetate", "undescended_testis_corrected": "Yes", "undescended_testis_corrected_age": "35", "undescended_testis_corrected_laterality": "Bilateral", "undescended_testis_corrected_method": "Hormones", "undescended_testis_history": "Yes", "undescended_testis_history_laterality": "Left" } ] } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedCaseFollowUpsPerStudydatapaginatedCaseFollowUpsPerStudyDef(optional){} paginatedCaseFollowUpsPerStudyDefpaginatedCaseFollowUpsPerStudypaginatedCaseFollowUpsPerStudyDesc(optional){} paginatedCaseFollowUpsPerStudyDesctotalnumber(optional)caseFollowUpsPerStudyarray[paginatedCaseFollowUps](optional)paginationPagination(optional){} paginatedCaseFollowUpscase_idstring(optional)case_submitter_idstring(optional)disease_typestring(optional)primary_sitestring(optional)follow_upsarray[FollowUp](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} FollowUpfollow_up_idstring(optional)follow_up_submitter_idstring(optional)adverse_eventstring(optional)barretts_esophagus_goblet_cells_presentstring(optional)bmifloat(optional)cause_of_responsestring(optional)comorbiditystring(optional)comorbidity_method_of_diagnosisstring(optional)days_to_adverse_eventinteger(optional)days_to_comorbidityinteger(optional)days_to_follow_upinteger(optional)days_to_progressioninteger(optional)days_to_progression_freeinteger(optional)days_to_recurrenceinteger(optional)diabetes_treatment_typestring(optional)disease_responsestring(optional)dlco_ref_predictive_percentfloat(optional)ecog_performance_statusstring(optional)fev1_ref_post_bronch_percentfloat(optional)fev1_ref_pre_bronch_percentfloat(optional)fev1_fvc_pre_bronch_percentfloat(optional)fev1_fvc_post_bronch_percentfloat(optional)heightfloat(optional)hepatitis_sustained_virological_responsestring(optional)hpv_positive_typestring(optional)karnofsky_performance_statusstring(optional)menopause_statusstring(optional)pancreatitis_onset_yearinteger(optional)progression_or_recurrencestring(optional)progression_or_recurrence_anatomic_sitestring(optional)progression_or_recurrence_typestring(optional)reflux_treatment_typestring(optional)risk_factorstring(optional)risk_factor_treatmentstring(optional)viral_hepatitis_serologiesstring(optional)weightfloat(optional)adverse_event_gradestring(optional)aids_risk_factorsstring(optional)body_surface_areafloat(optional)cd4_countfloat(optional)cdc_hiv_risk_factorsstring(optional)days_to_imaginginteger(optional)evidence_of_recurrence_typestring(optional)eye_colorstring(optional)haart_treatment_indicatorstring(optional)history_of_tumorstring(optional)history_of_tumor_typestring(optional)hiv_viral_loadfloat(optional)hormonal_contraceptive_typestring(optional)hormonal_contraceptive_usestring(optional)hormone_replacement_therapy_typestring(optional)hysterectomy_margins_involvedstring(optional)hysterectomy_typestring(optional)imaging_resultstring(optional)imaging_typestring(optional)immunosuppressive_treatment_typestring(optional)nadir_cd4_countfloat(optional)pregnancy_outcomestring(optional)procedures_performedstring(optional)recist_targeted_regions_numberinteger(optional)recist_targeted_regions_sumfloat(optional)scan_tracer_usedstring(optional)undescended_testis_correctedstring(optional)undescended_testis_corrected_ageinteger(optional)undescended_testis_corrected_lateralitystring(optional)undescended_testis_corrected_methodstring(optional)undescended_testis_historystring(optional)undescended_testis_history_lateralitystring(optional)
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Get Cases/Treatments Per Study
get ?query={paginatedCaseTreatmentsPerStudy (pdc_study_id: "{pdc_study_id}" offset: {offset} limit: {limit}) { total caseTreatmentsPerStudy { case_id case_submitter_id disease_type primary_site treatments { treatment_id treatment_submitter_id, days_to_treatment_end, days_to_treatment_start, initial_disease_status, regimen_or_line_of_therapy, therapeutic_agents, treatment_anatomic_site, treatment_effect, treatment_intent_type, treatment_or_therapy, treatment_outcome, treatment_type, chemo_concurrent_to_radiation, number_of_cycles, reason_treatment_ended, route_of_administration, treatment_arm, treatment_dose, treatment_dose_units, treatment_effect_indicator, treatment_frequency } } pagination { count sort from page total pages size } }}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 8961afcf-05de-4b7c-b471-ca1a4887ed36)
- study_submitter_id (example: APOLLO LUAD - Phosphoproteome - FeNTA)
- pdc_study_id (example: PDC000436)
- study_name (example: APOLLO LUAD - Phosphoproteome - FeNTA)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
It may take a long time to execute because of the huge volume of data.
Fields:- total
- caseTreatmentsPerStudy
- pagination
Response Sample
{ "data": { "paginatedCaseTreatmentsPerStudy": { "total": 230, "caseTreatmentsPerStudy": [ { "case_id": "e0d672dc-b42b-4721-82bd-deae88280c69", "case_submitter_id": "AP-27JZ", "disease_type": "Lung Adenocarcinoma", "primary_site": "Bronchus and lung", "treatments": [ { "treatment_id": "a2518568-1adc-43fe-852f-049ad21ec2df", "treatment_submitter_id": "AP-27JZ-TR", "days_to_treatment_end": " ", "days_to_treatment_start": " ", "initial_disease_status": " ", "regimen_or_line_of_therapy": " ", "therapeutic_agents": " ", "treatment_anatomic_site": " ", "treatment_effect": " ", "treatment_intent_type": "Adjuvant", "treatment_or_therapy": " ", "treatment_outcome": " ", "treatment_type": "Radiation Therapy, NOS", "chemo_concurrent_to_radiation": " ", "number_of_cycles": " ", "reason_treatment_ended": " ", "route_of_administration": " ", "treatment_arm": " ", "treatment_dose": " ", "treatment_dose_units": " ", "treatment_effect_indicator": " ", "treatment_frequency": " " } ] } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedCaseTreatmentsPerStudydatapaginatedCaseTreatmentsPerStudyDef(optional){} paginatedCaseTreatmentsPerStudyDefpaginatedCaseTreatmentsPerStudypaginatedCaseTreatmentsPerStudyDesc(optional){} paginatedCaseTreatmentsPerStudyDesctotalnumber(optional)caseTreatmentsPerStudyarray[paginatedCaseTreatments](optional)paginationPagination(optional){} paginatedCaseTreatmentscase_idstring(optional)case_submitter_idstring(optional)disease_typestring(optional)primary_sitestring(optional)treatmentsarray[Treatment](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} Treatmenttreatment_idstring(optional)treatment_submitter_idstring(optional)days_to_treatment_endinteger(optional)days_to_treatment_startinteger(optional)initial_disease_statusstring(optional)regimen_or_line_of_therapystring(optional)therapeutic_agentsstring(optional)treatment_anatomic_sitestring(optional)treatment_effectstring(optional)treatment_intent_typestring(optional)treatment_or_therapystring(optional)treatment_outcomestring(optional)treatment_typestring(optional)chemo_concurrent_to_radiationstring(optional)number_of_cyclesinteger(optional)reason_treatment_endedstring(optional)route_of_administrationstring(optional)treatment_armstring(optional)treatment_doseinteger(optional)treatment_dose_unitsstring(optional)treatment_effect_indicatorstring(optional)treatment_frequencystring(optional)
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Get Cases/Diagnoses Per Study
get ?query={paginatedCaseDiagnosesPerStudy (study_id: "{study_id}" offset: {offset} limit: {limit}) { total caseDiagnosesPerStudy { case_id case_submitter_id disease_type primary_site diagnoses{ diagnosis_id tissue_or_organ_of_origin age_at_diagnosis primary_diagnosis tumor_grade tumor_stage diagnosis_submitter_id classification_of_tumor days_to_last_follow_up days_to_last_known_disease_status days_to_recurrence last_known_disease_status morphology progression_or_recurrence site_of_resection_or_biopsy prior_malignancy ajcc_clinical_m ajcc_clinical_n ajcc_clinical_stage ajcc_clinical_t ajcc_pathologic_m ajcc_pathologic_n ajcc_pathologic_stage ajcc_pathologic_t ann_arbor_b_symptoms ann_arbor_clinical_stage ann_arbor_extranodal_involvement ann_arbor_pathologic_stage best_overall_response burkitt_lymphoma_clinical_variant circumferential_resection_margin colon_polyps_history days_to_best_overall_response days_to_diagnosis days_to_hiv_diagnosis days_to_new_event figo_stage hiv_positive hpv_positive_type hpv_status iss_stage laterality ldh_level_at_diagnosis ldh_normal_range_upper lymph_nodes_positive lymphatic_invasion_present method_of_diagnosis new_event_anatomic_site new_event_type overall_survival perineural_invasion_present prior_treatment progression_free_survival progression_free_survival_event residual_disease vascular_invasion_present year_of_diagnosis icd_10_code synchronous_malignancy tumor_largest_dimension_diameter anaplasia_present anaplasia_present_type child_pugh_classification cog_liver_stage cog_neuroblastoma_risk_group cog_renal_stage cog_rhabdomyosarcoma_risk_group enneking_msts_grade enneking_msts_metastasis enneking_msts_stage enneking_msts_tumor_site esophageal_columnar_dysplasia_degree esophageal_columnar_metaplasia_present first_symptom_prior_to_diagnosis gastric_esophageal_junction_involvement goblet_cells_columnar_mucosa_present gross_tumor_weight inpc_grade inpc_histologic_group inrg_stage inss_stage irs_group irs_stage ishak_fibrosis_score lymph_nodes_tested medulloblastoma_molecular_classification metastasis_at_diagnosis metastasis_at_diagnosis_site mitosis_karyorrhexis_index peripancreatic_lymph_nodes_positive peripancreatic_lymph_nodes_tested supratentorial_localization tumor_confined_to_organ_of_origin tumor_focality tumor_regression_grade vascular_invasion_type wilms_tumor_histologic_subtype breslow_thickness gleason_grade_group igcccg_stage international_prognostic_index largest_extrapelvic_peritoneal_focus masaoka_stage non_nodal_regional_disease non_nodal_tumor_deposits ovarian_specimen_status ovarian_surface_involvement percent_tumor_invasion peritoneal_fluid_cytological_status primary_gleason_grade secondary_gleason_grade weiss_assessment_score adrenal_hormone ann_arbor_b_symptoms_described diagnosis_is_primary_disease eln_risk_classification figo_staging_edition_year gleason_grade_tertiary gleason_patterns_percent margin_distance margins_involved_site pregnant_at_diagnosis satellite_nodule_present sites_of_involvement tumor_depth who_cns_grade who_nte_grade samples { sample_id sample_submitter_id annotation}} } pagination { count sort from page total pages size } }}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
Fields:- total
- caseDiagnosesPerStudy
- pagination
Response Sample
{ "data": { "paginatedCaseDiagnosesPerStudy": { "total": 90, "caseDiagnosesPerStudy": [ { "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490", "case_submitter_id": "C3N-00386", "disease_type": "Uterine Corpus Endometrial Carcinoma", "primary_site": "Uterus, NOS", "diagnoses": [ { "diagnosis_id": "f748299b-0f5a-11e9-a064-0a9c39d33490", "tissue_or_organ_of_origin": "Corpus uteri", "age_at_diagnosis": "16190", "primary_diagnosis": "Endometrioid adenocarcinoma, NOS", "tumor_grade": "G1", "tumor_stage": "Stage I", "diagnosis_submitter_id": "C3N-00386-DIAG", "classification_of_tumor": "Not Reported", "days_to_last_follow_up": "673", "days_to_last_known_disease_status": "673", "days_to_recurrence": "0", "last_known_disease_status": "Tumor free", "morphology": "8380/3", "progression_or_recurrence": "no", "site_of_resection_or_biopsy": "Corpus uteri", "prior_malignancy": "Not Reported", "ajcc_clinical_m": "Not Reported", "ajcc_clinical_n": "Not Reported", "ajcc_clinical_stage": "Not Reported", "ajcc_clinical_t": "Not Reported", "ajcc_pathologic_m": "Not Reported", "ajcc_pathologic_n": "Not Reported", "ajcc_pathologic_stage": "Not Reported", "ajcc_pathologic_t": "Not Reported", "ann_arbor_b_symptoms": "Not Reported", "ann_arbor_clinical_stage": "Not Reported", "ann_arbor_extranodal_involvement": "Not Reported", "ann_arbor_pathologic_stage": "Not Reported", "best_overall_response": "null", "burkitt_lymphoma_clinical_variant": "Not Reported", "circumferential_resection_margin": "null", "colon_polyps_history": "null", "days_to_best_overall_response": "null", "days_to_diagnosis": "null", "days_to_hiv_diagnosis": "null", "days_to_new_event": "null", "figo_stage": "Not Reported", "hiv_positive": "null", "hpv_positive_type": "null", "hpv_status": "null", "iss_stage": "Not Reported", "laterality": "Not Reported", "ldh_level_at_diagnosis": "null", "ldh_normal_range_upper": "null", "lymph_nodes_positive": "null", "lymphatic_invasion_present": "Not Reported", "method_of_diagnosis": "Not Reported", "new_event_anatomic_site": "null", "new_event_type": "null", "overall_survival": "null", "perineural_invasion_present": "Not Reported", "prior_treatment": "Not Reported", "progression_free_survival": "null", "progression_free_survival_event": "null", "residual_disease": "Not Reported", "vascular_invasion_present": "Not Reported", "year_of_diagnosis": "null", "icd_10_code": "null", "synchronous_malignancy": "null", "tumor_largest_dimension_diameter": "null", "anaplasia_present": "Yes", "anaplasia_present_type": "Diffuse", "child_pugh_classification": "A", "cog_liver_stage": "Stage I", "cog_neuroblastoma_risk_group": "High Risk", "cog_renal_stage": "Stage I", "cog_rhabdomyosarcoma_risk_group": "Low Risk", "enneking_msts_grade": "Low Grade (G1)", "enneking_msts_metastasis": "Regional or Distant Metastasis (M1)", "enneking_msts_stage": "Stage IA", "enneking_msts_tumor_site": "Extracompartmental (T2)", "esophageal_columnar_dysplasia_degree": "Indefinite for Dysplasia", "esophageal_columnar_metaplasia_present": "No", "first_symptom_prior_to_diagnosis": "Headaches", "gastric_esophageal_junction_involvement": "Yes", "goblet_cells_columnar_mucosa_present": "No", "gross_tumor_weight": "1", "inpc_grade": "Differentiating", "inpc_histologic_group": "Favorable", "inrg_stage": "L1", "inss_stage": "Stage 1", "irs_group": "Group I", "irs_stage": "1", "ishak_fibrosis_score": "1,2 - Portal Fibrosis", "lymph_nodes_tested": "1", "medulloblastoma_molecular_classification": "SHH-Activated", "metastasis_at_diagnosis": "Distant Metastasis", "metastasis_at_diagnosis_site": "Abdomen", "mitosis_karyorrhexis_index": "Low", "peripancreatic_lymph_nodes_positive": "0", "peripancreatic_lymph_nodes_tested": "1", "supratentorial_localization": "Cerebral Cortex", "tumor_confined_to_organ_of_origin": "Yes", "tumor_focality": "Unifocal", "tumor_regression_grade": "1", "vascular_invasion_type": "Extramural", "wilms_tumor_histologic_subtype": "Favorable", "breslow_thickness": "1", "gleason_grade_group": "Group 1", "igcccg_stage": "Good Prognosis", "international_prognostic_index": "Low Risk", "largest_extrapelvic_peritoneal_focus": "Macroscopic (2cm or less)", "masaoka_stage": "Stage I", "non_nodal_regional_disease": "Present", "non_nodal_tumor_deposits": "Yes", "ovarian_specimen_status": "Ovarian Capsule Intact", "ovarian_surface_involvement": "Present", "percent_tumor_invasion": "1", "peritoneal_fluid_cytological_status": "Atypical", "primary_gleason_grade": "Pattern 1", "secondary_gleason_grade": "Pattern 1", "weiss_assessment_score": "1", "adrenal_hormone": "No", "ann_arbor_b_symptoms_described": "Fever", "diagnosis_is_primary_disease": "false", "eln_risk_classification": "Favorable", "figo_staging_edition_year": "2009", "gleason_grade_tertiary": "Pattern 4", "gleason_patterns_percent": "1", "margin_distance": "1.5", "margins_involved_site": "Gerota Fascia", "pregnant_at_diagnosis": "Yes", "satellite_nodule_present": "Absent", "sites_of_involvement": "Unknown", "tumor_depth": "1.2", "who_cns_grade": "Grade I", "who_nte_grade": "G1", "samples": [ { "sample_id": "99a4bcef-1259-11e9-afb9-0a9c39d33490", "sample_submitter_id": "C3N-00386-02", "annotation": "The sample 7316-2901 is associated with this clinical record." } ] } ] } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedCaseDiagnosesPerStudydatapaginatedCaseDiagnosesPerStudyDef(optional){} paginatedCaseDiagnosesPerStudyDefpaginatedCaseDiagnosesPerStudypaginatedCaseDiagnosesPerStudyDesc(optional){} paginatedCaseDiagnosesPerStudyDesctotalnumber(optional)caseDiagnosesPerStudyarray[paginatedCaseDiagnosis](optional)paginationPagination(optional){} paginatedCaseDiagnosiscase_idstring(optional)case_submitter_idstring(optional)disease_typestring(optional)primary_sitestring(optional)diagnosesarray[Diagnosis](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} Diagnosisdiagnosis_idstring(optional)tissue_or_organ_of_originnumber(optional)age_at_diagnosisstring(optional)primary_diagnosisstring(optional)tumor_gradestring(optional)tumor_stagestring(optional)diagnosis_submitter_idstring(optional)classification_of_tumorstring(optional)days_to_last_follow_upstring(optional)days_to_last_known_disease_statusstring(optional)days_to_recurrencestring(optional)last_known_disease_statusstring(optional)morphologystring(optional)progression_or_recurrencestring(optional)site_of_resection_or_biopsystring(optional)prior_malignancystring(optional)ajcc_clinical_mstring(optional)ajcc_clinical_nstring(optional)ajcc_clinical_stagestring(optional)ajcc_clinical_tstring(optional)ajcc_pathologic_mstring(optional)ajcc_pathologic_nstring(optional)ajcc_pathologic_stagestring(optional)ajcc_pathologic_tstring(optional)ann_arbor_b_symptomsstring(optional)ann_arbor_clinical_stagestring(optional)ann_arbor_extranodal_involvementstring(optional)ann_arbor_pathologic_stagestring(optional)best_overall_responsestring(optional)burkitt_lymphoma_clinical_variantstring(optional)circumferential_resection_marginstring(optional)colon_polyps_historystring(optional)days_to_best_overall_responsestring(optional)days_to_diagnosisstring(optional)days_to_hiv_diagnosisstring(optional)days_to_new_eventstring(optional)figo_stagestring(optional)hiv_positivestring(optional)hpv_positive_typestring(optional)hpv_statusstring(optional)iss_stagestring(optional)lateralitystring(optional)ldh_level_at_diagnosisstring(optional)ldh_normal_range_upperstring(optional)lymph_nodes_positivestring(optional)lymphatic_invasion_presentstring(optional)method_of_diagnosisstring(optional)new_event_anatomic_sitestring(optional)new_event_typestring(optional)overall_survivalstring(optional)perineural_invasion_presentstring(optional)prior_treatmentstring(optional)progression_free_survivalstring(optional)progression_free_survival_eventstring(optional)residual_diseasestring(optional)vascular_invasion_presentstring(optional)year_of_diagnosisstring(optional)icd_10_codestring(optional)synchronous_malignancystring(optional)tumor_largest_dimension_diameterstring(optional)anaplasia_presentstring(optional)anaplasia_present_typestring(optional)child_pugh_classificationstring(optional)cog_liver_stagestring(optional)cog_neuroblastoma_risk_groupstring(optional)cog_renal_stagestring(optional)cog_rhabdomyosarcoma_risk_groupstring(optional)enneking_msts_gradestring(optional)enneking_msts_metastasisstring(optional)enneking_msts_stagestring(optional)enneking_msts_tumor_sitestring(optional)esophageal_columnar_dysplasia_degreestring(optional)esophageal_columnar_metaplasia_presentstring(optional)first_symptom_prior_to_diagnosisstring(optional)gastric_esophageal_junction_involvementstring(optional)goblet_cells_columnar_mucosa_presentstring(optional)gross_tumor_weightinteger(optional)inpc_gradestring(optional)inpc_histologic_groupstring(optional)inrg_stagestring(optional)inss_stagestring(optional)irs_groupstring(optional)irs_stagestring(optional)ishak_fibrosis_scorestring(optional)lymph_nodes_testedinteger(optional)medulloblastoma_molecular_classificationstring(optional)metastasis_at_diagnosisstring(optional)metastasis_at_diagnosis_sitestring(optional)mitosis_karyorrhexis_indexstring(optional)peripancreatic_lymph_nodes_positivestring(optional)peripancreatic_lymph_nodes_testedinteger(optional)supratentorial_localizationstring(optional)tumor_confined_to_organ_of_originstring(optional)tumor_focalitystring(optional)tumor_regression_gradestring(optional)vascular_invasion_typestring(optional)wilms_tumor_histologic_subtypestring(optional)breslow_thicknessinteger(optional)gleason_grade_groupstring(optional)igcccg_stagestring(optional)international_prognostic_indexstring(optional)largest_extrapelvic_peritoneal_focusstring(optional)masaoka_stagestring(optional)non_nodal_regional_diseasestring(optional)non_nodal_tumor_depositsstring(optional)ovarian_specimen_statusstring(optional)ovarian_surface_involvementstring(optional)percent_tumor_invasioninteger(optional)peritoneal_fluid_cytological_statusstring(optional)primary_gleason_gradestring(optional)secondary_gleason_gradestring(optional)weiss_assessment_scorestring(optional)adrenal_hormonestring(optional)ann_arbor_b_symptoms_describedstring(optional)diagnosis_is_primary_diseasestring(optional)eln_risk_classificationstring(optional)figo_staging_edition_yearstring(optional)gleason_grade_tertiarystring(optional)gleason_patterns_percentinteger(optional)margin_distancenumber(optional)margins_involved_sitestring(optional)pregnant_at_diagnosisstring(optional)satellite_nodule_presentstring(optional)sites_of_involvementstring(optional)tumor_depthnumber(optional)who_cns_gradestring(optional)who_nte_gradestring(optional)samplesarray[SampleRef](optional){} SampleRefsample_idstring(optional)sample_submitter_idstring(optional)annotationstring(optional)
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Get paginated case records
get ?query={ paginatedCasesSamplesAliquots(pdc_study_id:"{pdc_study_id}" offset:{offset} limit: {limit}) { total casesSamplesAliquots { case_id case_submitter_id days_to_lost_to_followup disease_type index_date lost_to_followup primary_site samples { sample_id sample_submitter_id sample_type sample_type_id gdc_sample_id gdc_project_id biospecimen_anatomic_site composition current_weight days_to_collection days_to_sample_procurement diagnosis_pathologically_confirmed freezing_method initial_weight intermediate_dimension longest_dimension method_of_sample_procurement pathology_report_uuid preservation_method sample_type_id shortest_dimension time_between_clamping_and_freezing time_between_excision_and_freezing tissue_type tumor_code tumor_code_id tumor_descriptor diagnoses{ diagnosis_id diagnosis_submitter_id annotation} aliquots { aliquot_id aliquot_submitter_id analyte_type aliquot_run_metadata { aliquot_run_metadata_id label experiment_number fraction replicate_number date alias analyte} } } } pagination { count sort from page total pages size } } }
Input Parameters (multiple parameters can be passed in one call):
- program_name (example: Clinical Proteomic Tumor Analysis Consortium)
- project_name (example: CPTAC3 Discovery and Confirmatory)
- program_submitter_id (example: Clinical Proteomic Tumor Analysis Consortium)
- project_submitter_id (example: CPTAC3 Discovery and Confirmatory)
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
Fields:- total
- casesSamplesAliquots
- pagination
Response Sample
{ "data": { "paginatedCasesSamplesAliquots": { "total": 958, "casesSamplesAliquots": [ { "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490", "case_submitter_id": "C3N-00386", "days_to_lost_to_followup": 0, "disease_type": "Uterine Corpus Endometrial Carcinoma", "index_date": "Diagnosis", "lost_to_followup": "string", "primary_site": "Uterus, NOS", "samples": [ { "sample_id": "99a4bcef-1259-11e9-afb9-0a9c39d33490", "sample_submitter_id": "C3N-00386-02", "sample_type": "Primary Tumor", "sample_type_id": "null", "gdc_sample_id": "null", "gdc_project_id": "null", "biospecimen_anatomic_site": "Not Reported", "composition": "Solid Tissue", "current_weight": "0", "days_to_collection": "0", "days_to_sample_procurement": "0", "diagnosis_pathologically_confirmed": "Not Reported", "freezing_method": "LN2", "initial_weight": "400", "intermediate_dimension": "null", "longest_dimension": "null", "method_of_sample_procurement": "Not Reported", "pathology_report_uuid": "null", "preservation_method": "Snap Frozen", "shortest_dimension": "null", "time_between_clamping_and_freezing": "0", "time_between_excision_and_freezing": "11", "tissue_type": "Tumor", "tumor_code": "null", "tumor_code_id": "null", "tumor_descriptor": "Not Reported", "biospecimen_laterality": "Bilateral", "catalog_reference": "Not Reported", "distance_normal_to_tumor": "Adjacent (< or = 2cm)", "distributor_reference": "Not Reported", "growth_rate": "1", "passage_count": "2", "sample_ordinal": "3", "tissue_collection_type": "Prospective", "diagnoses": [ { "diagnosis_id": "f748299b-0f5a-11e9-a064-0a9c39d33490", "diagnosis_submitter_id": "C3N-00386-DIAG", "annotation": "The sample 7316-2901 is associated with this clinical record." } ], "aliquots": [ { "aliquot_id": "141959ca-6424-11e8-bcf1-0a2705229b82", "aliquot_submitter_id": "3f957017-d081-45f4-b458-ec3f8d_D2", "analyte_type": "Protein", "aliquot_run_metadata": [ { "aliquot_run_metadata_id": "1661cee5-5731-11e8-b664-00a098d917f8", "label": "itraq_116", "experiment_number": "13", "fraction": "24-Jan", "replicate_number": "1", "date": "2013-02-28", "alias": "B1S6", "analyte": "Proteome" } ] } ] } ] } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedCasesSamplesAliquotsdatapaginatedCasesSamplesAliquotsDef(optional){} paginatedCasesSamplesAliquotsDefpaginatedCasesSamplesAliquotscasesSamplesAliquotsDesc(optional){} casesSamplesAliquotsDesctotalnumber(optional)casesSamplesAliquotsarray[Case](optional)paginationPagination(optional){} Casecase_idstring(optional)case_submitter_idstring(optional)days_to_lost_to_followupinteger(optional)disease_typestring(optional)index_datestring(optional)lost_to_followupstring(optional)primary_sitestring(optional)samplesarray[Sample](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} Samplesample_idstring(optional)sample_submitter_idstring(optional)sample_typestring(optional)sample_type_idstring(optional)gdc_sample_idstring(optional)gdc_project_idstring(optional)biospecimen_anatomic_sitestring(optional)compositionstring(optional)current_weightstring(optional)days_to_collectionstring(optional)days_to_sample_procurementstring(optional)diagnosis_pathologically_confirmedstring(optional)freezing_methodstring(optional)initial_weightstring(optional)intermediate_dimensionstring(optional)longest_dimensionstring(optional)method_of_sample_procurementstring(optional)pathology_report_uuidstring(optional)preservation_methodstring(optional)shortest_dimensionstring(optional)time_between_clamping_and_freezingstring(optional)time_between_excision_and_freezingstring(optional)tissue_typestring(optional)tumor_codestring(optional)tumor_code_idstring(optional)tumor_descriptorstring(optional)biospecimen_lateralitystring(optional)catalog_referencestring(optional)distance_normal_to_tumorstring(optional)distributor_referencestring(optional)growth_rateinteger(optional)passage_countinteger(optional)sample_ordinalinteger(optional)tissue_collection_typestring(optional)diagnosesarray[DiagnosisRef](optional)aliquotsarray[Aliquot](optional){} DiagnosisRefdiagnosis_idstring(optional)diagnosis_submitter_idstring(optional)annotationstring(optional){} Aliquotaliquot_idstringaliquot_submitter_idstringanalyte_typestring(optional)aliquot_run_metadataarray[aliquotRunMetaDataForPaginated](optional){} aliquotRunMetaDataForPaginatedaliquot_run_metadata_idstring(optional)labelstring(optional)experiment_numberstring(optional)fractionstring(optional)replicate_numberstring(optional)datestring(optional)aliasstring(optional)analytestring(optional)
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Gets all programs
get ?query={allPrograms {program_id program_submitter_id name projects {project_id project_submitter_id name studies {pdc_study_id study_id study_submitter_id submitter_id_name analytical_fraction study_name disease_types primary_sites experiment_type acquisition_type} }}}
Returns all available programs.
Fields:- program_id
- program_submitter_id
- name
- projects
Response Sample
{ "data": { "allPrograms": [ { "program_id": "10251935-5540-11e8-b664-00a098d917f8", "program_submitter_id": "Clinical Proteomic Tumor Analysis Consortium", "name": "Clinical Proteomic Tumor Analysis Consortium", "projects": [ { "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "project_submitter_id": "CPTAC3-Discovery", "name": "CPTAC3-Discovery", "studies": [ { "pdc_study_id": "PDC000206", "study_id": "0ea91a54-1798-11ea-9bfa-0a42f3c845fe", "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "submitter_id_name": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "analytical_fraction": "Phosphoproteome", "study_name": "CPTAC LSCC Discovery Study - Phosphoproteome", "disease_types": "[Lung Adenocarcinoma, Other]", "primary_sites": "[Lung, Bronchus and lung]", "experiment_type": "TMT11", "acquisition_type": "DDA" } ] } ] } ] } }
Response Schema
{} allProgramsdataallProgramsDef(optional){} allProgramsDefallProgramsarray[allProgramsDesc](optional){} allProgramsDescprogram_idstring(optional)program_submitter_idstring(optional)namestring(optional)projectsarray[allProgramsProject](optional){} allProgramsProjectproject_idstringPKproject_submitter_idstring(optional)namestring(optional)studiesarray[allProgramsStudy](optional){} allProgramsStudypdc_study_idstring(optional)study_idstringPKstudy_submitter_idstring(optional)submitter_id_namestring(optional)analytical_fractionstring(optional)study_namestring(optional)disease_typesstring(optional)primary_sitesstring(optional)experiment_typestring(optional)acquisition_typestring(optional)
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Find program by ID
get ?query={program(program_submitter_id: "{program_submitter_id}") {program_id program_submitter_id name projects {project_id project_submitter_id name studies {pdc_study_id study_id study_submitter_id submitter_id_name analytical_fraction study_name disease_types primary_sites experiment_type acquisition_type} } } }
Input Parameters:
- program_id (example: c3408a52-f1e8-11e9-9a07-0a80fada099c)
- program_submitter_id (example: Clinical Proteomic Tumor Analysis Consortium)
Fields:- program_id
- program_submitter_id
- name
- projects
Response Sample
{ "data": { "program": { "program_submitter_id": "CPTAC", "projects": [ { "program_id": "10251935-5540-11e8-b664-00a098d917f8", "program_submitter_id": "Clinical Proteomic Tumor Analysis Consortium", "name": "Clinical Proteomic Tumor Analysis Consortium", "projects": [ { "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "project_submitter_id": "CPTAC3-Discovery", "name": "CPTAC3-Discovery", "studies": [ { "pdc_study_id": "PDC000206", "study_id": "0ea91a54-1798-11ea-9bfa-0a42f3c845fe", "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "submitter_id_name": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "analytical_fraction": "Phosphoproteome", "study_name": "CPTAC LSCC Discovery Study - Phosphoproteome", "disease_types": "[Lung Adenocarcinoma, Other]", "primary_sites": "[Lung, Bronchus and lung]", "experiment_type": "TMT11", "acquisition_type": "DDA" } ] } ] } ] } } }
Response Schema
{} findProgramdatafindProgramObj(optional){} findProgramObjprogramfindProgramDef(optional){} findProgramDefprogram_submitter_idstring(optional)projectsarray[allProgramsDesc](optional){} allProgramsDescprogram_idstring(optional)program_submitter_idstring(optional)namestring(optional)projectsarray[allProgramsProject](optional){} allProgramsProjectproject_idstringPKproject_submitter_idstring(optional)namestring(optional)studiesarray[allProgramsStudy](optional){} allProgramsStudypdc_study_idstring(optional)study_idstringPKstudy_submitter_idstring(optional)submitter_id_namestring(optional)analytical_fractionstring(optional)study_namestring(optional)disease_typesstring(optional)primary_sitesstring(optional)experiment_typestring(optional)acquisition_typestring(optional)
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Get all programs/projects/studies
get ?query={programsProjectsStudies (disease_type: "{disease_type}") {program_id program_submitter_id name projects {project_id project_submitter_id name studies { pdc_study_id study_id study_submitter_id submitter_id_name analytical_fraction study_name disease_types primary_sites experiment_type acquisition_type} }}}
Input Parameters (multiple parameters can be passed in one call):
- disease_type (example: Lung Adenocarcinoma)
- instrument_model (example: Q Exactive)
- analytical_fraction (example: Phosphoproteome)
- experiment_type (example: iTRAQ4)
Fields:- program_id
- program_submitter_id
- name
- projects {project_id project_submitter_id name}
- studies {pdc_study_id study_id study_submitter_id submitter_id_name analytical_fraction study_name disease_types primary_sites experiment_type acquisition_type}
Response Sample
{ "data": { "programsProjectsStudies": [ { "program_id": "10251935-5540-11e8-b664-00a098d917f8", "program_submitter_id": "Clinical Proteomic Tumor Analysis Consortium", "name": "Clinical Proteomic Tumor Analysis Consortium", "projects": [ { "project_id": "PJ-CPTAC3", "project_submitter_id": "PJ-CPTAC3", "name": "PJ-CPTAC3", "studies": [ { "pdc_study_id": "PDC000125", "study_id": "c935c587-0cd1-11e9-a064-0a9c39d33490", "submitter_id_name": "CPTAC UCEC Discovery Study - Proteome", "study_submitter_id": "S043-1", "analytical_fraction": "Proteome", "study_name": "CPTAC LSCC Discovery Study - Phosphoproteome", "disease_types": "[Lung Adenocarcinoma, Other]", "primary_sites": "[Lung, Bronchus and lung]", "experiment_type": "TMT10", "acquisition_type": "DDA" } ] } ] } ] } }
Response Schema
{} programsProjectsStudiesdataprogramsProjectsStudiesDef(optional){} programsProjectsStudiesDefprogramsProjectsStudiesarray[programsProjectsStudiesDesc](optional){} programsProjectsStudiesDescprogram_idstring(optional)program_submitter_idstring(optional)namestring(optional)projectsarray[programsProjectsStudiesDefforProj](optional){} programsProjectsStudiesDefforProjproject_idstring(optional)project_submitter_idstring(optional)namestring(optional)studiesarray[programsProjectsStudiesDefforStudies](optional){} programsProjectsStudiesDefforStudiespdc_study_idstring(optional)study_idstring(optional)submitter_id_namestring(optional)study_submitter_idstring(optional)analytical_fractionstring(optional)study_namestring(optional)disease_typesstring(optional)primary_sitesstring(optional)experiment_typestring(optional)acquisition_typestring(optional)
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Returns the aliquot spectral counts
get ?query={aliquotSpectralCount(gene_name: "{gene_name}" dataset_alias: "{dataset_alias}" ){gene_id gene_name NCBI_gene_id authority description organism chromosome locus proteins assays spectral_counts { project_submitter_id plex spectral_count distinct_peptide unshared_peptide study_submitter_id pdc_study_id}}}
Input Parameters (multiple parameters can be passed in one call):
- gene_name (example: MYBBP1A)
- dataset_alias (example: FFPE_Discovery_Phospho_TMT_Gr12)
Fields:- gene_id
- gene_name
- NCBI_gene_id
- authority
- description
- organism
- chromosome
- locus
- proteins
- assays
- spectral_counts
Response Sample
{ "data": { "aliquotSpectralCount": { "gene_id": "f6ba4bc5-b814-11e8-907f-0a2705229b82", "gene_name": "A1BG", "NCBI_gene_id": "1", "authority": "HGNC:5", "description": "alpha-1-B glycoprotein", "organism": "Homo sapiens", "chromosome": "19", "locus": "19q13.43", "proteins": "M0R009;NP_570602.2;P04217;P04217-2", "assays": "non-CPTAC-1064", "spectral_counts": [ { "project_submitter_id": "CPTAC-TCGA", "project_id": "48653303-5546-11e8-b664-00a098d917f8", "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329", "spectral_count": "11", "distinct_peptide": "5", "unshared_peptide": "5", "study_id": "bb67ec40-57b8-11e8-b07a-00a098d917f8", "study_submitter_id": "S015-2", "pdc_study_id": "PDC000174" } ] } } }
Response Schema
{} aliquotSpectralCountdataaliquotSpectralCountDef(optional){} aliquotSpectralCountDefaliquotSpectralCountaliquotSpectralCountDesc(optional){} aliquotSpectralCountDescgene_idstring(optional)gene_namestring(optional)NCBI_gene_idnumber(optional)authoritystring(optional)descriptionstring(optional)organismstring(optional)chromosomestring(optional)locusstring(optional)proteinsstring(optional)assaysstring(optional)spectral_countsarray[spectralCountsDesc](optional){} spectralCountsDescproject_submitter_idstring(optional)project_idstring(optional)plexstring(optional)spectral_countnumber(optional)distinct_peptidenumber(optional)unshared_peptidenumber(optional)study_idstring(optional)study_submitter_idnumber(optional)pdc_study_idnumber(optional)
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Returns the gene spectral counts
get ?query={geneSpectralCount (gene_name: "{gene_name}"){gene_id gene_name NCBI_gene_id authority description organism chromosome locus proteins assays spectral_counts { project_submitter_id plex spectral_count distinct_peptide unshared_peptide study_submitter_id} }}
Input Parameter:
- gene_name (example: A1BG)
Fields:- gene_id
- gene_name
- NCBI_gene_id
- authority
- description
- organism
- chromosome
- locus
- proteins
- assays
- spectral_counts
Response Sample
{ "data": { "geneSpectralCount": { "gene_id": "f6ba4bc5-b814-11e8-907f-0a2705229b82", "gene_name": "A1BG", "NCBI_gene_id": "1", "authority": "HGNC:5", "description": "alpha-1-B glycoprotein", "organism": "Homo sapiens", "chromosome": "19", "locus": "19q13.43", "proteins": "M0R009;NP_570602.2;P04217;P04217-2", "assays": "non-CPTAC-1064", "spectral_counts": [ { "project_submitter_id": "CPTAC-TCGA", "project_id": "48653303-5546-11e8-b664-00a098d917f8", "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329", "spectral_count": "11", "distinct_peptide": "5", "unshared_peptide": "5", "study_id": "bb67ec40-57b8-11e8-b07a-00a098d917f8", "study_submitter_id": "S015-2", "pdc_study_id": "PDC000174" } ] } } }
Response Schema
{} geneSpectralCountdatageneSpectralCountDef(optional){} geneSpectralCountDefgeneSpectralCountaliquotSpectralCountDesc(optional){} aliquotSpectralCountDescgene_idstring(optional)gene_namestring(optional)NCBI_gene_idnumber(optional)authoritystring(optional)descriptionstring(optional)organismstring(optional)chromosomestring(optional)locusstring(optional)proteinsstring(optional)assaysstring(optional)spectral_countsarray[spectralCountsDesc](optional){} spectralCountsDescproject_submitter_idstring(optional)project_idstring(optional)plexstring(optional)spectral_countnumber(optional)distinct_peptidenumber(optional)unshared_peptidenumber(optional)study_idstring(optional)study_submitter_idnumber(optional)pdc_study_idnumber(optional)
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Get paginated gene records
get ?query={ getPaginatedGenes(gene_name: "{gene_name}") { total genesProper { gene_id gene_name NCBI_gene_id authority description organism chromosome locus proteins assays } pagination { count sort from page total pages size } } }
Input Parameters (multiple parameters can be passed in one call):
- gene_name (example: A1BG)
Fields:- total
- genesProper
- pagination
Response Sample
{ "data": { "getPaginatedGenes": { "total": 2, "genesProper": [ { "gene_id": "f6baad59-b814-11e8-907f-0a2705229b82", "gene_name": "A2ML1", "NCBI_gene_id": "144568", "authority": "HGNC:23336", "description": "alpha-2-macroglobulin like 1", "organism": "Homo sapiens", "chromosome": "12", "locus": "12p13.31", "proteins": "A8K2U0;A8K2U0-2;F5GXP1;F5GYG7;H0YGG5;H0YH14;NP_001269353.1;NP_653271.2;XP_011518868.1;XP_011518869.1;XP_016874357.1;XP_016874358.1;XP_016874359.1", "assays": "non-CPTAC-1064" } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} getPaginatedGenesdatagetPaginatedGenesDef(optional){} getPaginatedGenesDefgetPaginatedGenesgetPaginatedGenesDesc(optional){} getPaginatedGenesDesctotalnumber(optional)genesProperarray[genesProper](optional)paginationPagination(optional){} genesPropergene_idstring(optional)gene_namestring(optional)NCBI_gene_idnumber(optional)authoritystring(optional)descriptionstring(optional)organismstring(optional)chromosomestring(optional)locusstring(optional)proteinsstring(optional)assaysstring(optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger
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Get available info of diseases
get ?query={diseasesAvailable {disease_type project_id project_submitter_id cases_count tissue_or_organ_of_origin}}
Input Parameters (multiple parameters can be passed in one call):
- disease_type (example: Breast Invasive Carcinoma)
- tissue_or_organ_of_origin (example: Breast)
- project_submitter_id (example: CPTAC-2)
- project_id (example: 48653303-5546-11e8-b664-00a098d917f8)
Fields:- disease_type
- project_id
- project_submitter_id
- cases_count
- tissue_or_organ_of_origin
Response Sample
{ "data": { "diseasesAvailable": [ { "disease_type": "Breast Invasive Carcinoma", "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "project_submitter_id": "CPTAC-2", "cases_count": "116", "tissue_or_organ_of_origin": "Breast, NOS" } ] } }
Response Schema
{} diseasesAvailabledatadiseasesAvailableDef(optional){} diseasesAvailableDefdiseasesAvailablearray[diseasesAvailableDesc](optional){} diseasesAvailableDescdisease_typestring(optional)project_idstring(optional)project_submitter_idstring(optional)cases_countstring(optional)tissue_or_organ_of_originnumber(optional)
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Get disease types per project
get ?query={diseaseTypesPerProject {project_id project_submitter_id experiment_type analytical_fraction cases {disease_type count}}}
Input Parameters:
- project_submitter_id (example: CPTAC-2)
- project_id (example: 48653303-5546-11e8-b664-00a098d917f8)
Fields:- project_id
- project_submitter_id
- experiment_type
- analytical_fraction
- cases {disease_type count}
Response Sample
{ "data": { "diseaseTypesPerProject": [ { "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "project_submitter_id": "Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study", "experiment_type": "TMT11", "analytical_fraction": "Proteome", "cases": [ { "disease_type": "Clear Cell Renal Cell Carcinoma", "count": 6 } ] } ] } }
Response Schema
{} diseaseTypesPerProjectdatadiseaseTypesPerProjectDef(optional){} diseaseTypesPerProjectDefdiseaseTypesPerProjectarray[diseaseTypesPerProjectDesc](optional){} diseaseTypesPerProjectDescproject_idstring(optional)project_submitter_idstring(optional)experiment_typenumber(optional)analytical_fractionstring(optional)casesarray[casesForDiseaseTypeDesc](optional){} casesForDiseaseTypeDescdisease_typestring(optional)countnumber(optional)
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Get file count per study
get ?query={filesCountPerStudy (pdc_study_id: "{pdc_study_id}") {study_id pdc_study_id study_submitter_id file_type files_count data_category}}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- file_type (example: Proprietary)
- data_category (example: Raw Mass Spectra)
Fields:- study_id
- pdc_study_id
- study_submitter_id: ID of a study
- file_type
- files_count
- data_category
Response Sample
{ "data": { "filesCountPerStudy": [ { "study_id": "1c163e4c-e015-43e0-bd76-238eebd64e5a", "pdc_study_id": "PDC000206", "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "file_type": "Document", "files_count": 11, "data_category": "Other Metadata" } ] } }
Response Schema
{} filesCountPerStudydatafilesCountPerStudyDef(optional){} filesCountPerStudyDeffilesCountPerStudyarray[filesCountPerStudyDesc](optional){} filesCountPerStudyDescstudy_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)file_typenumber(optional)files_countnumber(optional)data_categorystring(optional)
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Get a list of file metadata
get ?query={ fileMetadata(offset: {offset} limit: {limit}) {file_id file_name file_size md5sum file_location file_submitter_id fraction_number experiment_type data_category file_type file_format plex_or_dataset_name analyte instrument study_run_metadata_submitter_id study_run_metadata_id aliquots { aliquot_id aliquot_submitter_id sample_id sample_submitter_id case_id case_submitter_id} } }
Input Parameters (multiple parameters can be passed in one call):
- file_id (example: 00046804-1b57-11e9-9ac1-005056921935)
- file_name (example: 20151104-P50-20ug-s35.mzML.gz)
- file_submitter_id (example: 20190125_30ug_OCb5_T_p_s40.raw)
- data_category (example: Raw Mass Spectra)
- file_type (example: Proprietary)
- file_format (example: vendor-specific)
- offset (example: 0)
- limit (example: 10 cannot exceed 25000)
Fields:- file_id
- file_name
- file_size
- md5sum
- file_location
- file_submitter_id
- fraction_number
- experiment_type
- data_category
- file_type
- file_format
- plex_or_dataset_name
- analyte
- instrument
- study_run_metadata_submitter_id
- study_run_metadata_id
- aliquots
Response Sample
{ "data": { "fileMetadata": [ { "file_id": "00046804-1b57-11e9-9ac1-005056921935", "file_name": "06CPTAC_CCRCC_W_JHU_20171120_LUMOS_f09.mzid.gz", "file_size": "7290779", "md5sum": "e8d4417af70878bb1cf45f8a0fca9433", "file_location": "studies/127/PSM/mzid/06CPTAC_CCRCC_W_JHU_20171120_LUMOS_f09.mzid.gz", "file_submitter_id": "06CPTAC_CCRCC_W_JHU_20171120_LUMOS_f09.mzid.gz", "fraction_number": "9", "experiment_type": "TMT10", "data_category": "Peptide Spectral Matches", "file_type": "Open Standard", "file_format": "mzIdentML", "plex_or_dataset_name": "06CPTAC_CCRCC_Proteome_JHU_20171120", "analyte": "Proteome", "instrument": "Orbitrap Fusion Lumos", "study_run_metadata_submitter_id": "S044-1-9", "study_run_metadata_id": "f7fdea37-2074-11e9-b7f8-0a80fada099c", "aliquots": [ { "aliquot_id": "4f9821f1-2053-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0000790001", "sample_id": "7e25284f-204c-11e9-b7f8-0a80fada099c", "sample_submitter_id": "C3L-00097-06", "case_id": "b76d3749-1fb8-11e9-b7f8-0a80fada099c", "case_submitter_id": "C3L-00097" } ] } ] } }
Response Schema
{} fileMetadatadatafileMetadataDef(optional){} fileMetadataDeffileMetadataarray[fileMetadataDesc](optional){} fileMetadataDescfile_idstring(optional)file_namestring(optional)file_sizestring(optional)md5sumstring(optional)file_locationstring(optional)file_submitter_idstring(optional)fraction_numberstring(optional)experiment_typestring(optional)data_categorystring(optional)file_typestring(optional)file_formatstring(optional)plex_or_dataset_namestring(optional)analytestring(optional)instrumentstring(optional)study_run_metadata_submitter_idstring(optional)study_run_metadata_idstring(optional)aliquotsarray[fileMetadataAliquotsDesc](optional){} fileMetadataAliquotsDescaliquot_idstring(optional)aliquot_submitter_idstring(optional)sample_idstring(optional)sample_submitter_idstring(optional)case_idstring(optional)case_submitter_idstring(optional)
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Get paginated file records
get ?query={getPaginatedFiles(study_id: "{study_id}" offset: {offset} limit: {limit}) {total files {study_id pdc_study_id study_submitter_id file_id file_name file_type file_format data_category md5sum} pagination {count sort from page total pages size}}}
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- file_type (example: Proprietary)
- file_name (example: BL20161004_BI_FM_Medullo_pY_Plex02_Fxn1.raw)
- file_format (example: vendor-specific)
- data_category (example: Raw Mass Spectra)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
Fields:- total
- files
- pagination
Response Sample
{ "data": { "getPaginatedFiles": { "total": 37809, "files": [ { "study_id": "0fe15489-1381-4864-8b17-6159e14a65a8", "pdc_study_id": "PDC000431", "study_submitter_id": "Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments", "file_name": "BA20161122_BI_FM_Medullo_pY_Plex04_Fxn1.raw", "file_id": "18ff9bcd-4e60-4949-9db0-b859c8d0b7bc", "file_type": "Proprietary", "file_format": "vendor-specific", "data_category": "Raw Mass Spectra", "md5sum": "058ab22afbf1fb18563f8e499ad3ad8d" } ] }, "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } }
Response Schema
{} getPaginatedFilesdatagetPaginatedFilesDef(optional){} getPaginatedFilesDefgetPaginatedFilesgetPaginatedFilesDesc(optional)paginationPagination(optional){} getPaginatedFilesDesctotalnumber(optional)filesarray[filesForPaginatedRecords](optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} filesForPaginatedRecordsstudy_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)file_namestring(optional)file_idstring(optional)file_typestring(optional)file_formatstring(optional)data_categorystring(optional)md5sumstring(optional)
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Get files per Study ID
get ?query={ filesPerStudy (study_id: "{study_id}") {study_id pdc_study_id study_submitter_id study_name file_id file_name file_submitter_id file_type md5sum file_location file_size data_category file_format signedUrl {url}} }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- file_name (example: 20151104-P50-20ug-s35.mzML.gz)
- file_type (example: Proprietary)
- data_category (example: Raw Mass Spectra)
- file_format (example: vendor-specific)
It may take a long time to execute because of the huge volume of data.
Fields:- study_id
- pdc_study_id
- study_submitter_id
- study_name
- file_id
- file_name
- file_submitter_id
- file_type
- md5sum
- file_location
- file_size
- data_category
- file_format
- signedUrl {url}
Response Sample
{ "data": { "filesPerStudy": [ { "study_id": "0ea91a54-1798-11ea-9bfa-0a42f3c845fe", "pdc_study_id": "PDC000206", "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "study_name": "CPTAC GBM Discovery Study - CompRef Phosphoproteome", "file_id": "057a5b76-a582-4a3b-87d7-4897750d18c3", "file_name": "02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz", "file_submitter_id": "02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz", "file_type": "Open Standard", "md5sum": "058ab22afbf1fb18563f8e499ad3ad8d", "file_location": "studies/206/mzml/02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz", "file_size": "145180612", "data_category": "Processed Mass Spectra", "file_format": "mzML", "signedUrl": [ { "url": "https://pdcdatastore.s3.amazonaws.com/studies/206/mzml/02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz?AWSAccessKeyId=AKIAQPWI5WIU7M4BLQXG&Expires=1602261172&Signature=W2wF3metuSJUtoZQQFkrfVX0dek%3D" } ] } ] } }
Response Schema
{} filesPerStudydatafilesPerStudyDef(optional){} filesPerStudyDeffilesPerStudyarray[filesPerStudyDesc](optional){} filesPerStudyDescstudy_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)study_namestring(optional)file_idstring(optional)file_namestring(optional)file_submitter_idstring(optional)file_typestring(optional)md5sumstring(optional)file_locationstring(optional)file_sizestring(optional)data_categorystring(optional)file_formatstring(optional)signedUrlarray[signedUrlDesc](optional){} signedUrlDescurlstring(optional)
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Get spectral counts per study/aliquot/gene
get ?query={paginatedSpectralCountPerStudyAliquot(study_id: "{study_id}" plex_name: "{plex_name}" gene_name: "{gene_name}" offset: 0 limit: 10) { total spectralCounts { study_id study_submitter_id pdc_study_id plex spectral_count distinct_peptide unshared_peptide } pagination { count sort from page total pages size } }}
Returns spectral counts per study/aliquot/gene. This API can also be used with multiple input parameters.
Fields:- total
- spectralCounts
- pagination
Response Sample
{ "data": { "paginatedSpectralCountPerStudyAliquot": { "total": 1, "spectralCounts": [ { "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8", "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2", "pdc_study_id": "PDC000174", "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329", "spectral_count": 94, "distinct_peptide": 37, "unshared_peptide": 36 } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedSpectralCountPerStudyAliquotdatapaginatedSpectralCountPerStudyAliquotDef(optional){} paginatedSpectralCountPerStudyAliquotDefpaginatedSpectralCountPerStudyAliquotpaginatedSpectralCountPerStudyAliquotDesc(optional){} paginatedSpectralCountPerStudyAliquotDesctotalnumber(optional)spectralCountsarray[spectralCountsPaginatedAliquot](optional)paginationPagination(optional){} spectralCountsPaginatedAliquotstudy_idstring(optional)study_submitter_idstring(optional)pdc_study_idstring(optional)plexstring(optional)spectral_countnumber(optional)distinct_peptidenumber(optional)unshared_peptidenumber(optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger
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Get spectral counts per study/aliquot/gene
get ?query={paginatedSpectralCountPerStudyAliquot(study_submitter_id: "{study_submitter_id}" plex_name: "{plex_name}" gene_name: "{gene_name}" offset: 0 limit: 10) { total spectralCounts { study_id study_submitter_id pdc_study_id plex spectral_count distinct_peptide unshared_peptide } pagination { count sort from page total pages size } }}
Returns spectral counts per study/aliquot/gene. This API can also be used with multiple input parameters.
Fields:- total
- spectralCounts
- pagination
Response Sample
{ "data": { "paginatedSpectralCountPerStudyAliquot": { "total": 1, "spectralCounts": [ { "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8", "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2", "pdc_study_id": "PDC000174", "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329", "spectral_count": 94, "distinct_peptide": 37, "unshared_peptide": 36 } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedSpectralCountPerStudyAliquotdatapaginatedSpectralCountPerStudyAliquotDef(optional){} paginatedSpectralCountPerStudyAliquotDefpaginatedSpectralCountPerStudyAliquotpaginatedSpectralCountPerStudyAliquotDesc(optional){} paginatedSpectralCountPerStudyAliquotDesctotalnumber(optional)spectralCountsarray[spectralCountsPaginatedAliquot](optional)paginationPagination(optional){} spectralCountsPaginatedAliquotstudy_idstring(optional)study_submitter_idstring(optional)pdc_study_idstring(optional)plexstring(optional)spectral_countnumber(optional)distinct_peptidenumber(optional)unshared_peptidenumber(optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger
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Get spectral counts per study/aliquot/gene for a PDC Study ID
get ?query={paginatedSpectralCountPerStudyAliquot(pdc_study_id: "{pdc_study_id}" gene_name: "{gene_name}" offset: 0 limit: 10) { total spectralCounts { study_id study_submitter_id pdc_study_id plex spectral_count distinct_peptide unshared_peptide } pagination { count sort from page total pages size } }}
Returns spectral counts per study/aliquot/gene. This API can also be used with multiple input parameters.
Fields:- total
- spectralCounts
- pagination
Response Sample
{ "data": { "paginatedSpectralCountPerStudyAliquot": { "total": 1, "spectralCounts": [ { "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8", "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2", "pdc_study_id": "PDC000174", "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329", "spectral_count": 94, "distinct_peptide": 37, "unshared_peptide": 36 } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} paginatedSpectralCountPerStudyAliquotdatapaginatedSpectralCountPerStudyAliquotDef(optional){} paginatedSpectralCountPerStudyAliquotDefpaginatedSpectralCountPerStudyAliquotpaginatedSpectralCountPerStudyAliquotDesc(optional){} paginatedSpectralCountPerStudyAliquotDesctotalnumber(optional)spectralCountsarray[spectralCountsPaginatedAliquot](optional)paginationPagination(optional){} spectralCountsPaginatedAliquotstudy_idstring(optional)study_submitter_idstring(optional)pdc_study_idstring(optional)plexstring(optional)spectral_countnumber(optional)distinct_peptidenumber(optional)unshared_peptidenumber(optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger
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Get spectral counts and plex in available projects for a protein
get ?query={protein(protein: "{protein}"){gene_name NCBI_gene_id authority description organism chromosome locus proteins assays spectral_counts {project_id project_submitter_id plex spectral_count distinct_peptide unshared_peptide study_id study_submitter_id pdc_study_id}}}
Input Parameter:
- protein (example: M0R009)
Fields:- gene_name
- NCBI_gene_id
- authority
- description
- organism
- chromosome
- locus
- proteins
- assays
- spectral_counts
Response Sample
{ "data": { "protein": { "gene_name": "A1BG", "NCBI_gene_id": 1, "authority": "HGNC:5", "description": "alpha-1-B glycoprotein", "organism": "Homo sapiens", "chromosome": "19", "locus": "19q13.43", "proteins": "M0R009;NP_570602.2;P04217;P04217-2", "assays": "non-CPTAC-1064", "spectral_counts": [ { "project_submitter_id": "CPTAC-TCGA", "project_id": "48653303-5546-11e8-b664-00a098d917f8", "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329", "spectral_count": "11", "distinct_peptide": "5", "unshared_peptide": "5", "study_id": "bb67ec40-57b8-11e8-b07a-00a098d917f8", "study_submitter_id": "S015-2", "pdc_study_id": "PDC000174" } ] } } }
Response Schema
{} ProteindataProteinDef(optional){} ProteinDefproteinGene(optional){} Genegene_namestring(optional)NCBI_gene_idinteger(optional)authoritystring(optional)descriptionstring(optional)organismstring(optional)chromosomestring(optional)locusstring(optional)proteinsstring(optional)assaysstring(optional)spectral_countsarray[spectralCountsDesc](optional){} spectralCountsDescproject_submitter_idstring(optional)project_idstring(optional)plexstring(optional)spectral_countnumber(optional)distinct_peptidenumber(optional)unshared_peptidenumber(optional)study_idstring(optional)study_submitter_idnumber(optional)pdc_study_idnumber(optional)
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Returns quant data matrix for a PDC Study ID
get ?query={ quantDataMatrix(pdc_study_id: "{pdc_study_id}" data_type: "{data_type}" acceptDUA: {acceptDUA}) }
Returns quant data matrix for a PDC Study ID.
Fields:- pdc_study_id: PDC Study ID, example: PDC000127
- data_type: Data type, example: log2_ratio/unshared_log2_ratio
- acceptDUA: Accept DUA , example: true/false
?query= { quantDataMatrix(study_id: '{study_id}' data_type: '{data_type}' acceptDUA: {acceptDUA}) }
Fields:- study_id: Study ID, example: dbe94609-1fb3-11e9-b7f8-0a80fada099c
- data_type: Data type, example: log2_ratio/unshared_log2_ratio
- acceptDUA: Accept DUA , example: true/false
Please click here to know more on how to test this API.Response Sample
{ "data": { "quantDataMatrix": [ { "Gene/Aliquot": "string" } ] } }
Response Schema
{} quantDataMatrixdataquantDataMatrixDef(optional){} quantDataMatrixDefquantDataMatrixarray[quantDataMatrixDesc](optional){} quantDataMatrixDescGene/Aliquotstring(optional)
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Show samples
Gets the following PDC metrics.
Fields:- programs
- projects
- studies
- cases
- files
- data_size_TB
Response Sample
{ "data": { "getPDCMetrics": [ { "programs": 6, "projects": 13, "studies": 75, "cases": 2419, "files": 31172, "data_size_TB": 30 } ] } }
Response Schema
{} getPDCMetricsdatagetPDCMetricsDef(optional){} getPDCMetricsDefgetPDCMetricsarray[getPDCMetricsDesc](optional){} getPDCMetricsDescprogramsinteger(optional)projectsinteger(optional)studiesinteger(optional)casesinteger(optional)filesinteger(optional)data_size_TBinteger(optional)
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Gets PDC statistics per program
get ?query={dataStatsPerProgram {program_id program_submitter_id name project_count study_count data_file_count data_size_TB}}
Gets the following PDC statistics.
Fields:- program_id
- program_submitter_id
- name
- project_count
- study_count
- data_file_count
- data_size_TB
Response Sample
{ "data": { "dataStatsPerProgram": [ { "program_id": "10251935-5540-11e8-b664-00a098d917f8", "program_submitter_id": "Georgetown Proteomics Research Program", "name": "Georgetown Proteomics Research Program", "project_count": 13, "study_count": 101, "data_file_count": 31172, "data_size_TB": 29 } ] } }
Response Schema
{} dataStatsPerProgramdatadataStatsPerProgramDef(optional){} dataStatsPerProgramDefdataStatsPerProgramarray[dataStatsPerProgramDesc](optional){} dataStatsPerProgramDescprogram_idstring(optional)program_submitter_idstring(optional)namestring(optional)project_countinteger(optional)study_countinteger(optional)data_file_countinteger(optional)data_size_TBinteger(optional)
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Returns biospecimen details per study
get ?query={ biospecimenPerStudy (pdc_study_id: "{pdc_study_id}"){ aliquot_id sample_id case_id aliquot_submitter_id sample_submitter_id case_submitter_id aliquot_status case_status sample_status project_name sample_type disease_type primary_site pool taxon externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location }} }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000127)
Fields:- aliquot_id
- sample_id
- case_id
- aliquot_submitter_id
- sample_submitter_id
- case_submitter_id
- aliquot_status
- case_status
- sample_status
- project_name
- sample_type
- disease_type
- primary_site
- pool
- taxon
- externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location }
Response Sample
{ "data": { "biospecimenPerStudy": [ { "aliquot_id": "bd34fbb3-2053-11e9-b7f8-0a80fada099c", "sample_id": "b72322c6-204c-11e9-b7f8-0a80fada099c", "case_id": "dae8930e-1fb8-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0026410003", "sample_submitter_id": "C3L-00791-01", "case_submitter_id": "C3L-00791", "aliquot_status": "Qualified", "case_status": "Qualified", "sample_status": "Qualified", "project_name": "CPTAC3 Discovery", "sample_type": "Primary Tumor", "disease_type": "Clear Cell Renal Cell Carcinoma", "primary_site": "Kidney", "pool": "No", "taxon": "Homo sapiens", "externalReferences": [ { "external_reference_id": "ad9a7ce1-9f9e-4092-8eae-493297289022", "reference_resource_shortname": "GDC", "reference_resource_name": "Genomic Data Commons", "reference_entity_location": "https://portal.gdc.cancer.gov/cases/ad9a7ce1-9f9e-4092-8eae-493297289022" } ] } ] } }
Response Schema
{} biospecimenPerStudydatabiospecimenPerStudyDef(optional){} biospecimenPerStudyDefbiospecimenPerStudyarray[biospecimenPerStudyDesc](optional){} biospecimenPerStudyDescaliquot_idstring(optional)sample_idstring(optional)case_idstring(optional)aliquot_submitter_idstring(optional)sample_submitter_idstring(optional)case_submitter_idstring(optional)aliquot_statusstring(optional)case_statusstring(optional)sample_statusstring(optional)project_namestring(optional)sample_typestring(optional)disease_typestring(optional)primary_sitestring(optional)poolstring(optional)taxonstring(optional)externalReferencesarray[ExternalReferencesBipspecimen](optional){} ExternalReferencesBipspecimenexternal_reference_idstring(optional)reference_resource_shortnamestring(optional)reference_resource_namestring(optional)reference_entity_locationstring(optional)
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Gets protocols per Study
get ?query={ protocolPerStudy(study_submitter_id: "{study_submitter_id}"){ protocol_id protocol_submitter_id study_id pdc_study_id study_submitter_id program_id program_submitter_id protocol_name protocol_date document_name quantitation_strategy experiment_type label_free_quantitation labeled_quantitation isobaric_labeling_reagent reporter_ion_ms_level starting_amount starting_amount_uom digestion_reagent alkylation_reagent enrichment_strategy enrichment chromatography_dimensions_count one_d_chromatography_type two_d_chromatography_type fractions_analyzed_count column_type amount_on_column amount_on_column_uom column_length column_length_uom column_inner_diameter column_inner_diameter_uom particle_size particle_size_uom particle_type gradient_length gradient_length_uom instrument_make instrument_model dissociation_type ms1_resolution ms2_resolution dda_topn normalized_collision_energy acquistion_type dia_multiplexing dia_ims analytical_technique chromatography_instrument_make chromatography_instrument_model polarity reconstitution_solvent reconstitution_volume reconstitution_volume_uom internal_standards extraction_method ionization_mode } }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000127)
Fields:- protocol_id
- protocol_submitter_id
- study_id
- pdc_study_id
- study_submitter_id
- program_id
- program_submitter_id
- protocol_name
- protocol_date
- document_name
- quantitation_strategy
- experiment_type
- label_free_quantitation
- labeled_quantitation
- isobaric_labeling_reagent
- reporter_ion_ms_level
- starting_amount
- starting_amount_uom
- digestion_reagent
- alkylation_reagent
- enrichment_strategy
- enrichment
- chromatography_dimensions_count
- one_d_chromatography_type
- two_d_chromatography_type
- fractions_analyzed_count
- column_type
- amount_on_column
- amount_on_column_uom
- column_length
- column_length_uom
- column_inner_diameter
- column_inner_diameter_uom
- particle_size
- particle_size_uom
- particle_type
- gradient_length
- gradient_length_uom
- instrument_make
- instrument_model
- dissociation_type
- ms1_resolution
- ms2_resolution
- dda_topn
- normalized_collision_energy
- acquistion_type
- dia_multiplexing
- dia_ims
- analytical_technique
- chromatography_instrument_make
- chromatography_instrument_model
- polarity
- reconstitution_solvent
- reconstitution_volume
- reconstitution_volume_uom
- internal_standards
- extraction_method
- ionization_mode
Response Sample
{ "data": { "protocolPerStudy": [ { "protocol_id": "1c06aff5-3b26-11e9-9a07-0a80fada099c", "protocol_submitter_id": "P-S015-2", "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8", "pdc_study_id": "PDC000174", "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2", "program_id": "10251935-5540-11e8-b664-00a098d917f8", "program_submitter_id": "CPTAC", "protocol_name": "TCGA_Breast_Cancer_Phosphoproteome", "protocol_date": "2013-02-02", "document_name": " ", "quantitation_strategy": "Isobaric label quantitation", "experiment_type": "iTRAQ4", "label_free_quantitation": " ", "labeled_quantitation": "iTRAQ quantitation", "isobaric_labeling_reagent": "iTRAQ", "reporter_ion_ms_level": "2", "starting_amount": "4.00", "starting_amount_uom": "mg", "digestion_reagent": "Lys-C/Trypsin", "alkylation_reagent": "Iodoacetamide", "enrichment_strategy": "Phosphoproteome", "enrichment": "Phosphopeptide enrichment with immobilized metal affinity chromatography (NiNTA beads stripped with EDTA and loaded with FeCl3; Qiagen)", "chromatography_dimensions_count": "2", "one_d_chromatography_type": "bRPLC (pH 10)", "two_d_chromatography_type": "RPLC", "fractions_analyzed_count": "13", "column_type": "New Objective; PicoFrit SELF/P", "amount_on_column": " ", "amount_on_column_uom": " ", "column_length": "20", "column_length_uom": "cm", "column_inner_diameter": "75", "column_inner_diameter_uom": "µm", "particle_size": "1.9", "particle_size_uom": "µm", "particle_type": "Dr Maisch GmbH; ReproSil-Pur 120 C18-AQ; 1.9 um", "gradient_length": "110", "gradient_length_uom": "min", "instrument_make": "Thermo Scientific", "instrument_model": "Q Exactive", "dissociation_type": "HCD", "ms1_resolution": "70000", "ms2_resolution": "17500", "dda_topn": "Top12", "normalized_collision_energy": "28%", "acquistion_type": "DDA", "dia_multiplexing": "N/A", "dia_ims": "N/A", "analytical_technique": "N/A", "chromatography_instrument_make": "N/A", "chromatography_instrument_model": "N/A", "polarity": "N/A", "reconstitution_solvent": "N/A", "reconstitution_volume": "N/A", "reconstitution_volume_uom": "N/A", "internal_standards": "N/A", "extraction_method": "N/A", "ionization_mode": "N/A" } ] } }
Response Schema
{} protocolPerStudydataprotocolPerStudyDef(optional){} protocolPerStudyDefprotocolPerStudyarray[protocolPerStudyDesc](optional){} protocolPerStudyDescprotocol_idstring(optional)protocol_submitter_idstring(optional)study_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)program_idstring(optional)program_submitter_idstring(optional)protocol_namestring(optional)protocol_datestring(optional)document_namestring(optional)quantitation_strategystring(optional)experiment_typestring(optional)label_free_quantitationstring(optional)labeled_quantitationstring(optional)isobaric_labeling_reagentstring(optional)reporter_ion_ms_levelstring(optional)starting_amountstring(optional)starting_amount_uomstring(optional)digestion_reagentstring(optional)alkylation_reagentstring(optional)enrichment_strategystring(optional)enrichmentstring(optional)chromatography_dimensions_countstring(optional)one_d_chromatography_typestring(optional)two_d_chromatography_typestring(optional)fractions_analyzed_countstring(optional)column_typestring(optional)amount_on_columnstring(optional)amount_on_column_uomstring(optional)column_lengthstring(optional)column_length_uomstring(optional)column_inner_diameterstring(optional)column_inner_diameter_uomstring(optional)particle_sizestring(optional)particle_size_uomstring(optional)particle_typestring(optional)gradient_lengthstring(optional)gradient_length_uomstring(optional)instrument_makestring(optional)instrument_modelstring(optional)dissociation_typestring(optional)ms1_resolutionstring(optional)ms2_resolutionstring(optional)dda_topnstring(optional)normalized_collision_energystring(optional)acquistion_typestring(optional)dia_multiplexingstring(optional)dia_imsstring(optional)analytical_techniquestring(optional)chromatography_instrument_makestring(optional)chromatography_instrument_modelstring(optional)polaritystring(optional)reconstitution_solventstring(optional)reconstitution_volumestring(optional)reconstitution_volume_uomstring(optional)internal_standardsstring(optional)extraction_methodstring(optional)ionization_modestring(optional)
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Find Entity References for a Study or a Case
get ?query={ pdcEntityReference(entity_type:"{entity_type}", entity_id: "{entity_id}", reference_type: "{reference_type}") { reference_id entity_type entity_id reference_type reference_entity_type reference_entity_alias reference_resource_name reference_resource_shortname reference_entity_location } }
Input Parameters (multiple parameters can be passed in one call):
- entity_type (example: study or case)
- entity_id (must be the id of an object of the entity_type entered. example: dbe94609-1fb3-11e9-b7f8-0a80fada099c)
- reference_type (example: internal/external)
Fields:- pdcEntityReference
Response Sample
{ "data": { "pdcEntityReference": [ { "reference_id": "25b2ff66-88bc-11ea-bc9a-0a16d369a41f", "entity_type": "study", "entity_id": "dbe94609-1fb3-11e9-b7f8-0a80fada099c", "reference_type": "external", "reference_entity_type": "study", "reference_entity_alias": "S044", "reference_resource_name": "Clinical Proteomic Tumor Analysis Consortium", "reference_resource_shortname": "CPTAC", "reference_entity_location": "https://cptac-data-portal.georgetown.edu/cptac/s/S044\r" } ] } }
Response Schema
{} pdcEntityReferencedatapdcEntityReferenceDef(optional){} pdcEntityReferenceDefpdcEntityReferencearray[pdcEntityReferenceDetails](optional){} pdcEntityReferenceDetailsreference_idstring(optional)entity_typestring(optional)entity_idstring(optional)reference_typestring(optional)reference_entity_typestring(optional)reference_entity_aliasstring(optional)reference_resource_namestring(optional)reference_resource_shortnamestring(optional)reference_entity_locationstring(optional)
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Find Entity References
get ?query={ reference(entity_type:"{entity_type}", entity_id: "{entity_id}", reference_type: "{reference_type}") { reference_id entity_type entity_id reference_type reference_entity_type reference_entity_alias reference_resource_name reference_resource_shortname reference_entity_location } }
Input Parameters (multiple parameters can be passed in one call):
- entity_type (example: diagnosis)
- entity_id (must be the id of an object of the entity_type entered. example: d0913803-ff5e-11e9-9a07-0a80fada099c)
- reference_type (example: internal)
Fields:- reference
Response Sample
{ "data": { "reference": [ { "reference_id": "25b2ff66-88bc-11ea-bc9a-0a16d369a41f", "entity_type": "diagnosis", "entity_id": "d0913803-ff5e-11e9-9a07-0a80fada099c", "reference_type": "internal", "reference_entity_type": "sample", "reference_entity_alias": "7316-496", "reference_resource_name": "Proteomic Data Commons", "reference_resource_shortname": "PDC", "reference_entity_location": "string" } ] } }
Response Schema
{} referencedatareferenceDef(optional){} referenceDefreferencearray[referenceDetails](optional){} referenceDetailsreference_idstring(optional)entity_typestring(optional)entity_idstring(optional)reference_typestring(optional)reference_entity_typestring(optional)reference_entity_aliasstring(optional)reference_resource_namestring(optional)reference_resource_shortnamestring(optional)reference_entity_locationstring(optional)
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Get available Tissue Sites
get ?query={tissueSitesAvailable { tissue_or_organ_of_origin project_id project_submitter_id cases_count }}
Input Parameters (multiple parameters can be passed in one call):
- tissue_or_organ_of_origin (example: Breast)
- project_submitter_id (example: CPTAC-2)
- project_id (example: d78374f9-5fd5-4776-aa41-b1fe7ef338ab)
Fields:- tissue_or_organ_of_origin:Text term that describes the anatomic site of the tumor or disease. caDSR: 3427536, example: Breast
- project_id
- project_submitter_id
- cases_count
Response Sample
{ "data": { "tissueSitesAvailable": [ { "tissue_or_organ_of_origin": "Breast", "project_id": "d78374f9-5fd5-4776-aa41-b1fe7ef338ab", "project_submitter_id": "CPTAC-2", "cases_count": 119 } ] } }
Response Schema
{} tissueSitesAvailabledatatissueSitesAvailableDef(optional){} tissueSitesAvailableDeftissueSitesAvailablearray[tissueSitesAvailableDesc](optional){} tissueSitesAvailableDesctissue_or_organ_of_originstring(optional)project_idstring(optional)project_submitter_idstring(optional)cases_countnumber(optional)
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Get available publications
get ?query={getPaginatedPublications(offset: 0, limit: 50) {total uiPublication {publication_id pubmed_id doi author title journal journal_url year abstract citation studies {pdc_study_id submitter_id_name} disease_types}pagination {count sort from page total pages size}}}
Input Parameters (multiple parameters can be passed in one call):
- disease_type (example: Colon Adenocarcinoma)
- year (example: 2015)
- pubmed_id (example: 26110064)
- offset (required for pagination, example: 0)
- limit (required for pagination, example: 10)
Fields:- publication_id
- pubmed_id
- doi
- author
- title
- journal
- journal_url
- year
- abstract
- citation
- studies
- disease_types
Response Sample
{ "data": { "getPaginatedPublications": { "total": "44", "uiPublication": [ { "publication_id": "18a56fbd-10d5-11e9-afb9-0a9c39d33490", "pubmed_id": "25730263", "doi": "10.1038/nm.3807", "author": "Guo, T.; Kouvonen, P.; Koh, C. C.; Gillet, L. C.; Wolski, W. E.; Röst, H. L....", "title": "Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps", "journal": "Nat Med", "journal_url": "https://www.nature.com/articles/nm.3807", "year": "2015", "abstract": "Clinical specimens are each inherently unique, limited and nonrenewable....", "citation": "uo, T., Kouvonen, P., Koh, C.C., et al. (2015)....", "studies": [ { "pdc_study_id": "PDC000152", "submitter_id_name": "PCT SWATH Kidney" } ], "disease_types": " [Clear Cell Renal Cell Carcinoma, Papillary Renal Cell Carcinoma, Chromophobe Renal Cell Carcinoma]" } ], "pagination": { "count": "10", "sort": "string", "from": "0", "page": "1", "total": "10", "pages": "1", "size": "10" } } } }
Response Schema
{} getPaginatedPublicationsdatagetPaginatedPublicationsDef(optional){} getPaginatedPublicationsDefgetPaginatedPublicationsgetPaginatedPublicationsDesc(optional){} getPaginatedPublicationsDesctotalnumber(optional)uiPublicationarray[uiPublication](optional)paginationPagination(optional){} uiPublicationpublication_idstring(optional)pubmed_idstring(optional)doinumber(optional)authorstring(optional)titlestring(optional)journalstring(optional)journal_urlstring(optional)yearstring(optional)abstractstring(optional)citationstring(optional)studiesarray[pubStudies](optional)disease_typesstring(optional){} Paginationcountintegersortstring(optional)fromintegerpageintegertotalintegerpagesintegersizeinteger{} pubStudiespdc_study_idstring(optional)submitter_id_namestring(optional)
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Gets experimental design for a PDC Study ID
get ?query={ studyExperimentalDesign (pdc_study_id: "{pdc_study_id}"){ pdc_study_id, study_run_metadata_id, study_run_metadata_submitter_id, study_id, study_submitter_id, analyte, acquisition_type, polarity, experiment_type, plex_dataset_name, experiment_number, number_of_fractions, label_free{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_113{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_114{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_115{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_116{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_117{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_118{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_119{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, itraq_121{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_126{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_127n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_127c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_128n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_128c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_129n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_129c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_130n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_130c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_131{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_131c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_132n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_132c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_133n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_133c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_134n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_134c{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id}, tmt_135n{aliquot_id, aliquot_run_metadata_id, aliquot_submitter_id} } }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- pdc_study_id
- study_run_metadata_id
- study_run_metadata_submitter_id
- study_id
- study_submitter_id
- analyte
- acquisition_type
- polarity
- experiment_type
- plex_dataset_name
- experiment_number
- number_of_fractions
- label_free
- itraq_113
- itraq_114
- itraq_115
- itraq_116
- itraq_117
- itraq_118
- itraq_119
- itraq_121
- tmt_126
- tmt_127n
- tmt_127c
- tmt_128n
- tmt_128c
- tmt_129n
- tmt_129c
- tmt_130n
- tmt_130c
- tmt_131
- tmt_131c
- tmt_132n
- tmt_132c
- tmt_133n
- tmt_133c
- tmt_134n
- tmt_134c
- tmt_135n
Response Sample
{ "data": { "studyExperimentalDesign": [ { "pdc_study_id": "PDC000127", "study_run_metadata_id": "de9ebff4-2074-11e9-b7f8-0a80fada099c", "study_run_metadata_submitter_id": "S044-1-1", "study_id": "dbe94609-1fb3-11e9-b7f8-0a80fada099c", "study_submitter_id": "S044-1", "analyte": "Proteome", "acquisition_type": "DDA", "polarity": "Negative", "experiment_type": "TMT10", "plex_dataset_name": "01CPTAC_CCRCC_Proteome_JHU_20171007", "experiment_number": "1", "number_of_fractions": "25", "label_free": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_113": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_114": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_115": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_116": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_117": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_118": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_119": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "itraq_121": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_126": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_127n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_127c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_128n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_128c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_129n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_129c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_130n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_130c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_131": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_131c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_132n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_132c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_133n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_133c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_134n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_134c": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ], "tmt_135n": [ { "aliquot_id": "f02c5363-2053-11e9-b7f8-0a80fada099c", "aliquot_run_metadata_id": "f663550c-207a-11e9-b7f8-0a80fada099c", "aliquot_submitter_id": "CPT0079430001" } ] } ] } }
Response Schema
{} studyExperimentalDesigndatastudyExperimentalDesignDef(optional){} studyExperimentalDesignDefstudyExperimentalDesignarray[studyExperimentalDesignDesc](optional){} studyExperimentalDesignDescpdc_study_idstring(optional)study_run_metadata_idstring(optional)study_run_metadata_submitter_idstring(optional)study_idstring(optional)study_submitter_idstring(optional)analytestring(optional)acquisition_typestring(optional)polaritystring(optional)experiment_typestring(optional)plex_dataset_namestring(optional)experiment_numberstring(optional)number_of_fractionsstring(optional)label_freearray[labelAliguots](optional)itraq_113array[labelAliguots](optional)itraq_114array[labelAliguots](optional)itraq_115array[labelAliguots](optional)itraq_116array[labelAliguots](optional)itraq_117array[labelAliguots](optional)itraq_118array[labelAliguots](optional)itraq_119array[labelAliguots](optional)itraq_121array[labelAliguots](optional)tmt_126array[labelAliguots](optional)tmt_127narray[labelAliguots](optional)tmt_127carray[labelAliguots](optional)tmt_128narray[labelAliguots](optional)tmt_128carray[labelAliguots](optional)tmt_129narray[labelAliguots](optional)tmt_129carray[labelAliguots](optional)tmt_130narray[labelAliguots](optional)tmt_130carray[labelAliguots](optional)tmt_131array[labelAliguots](optional)tmt_131carray[labelAliguots](optional)tmt_132narray[labelAliguots](optional)tmt_132carray[labelAliguots](optional)tmt_133narray[labelAliguots](optional)tmt_133carray[labelAliguots](optional)tmt_134narray[labelAliguots](optional)tmt_134carray[labelAliguots](optional)tmt_135narray[labelAliguots](optional){} labelAliguotsaliquot_idstring(optional)aliquot_run_metadata_idstring(optional)aliquot_submitter_idstring(optional)
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Find experimental metadata for a study
get ?query={ experimentalMetadata(study_submitter_id: "{study_submitter_id}"){ experiment_type analytical_fraction instrument study_run_metadata { study_run_metadata_id study_run_metadata_submitter_id fraction aliquot_run_metadata { aliquot_id aliquot_submitter_id aliquot_run_metadata_id label experiment_number fraction replicate_number date alias analyte} files { file_type data_category file_location} } } }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000431)
- experiment_type
- analytical_fraction
- instrument
- study_run_metadata
- files
Response Sample
{ "data": { "experimentalMetadata": [ { "experiment_type": "iTRAQ4", "analytical_fraction": "Phosphoproteome", "instrument": "Q Exactive", "study_run_metadata": [ { "study_run_metadata_id": "d9b03458-56ca-11e8-b664-00a098d917f8", "study_run_metadata_submitter_id": "S015-2-27", "fraction": "1-12, A", "aliquot_run_metadata": [ { "aliquot_id": "141959ca-6424-11e8-bcf1-0a2705229b82", "aliquot_submitter_id": "TCGA-AO-A12B-01A-41-A21V-30", "aliquot_run_metadata_id": "2384aae1-5732-11e8-b664-00a098d917f8", "label": "itraq_116", "experiment_number": "13", "fraction": "24-Jan", "replicate_number": "1", "date": "2013-02-28", "alias": "B1S6", "analyte": "Proteome" } ], "files": [ { "file_type": "Proprietary", "data_category": "Raw Mass Spectra", "file_location": "raw-files/10/30/TCGA_A2-A0YG_E2-A150_BH-A18N_117C_P_BI_20130920_H-PM_f07.raw" } ] } ] } ] } }
Response Schema
{} experimentalMetadatadataexperimentalMetadataDef(optional){} experimentalMetadataDefexperimentalMetadataarray[experimentalMetadataDesc](optional){} experimentalMetadataDescexperiment_typestring(optional)analytical_fractionstring(optional)instrumentstring(optional)study_run_metadataarray[Study_run_metadata](optional){} Study_run_metadatastudy_run_metadata_idstring(optional)study_run_metadata_submitter_idstring(optional)fractionstring(optional)aliquot_run_metadataarray[Aliquot_run_metadata](optional)filesarray[fileInformation](optional){} Aliquot_run_metadataaliquot_idstring(optional)aliquot_submitter_idstring(optional)aliquot_run_metadata_idstring(optional)labelstring(optional)experiment_numberstring(optional)fractionstring(optional)replicate_numberstring(optional)datestring(optional)aliasstring(optional)analytestring(optional){} fileInformationfile_typestring(optional)data_categorystring(optional)file_locationstring(optional)
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Returns clinical details per study
get ?query={ clinicalPerStudy(pdc_study_id: "{pdc_study_id}"){ case_id case_submitter_id status disease_type primary_site consent_type days_to_consent ethnicity gender race cause_of_death days_to_birth days_to_death year_of_birth year_of_death age_at_index premature_at_birth weeks_gestation_at_birth age_is_obfuscated cause_of_death_source occupation_duration_years country_of_residence_at_enrollment morphology primary_diagnosis site_of_resection_or_biopsy tissue_or_organ_of_origin tumor_grade tumor_stage icd_10_code synchronous_malignancy tumor_largest_dimension_diameter anaplasia_present anaplasia_present_type child_pugh_classification cog_liver_stage cog_neuroblastoma_risk_group cog_renal_stage cog_rhabdomyosarcoma_risk_group enneking_msts_grade enneking_msts_metastasis enneking_msts_stage enneking_msts_tumor_site esophageal_columnar_dysplasia_degree esophageal_columnar_metaplasia_present first_symptom_prior_to_diagnosis gastric_esophageal_junction_involvement goblet_cells_columnar_mucosa_present gross_tumor_weight inpc_grade inpc_histologic_group inrg_stage inss_stage irs_group irs_stage ishak_fibrosis_score lymph_nodes_tested medulloblastoma_molecular_classification metastasis_at_diagnosis metastasis_at_diagnosis_site mitosis_karyorrhexis_index peripancreatic_lymph_nodes_positive peripancreatic_lymph_nodes_tested supratentorial_localization tumor_confined_to_organ_of_origin tumor_focality tumor_regression_grade vascular_invasion_type wilms_tumor_histologic_subtype breslow_thickness gleason_grade_group igcccg_stage international_prognostic_index largest_extrapelvic_peritoneal_focus masaoka_stage non_nodal_regional_disease non_nodal_tumor_deposits ovarian_specimen_status ovarian_surface_involvement percent_tumor_invasion peritoneal_fluid_cytological_status primary_gleason_grade secondary_gleason_grade weiss_assessment_score adrenal_hormone ann_arbor_b_symptoms_described diagnosis_is_primary_disease eln_risk_classification figo_staging_edition_year gleason_grade_tertiary gleason_patterns_percent margin_distance margins_involved_site pregnant_at_diagnosis satellite_nodule_present sites_of_involvement tumor_depth who_cns_grade who_nte_grade exposures { exposure_id exposure_submitter_id alcohol_days_per_week alcohol_drinks_per_day alcohol_history alcohol_intensity asbestos_exposure cigarettes_per_day coal_dust_exposure environmental_tobacco_smoke_exposure pack_years_smoked radon_exposure respirable_crystalline_silica_exposure smoking_frequency time_between_waking_and_first_smoke tobacco_smoking_onset_year tobacco_smoking_quit_year tobacco_smoking_status type_of_smoke_exposure type_of_tobacco_used years_smoked age_at_onset, alcohol_type, exposure_duration, exposure_duration_years, exposure_type, marijuana_use_per_week, parent_with_radiation_exposure, secondhand_smoke_as_child, smokeless_tobacco_quit_age, tobacco_use_per_day} follow_ups {follow_up_id, follow_up_submitter_id, adverse_event, barretts_esophagus_goblet_cells_present, bmi, cause_of_response, comorbidity, comorbidity_method_of_diagnosis, days_to_adverse_event, days_to_comorbidity, days_to_follow_up, days_to_progression, days_to_progression_free, days_to_recurrence, diabetes_treatment_type, disease_response, dlco_ref_predictive_percent, ecog_performance_status, fev1_ref_post_bronch_percent, fev1_ref_pre_bronch_percent, fev1_fvc_pre_bronch_percent, fev1_fvc_post_bronch_percent, height, hepatitis_sustained_virological_response, hpv_positive_type, karnofsky_performance_status, menopause_status, pancreatitis_onset_year, progression_or_recurrence, progression_or_recurrence_anatomic_site, progression_or_recurrence_type, reflux_treatment_type, risk_factor, risk_factor_treatment, viral_hepatitis_serologies, weight, adverse_event_grade, aids_risk_factors, body_surface_area, cd4_count, cdc_hiv_risk_factors, days_to_imaging, evidence_of_recurrence_type, eye_color, haart_treatment_indicator, history_of_tumor, history_of_tumor_type, hiv_viral_load, hormonal_contraceptive_type, hormonal_contraceptive_use, hormone_replacement_therapy_type, hysterectomy_margins_involved, hysterectomy_type, imaging_result, imaging_type, immunosuppressive_treatment_type, nadir_cd4_count, pregnancy_outcome, procedures_performed, recist_targeted_regions_number, recist_targeted_regions_sum, scan_tracer_used, undescended_testis_corrected, undescended_testis_corrected_age, undescended_testis_corrected_laterality, undescended_testis_corrected_method, undescended_testis_history, undescended_testis_history_laterality} treatments { treatment_id treatment_submitter_id, days_to_treatment_end, days_to_treatment_start, initial_disease_status, regimen_or_line_of_therapy, therapeutic_agents, treatment_anatomic_site, treatment_effect, treatment_intent_type, treatment_or_therapy, treatment_outcome, treatment_type, chemo_concurrent_to_radiation, number_of_cycles, reason_treatment_ended, route_of_administration, treatment_arm, treatment_dose, treatment_dose_units, treatment_effect_indicator, treatment_frequency} samples { sample_id sample_submitter_id annotation} externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location}} }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000127)
A test call can be issued with the following parameter:Response Sample
{ "data": { "clinicalPerStudy": [ { "case_id": "f98c2cb5-63d8-11e8-bcf1-0a2705229b82", "case_submitter_id": "TCGA-C8-A131", "status": "Qualified", "ethnicity": "not hispanic or latino", "gender": "Female", "race": "asian", "days_to_birth": "-16190", "days_to_death": "0", "vital_status": "Alive", "year_of_birth": "1972", "year_of_death": "0", "age_at_index": "50", "premature_at_birth": "Yes", "weeks_gestation_at_birth": "6", "age_is_obfuscated": "true", "cause_of_death_source": "Autopsy", "occupation_duration_years": "30", "country_of_residence_at_enrollment": "Afghanistan", "morphology": "8500/3", "primary_diagnosis": "Infiltrating duct carcinoma, NOS", "site_of_resection_or_biopsy": "Breast, NOS", "tissue_or_organ_of_origin": "Breast, NOS", "tumor_grade": "Not Reported", "tumor_stage": "Stage IIIA", "icd_10_code": "null", "synchronous_malignancy": "null", "tumor_largest_dimension_diameter": "0.8", "anaplasia_present": "Yes", "anaplasia_present_type": "Diffuse", "child_pugh_classification": "A", "cog_liver_stage": "Stage I", "cog_neuroblastoma_risk_group": "High Risk", "cog_renal_stage": "Stage I", "cog_rhabdomyosarcoma_risk_group": "Low Risk", "enneking_msts_grade": "Low Grade (G1)", "enneking_msts_metastasis": "Regional or Distant Metastasis (M1)", "enneking_msts_stage": "Stage IA", "enneking_msts_tumor_site": "Extracompartmental (T2)", "esophageal_columnar_dysplasia_degree": "Indefinite for Dysplasia", "esophageal_columnar_metaplasia_present": "No", "first_symptom_prior_to_diagnosis": "Headaches", "gastric_esophageal_junction_involvement": "Yes", "goblet_cells_columnar_mucosa_present": "No", "gross_tumor_weight": "1", "inpc_grade": "Differentiating", "inpc_histologic_group": "Favorable", "inrg_stage": "L1", "inss_stage": "Stage 1", "irs_group": "Group I", "irs_stage": "1", "ishak_fibrosis_score": "1,2 - Portal Fibrosis", "lymph_nodes_tested": "1", "medulloblastoma_molecular_classification": "SHH-Activated", "metastasis_at_diagnosis": "Distant Metastasis", "metastasis_at_diagnosis_site": "Abdomen", "mitosis_karyorrhexis_index": "Low", "peripancreatic_lymph_nodes_positive": "0", "peripancreatic_lymph_nodes_tested": "1", "supratentorial_localization": "Cerebral Cortex", "tumor_confined_to_organ_of_origin": "Yes", "tumor_focality": "Unifocal", "tumor_regression_grade": "1", "vascular_invasion_type": "Extramural", "wilms_tumor_histologic_subtype": "Favorable", "breslow_thickness": "1", "gleason_grade_group": "Group 1", "igcccg_stage": "Good Prognosis", "international_prognostic_index": "Low Risk", "largest_extrapelvic_peritoneal_focus": "Macroscopic (2cm or less)", "masaoka_stage": "Stage I", "non_nodal_regional_disease": "Present", "non_nodal_tumor_deposits": "Yes", "ovarian_specimen_status": "Ovarian Capsule Intact", "ovarian_surface_involvement": "Present", "percent_tumor_invasion": "1", "peritoneal_fluid_cytological_status": "Atypical", "primary_gleason_grade": "Pattern 1", "secondary_gleason_grade": "Pattern 1", "weiss_assessment_score": "1", "adrenal_hormone": "No", "ann_arbor_b_symptoms_described": "Fever", "diagnosis_is_primary_disease": "false", "eln_risk_classification": "Favorable", "figo_staging_edition_year": "2009", "gleason_grade_tertiary": "Pattern 4", "gleason_patterns_percent": "1", "margin_distance": "1.5", "margins_involved_site": "Gerota Fascia", "pregnant_at_diagnosis": "Yes", "satellite_nodule_present": "Absent", "sites_of_involvement": "Unknown", "tumor_depth": "1.2", "who_cns_grade": "Grade I", "who_nte_grade": "G1", "exposures": [ { "exposure_id": "848b480c-0f56-11e9-a064-0a9c39d33490", "exposure_submitter_id": "C3N-00386-EX", "alcohol_days_per_week": "3", "alcohol_drinks_per_day": "2", "alcohol_history": "Yes", "alcohol_intensity": "Lifelong Non-Drinker", "asbestos_exposure": "Not Reported", "cigarettes_per_day": "5", "coal_dust_exposure": "Not Reported", "environmental_tobacco_smoke_exposure": "Not Reported", "pack_years_smoked": "52", "radon_exposure": "Not Reported", "respirable_crystalline_silica_exposure": "Not Reported", "smoking_frequency": "Not Reported", "time_between_waking_and_first_smoke": "Not Reported", "tobacco_smoking_onset_year": "1972", "tobacco_smoking_quit_year": "1992", "tobacco_smoking_status": "Not Reported", "type_of_smoke_exposure": "Smoke exposure, NOS", "type_of_tobacco_used": "pipe", "years_smoked": "20", "age_at_onset": "45", "alcohol_type": "Liquor", "exposure_duration": "Six Weeks or More", "exposure_duration_years": "15", "exposure_type": "Marijuana", "marijuana_use_per_week": "3.5", "parent_with_radiation_exposure": "Not Reported", "secondhand_smoke_as_child": "Unknown", "smokeless_tobacco_quit_age": "48", "tobacco_use_per_day": "7.5" } ], "follow_ups": [ { "follow_up_id": "d12a10c4-1075-11ec-b712-0a4e2186f121", "follow_up_submitter_id": "C3N-03662-FL", "adverse_event": "Abdominal Distension", "barretts_esophagus_goblet_cells_present": "Yes", "bmi": "1.75", "cause_of_response": "Not Reported", "comorbidity": "Adenocarcinoma", "comorbidity_method_of_diagnosis": "Histology", "days_to_adverse_event": "10", "days_to_comorbidity": "15", "days_to_follow_up": "14", "days_to_progression": "14", "days_to_progression_free": "14", "days_to_recurrence": "14", "diabetes_treatment_type": "Biguanide", "disease_response": "AJ-Adjuvant Therapy", "dlco_ref_predictive_percent": "25.0", "ecog_performance_status": "0", "fev1_ref_post_bronch_percent": "10", "fev1_ref_pre_bronch_percent": "10", "fev1_fvc_pre_bronch_percent": "10", "fev1_fvc_post_bronch_percent": "10", "height": "1.75", "hepatitis_sustained_virological_response": "Unknown", "hpv_positive_type": "16", "karnofsky_performance_status": "50", "menopause_status": "Postmenopausal", "pancreatitis_onset_year": "45", "progression_or_recurrence": "Yes", "progression_or_recurrence_anatomic_site": "Abdomen, NOS", "progression_or_recurrence_type": "Biochemical", "reflux_treatment_type": "Antacids", "risk_factor": "Alcoholic Liver Disease", "risk_factor_treatment": "Yes", "viral_hepatitis_serologies": "HBV DNA", "weight": "178.5", "adverse_event_grade": "Grade 1", "aids_risk_factors": "Coccidioidomycosis", "body_surface_area": "15", "cd4_count": "2.5", "cdc_hiv_risk_factors": "Hemophiliac", "days_to_imaging": "14", "evidence_of_recurrence_type": "Physical Examination", "eye_color": "Hazel", "haart_treatment_indicator": "No", "history_of_tumor": "No", "history_of_tumor_type": "Phenochromocytoma", "hiv_viral_load": "2.0", "hormonal_contraceptive_type": "Progestin", "hormonal_contraceptive_use": "Never Used", "hormone_replacement_therapy_type": "Estrogen only", "hysterectomy_margins_involved": "Bladder", "hysterectomy_type": "Simple Hysterectomy", "imaging_result": "Positive", "imaging_type": "MRI", "immunosuppressive_treatment_type": "Azathioprine", "nadir_cd4_count": "1.5", "pregnancy_outcome": "Live Birth", "procedures_performed": "Colonoscopy", "recist_targeted_regions_number": "2", "recist_targeted_regions_sum": "2.5", "scan_tracer_used": "Acetate", "undescended_testis_corrected": "Yes", "undescended_testis_corrected_age": "35", "undescended_testis_corrected_laterality": "Bilateral", "undescended_testis_corrected_method": "Hormones", "undescended_testis_history": "Yes", "undescended_testis_history_laterality": "Left" } ], "treatments": [ { "treatment_id": "a2518568-1adc-43fe-852f-049ad21ec2df", "treatment_submitter_id": "AP-27JZ-TR", "days_to_treatment_end": " ", "days_to_treatment_start": " ", "initial_disease_status": " ", "regimen_or_line_of_therapy": " ", "therapeutic_agents": " ", "treatment_anatomic_site": " ", "treatment_effect": " ", "treatment_intent_type": "Adjuvant", "treatment_or_therapy": " ", "treatment_outcome": " ", "treatment_type": "Radiation Therapy, NOS", "chemo_concurrent_to_radiation": " ", "number_of_cycles": " ", "reason_treatment_ended": " ", "route_of_administration": " ", "treatment_arm": " ", "treatment_dose": " ", "treatment_dose_units": " ", "treatment_effect_indicator": " ", "treatment_frequency": " " } ], "samples": [ { "sample_id": "99a4bcef-1259-11e9-afb9-0a9c39d33490", "sample_submitter_id": "C3N-00386-02", "annotation": "The sample 7316-2901 is associated with this clinical record." } ], "externalReferences": [ { "external_reference_id": "c49e3b18-fd88-48f4-8b01-300692ceb367", "reference_resource_shortname": "GDC", "reference_resource_name": "Genomic Data Commons", "reference_entity_location": "https://portal.gdc.cancer.gov/cases/c49e3b18-fd88-48f4-8b01-300692ceb367" } ] } ] } }
Response Schema
{} clinicalPerStudydataclinicalPerStudyDef(optional){} clinicalPerStudyDefclinicalPerStudyarray[clinicalPerStudyDesc](optional){} clinicalPerStudyDesccase_idstring(optional)case_submitter_idstring(optional)statusstring(optional)ethnicitystring(optional)genderstring(optional)racestring(optional)days_to_birthinteger(optional)days_to_deathinteger(optional)vital_statusstring(optional)year_of_birthinteger(optional)year_of_deathinteger(optional)age_at_indexinteger(optional)premature_at_birthstring(optional)weeks_gestation_at_birthinteger(optional)age_is_obfuscatedboolean(optional)cause_of_death_sourcestring(optional)occupation_duration_yearsinteger(optional)country_of_residence_at_enrollmentstring(optional)morphologystring(optional)primary_diagnosisstring(optional)site_of_resection_or_biopsystring(optional)tissue_or_organ_of_originstring(optional)tumor_gradestring(optional)tumor_stagestring(optional)icd_10_codestring(optional)synchronous_malignancystring(optional)tumor_largest_dimension_diameterstring(optional)anaplasia_presentstring(optional)anaplasia_present_typestring(optional)child_pugh_classificationstring(optional)cog_liver_stagestring(optional)cog_neuroblastoma_risk_groupstring(optional)cog_renal_stagestring(optional)cog_rhabdomyosarcoma_risk_groupstring(optional)enneking_msts_gradestring(optional)enneking_msts_metastasisstring(optional)enneking_msts_stagestring(optional)enneking_msts_tumor_sitestring(optional)esophageal_columnar_dysplasia_degreestring(optional)esophageal_columnar_metaplasia_presentstring(optional)first_symptom_prior_to_diagnosisstring(optional)gastric_esophageal_junction_involvementstring(optional)goblet_cells_columnar_mucosa_presentstring(optional)gross_tumor_weightinteger(optional)inpc_gradestring(optional)inpc_histologic_groupstring(optional)inrg_stagestring(optional)inss_stagestring(optional)irs_groupstring(optional)irs_stagestring(optional)ishak_fibrosis_scorestring(optional)lymph_nodes_testedinteger(optional)medulloblastoma_molecular_classificationstring(optional)metastasis_at_diagnosisstring(optional)metastasis_at_diagnosis_sitestring(optional)mitosis_karyorrhexis_indexstring(optional)peripancreatic_lymph_nodes_positivestring(optional)peripancreatic_lymph_nodes_testedinteger(optional)supratentorial_localizationstring(optional)tumor_confined_to_organ_of_originstring(optional)tumor_focalitystring(optional)tumor_regression_gradestring(optional)vascular_invasion_typestring(optional)wilms_tumor_histologic_subtypestring(optional)breslow_thicknessinteger(optional)gleason_grade_groupstring(optional)igcccg_stagestring(optional)international_prognostic_indexstring(optional)largest_extrapelvic_peritoneal_focusstring(optional)masaoka_stagestring(optional)non_nodal_regional_diseasestring(optional)non_nodal_tumor_depositsstring(optional)ovarian_specimen_statusstring(optional)ovarian_surface_involvementstring(optional)percent_tumor_invasioninteger(optional)peritoneal_fluid_cytological_statusstring(optional)primary_gleason_gradestring(optional)secondary_gleason_gradestring(optional)weiss_assessment_scorestring(optional)adrenal_hormonestring(optional)ann_arbor_b_symptoms_describedstring(optional)diagnosis_is_primary_diseasestring(optional)eln_risk_classificationstring(optional)figo_staging_edition_yearstring(optional)gleason_grade_tertiarystring(optional)gleason_patterns_percentinteger(optional)margin_distancenumber(optional)margins_involved_sitestring(optional)pregnant_at_diagnosisstring(optional)satellite_nodule_presentstring(optional)sites_of_involvementstring(optional)tumor_depthnumber(optional)who_cns_gradestring(optional)who_nte_gradestring(optional)exposuresarray[Exposure](optional)follow_upsarray[FollowUp](optional)treatmentsarray[Treatment](optional)samplesarray[SampleRef](optional)externalReferencesarray[ExternalReferencesClinical](optional){} Exposureexposure_idstring(optional)exposure_submitter_idstring(optional)alcohol_days_per_weekinteger(optional)alcohol_drinks_per_dayinteger(optional)alcohol_historystring(optional)alcohol_intensitystring(optional)asbestos_exposurestring(optional)cigarettes_per_dayinteger(optional)coal_dust_exposurestring(optional)environmental_tobacco_smoke_exposurestring(optional)pack_years_smokedinteger(optional)radon_exposurestring(optional)respirable_crystalline_silica_exposurestring(optional)smoking_frequencystring(optional)time_between_waking_and_first_smokestring(optional)tobacco_smoking_onset_yearinteger(optional)tobacco_smoking_quit_yearinteger(optional)tobacco_smoking_statusstring(optional)type_of_smoke_exposurestring(optional)type_of_tobacco_usedstring(optional)years_smokedinteger(optional)age_at_onsetinteger(optional)alcohol_typestring(optional)exposure_durationstring(optional)exposure_duration_yearsinteger(optional)exposure_typestring(optional)marijuana_use_per_weeknumber(optional)parent_with_radiation_exposurestring(optional)secondhand_smoke_as_childstring(optional)smokeless_tobacco_quit_ageinteger(optional)tobacco_use_per_daynumber(optional){} FollowUpfollow_up_idstring(optional)follow_up_submitter_idstring(optional)adverse_eventstring(optional)barretts_esophagus_goblet_cells_presentstring(optional)bmifloat(optional)cause_of_responsestring(optional)comorbiditystring(optional)comorbidity_method_of_diagnosisstring(optional)days_to_adverse_eventinteger(optional)days_to_comorbidityinteger(optional)days_to_follow_upinteger(optional)days_to_progressioninteger(optional)days_to_progression_freeinteger(optional)days_to_recurrenceinteger(optional)diabetes_treatment_typestring(optional)disease_responsestring(optional)dlco_ref_predictive_percentfloat(optional)ecog_performance_statusstring(optional)fev1_ref_post_bronch_percentfloat(optional)fev1_ref_pre_bronch_percentfloat(optional)fev1_fvc_pre_bronch_percentfloat(optional)fev1_fvc_post_bronch_percentfloat(optional)heightfloat(optional)hepatitis_sustained_virological_responsestring(optional)hpv_positive_typestring(optional)karnofsky_performance_statusstring(optional)menopause_statusstring(optional)pancreatitis_onset_yearinteger(optional)progression_or_recurrencestring(optional)progression_or_recurrence_anatomic_sitestring(optional)progression_or_recurrence_typestring(optional)reflux_treatment_typestring(optional)risk_factorstring(optional)risk_factor_treatmentstring(optional)viral_hepatitis_serologiesstring(optional)weightfloat(optional)adverse_event_gradestring(optional)aids_risk_factorsstring(optional)body_surface_areafloat(optional)cd4_countfloat(optional)cdc_hiv_risk_factorsstring(optional)days_to_imaginginteger(optional)evidence_of_recurrence_typestring(optional)eye_colorstring(optional)haart_treatment_indicatorstring(optional)history_of_tumorstring(optional)history_of_tumor_typestring(optional)hiv_viral_loadfloat(optional)hormonal_contraceptive_typestring(optional)hormonal_contraceptive_usestring(optional)hormone_replacement_therapy_typestring(optional)hysterectomy_margins_involvedstring(optional)hysterectomy_typestring(optional)imaging_resultstring(optional)imaging_typestring(optional)immunosuppressive_treatment_typestring(optional)nadir_cd4_countfloat(optional)pregnancy_outcomestring(optional)procedures_performedstring(optional)recist_targeted_regions_numberinteger(optional)recist_targeted_regions_sumfloat(optional)scan_tracer_usedstring(optional)undescended_testis_correctedstring(optional)undescended_testis_corrected_ageinteger(optional)undescended_testis_corrected_lateralitystring(optional)undescended_testis_corrected_methodstring(optional)undescended_testis_historystring(optional)undescended_testis_history_lateralitystring(optional){} Treatmenttreatment_idstring(optional)treatment_submitter_idstring(optional)days_to_treatment_endinteger(optional)days_to_treatment_startinteger(optional)initial_disease_statusstring(optional)regimen_or_line_of_therapystring(optional)therapeutic_agentsstring(optional)treatment_anatomic_sitestring(optional)treatment_effectstring(optional)treatment_intent_typestring(optional)treatment_or_therapystring(optional)treatment_outcomestring(optional)treatment_typestring(optional)chemo_concurrent_to_radiationstring(optional)number_of_cyclesinteger(optional)reason_treatment_endedstring(optional)route_of_administrationstring(optional)treatment_armstring(optional)treatment_doseinteger(optional)treatment_dose_unitsstring(optional)treatment_effect_indicatorstring(optional)treatment_frequencystring(optional){} SampleRefsample_idstring(optional)sample_submitter_idstring(optional)annotationstring(optional){} ExternalReferencesClinicalexternal_reference_idstring(optional)reference_resource_shortnamestring(optional)reference_resource_namestring(optional)reference_entity_locationstring(optional)
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Find clinical metadata for a study
get ?query={ clinicalMetadata(study_id: "{study_id}") { aliquot_id aliquot_submitter_id morphology primary_diagnosis tumor_grade tumor_stage tumor_largest_dimension_diameter} }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
- study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
- pdc_study_id (example: PDC000127)
Fields:- aliquot_id
- aliquot_submitter_id
- morphology
- primary_diagnosis
- tumor_grade
- tumor_stage
- tumor_largest_dimension_diameter
Response Sample
{ "data": { "clinicalMetadata": [ { "aliquot_id": "1c671301-d028-11ea-b1fd-0aad30af8a83", "aliquot_submitter_id": "TCGA-BH-A18U-01A-61-A21W-30", "morphology": "8500/3", "primary_diagnosis": "Infiltrating duct carcinoma, NOS", "tumor_grade": "Not Reported", "tumor_stage": "Stage IIIA", "tumor_largest_dimension_diameter": "null" } ] } }
Response Schema
{} clinicalMetadatadataclinicalMetadataDef(optional){} clinicalMetadataDefclinicalMetadataarray[clinicalMetadataDesc](optional){} clinicalMetadataDescaliquot_idstring(optional)aliquot_submitter_idstring(optional)morphologystring(optional)primary_diagnosisstring(optional)tumor_gradestring(optional)tumor_stagestring(optional)tumor_largest_dimension_diameterstring(optional)
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Gets Study details for PDC Study ID
get ?query={ study (pdc_study_id: "{pdc_study_id}") { study_id pdc_study_id study_submitter_id program_id project_id study_name study_description program_name project_name disease_type primary_site analytical_fraction experiment_type cases_count aliquots_count filesCount { data_category file_type files_count } } }
Input Parameters (multiple parameters can be passed in one call):
- study_id (example: dbe94609-1fb3-11e9-b7f8-0a80fada099c)
- study_submitter_id (example: CPTAC CCRCC Discovery Study - Proteome S044-1)
- pdc_study_id (example: PDC000127)
Fields:- study_id
- pdc_study_id
- study_submitter_id
- program_id
- project_id
- study_name
- study_description
- program_name
- project_name
- disease_type
- primary_site
- analytical_fraction
- experiment_type
- cases_count
- aliquots_count
- filesCount
Response Sample
{ "data": { "study": [ { "study_id": "dbe94609-1fb3-11e9-b7f8-0a80fada099c", "pdc_study_id": "PDC000127", "study_submitter_id": "S044-1", "program_id": "10251935-5540-11e8-b664-00a098d917f8", "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490", "study_name": "CPTAC CCRCC Discovery Study - Proteome", "study_description": "Kidney cancer is among the 10 most common cancers...", "program_name": "Clinical Proteomic Tumor Analysis Consortium", "project_name": "CPTAC3 Discovery", "disease_type": "Clear Cell Renal Cell Carcinoma;Other", "primary_site": "Kidney;N/A", "analytical_fraction": "Proteome", "experiment_type": "TMT10", "cases_count": 126, "aliquots_count": 218, "filesCount": [ { "data_category": "Other Metadata", "file_type": "Document", "files_count": 7 } ] } ] } }
Response Schema
{} studyDetailsPerStudyIDdatastudyDetailsPerStudyIDDef(optional){} studyDetailsPerStudyIDDefstudyarray[studyDetailsPerStudyIDDesc](optional){} studyDetailsPerStudyIDDescstudy_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)program_idstring(optional)project_idstring(optional)study_namestring(optional)study_descriptionstring(optional)program_namestring(optional)project_namestring(optional)disease_typestring(optional)primary_sitestring(optional)analytical_fractionstring(optional)experiment_typestring(optional)cases_countnumber(optional)aliquots_countnumber(optional)filesCountarray[fileDetailsPerStudyIDDesc](optional){} fileDetailsPerStudyIDDescdata_categorystring(optional)file_typenumber(optional)files_countnumber(optional)
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Gets Studies with version information
get ?query={ studyCatalog (acceptDUA: {acceptDUA}) { pdc_study_id versions { study_id study_submitter_id submitter_id_name study_shortname study_version is_latest_version } } }
Gets Studies with version information.
Fields:- pdc_study_id
- versions
Response Sample
{ "data": { "studyCatalog": [ { "pdc_study_id": "PDC000121", "versions": [ { "study_id": "b91a0e5f-f3a0-11ea-b1fd-0aad30af8a83", "study_submitter_id": "Prospective Breast BI Phosphoproteome v2", "submitter_id_name": "Prospective Breast BI Phosphoproteome", "study_shortname": "Prospective BRCA Phosphoproteome S039-2", "study_version": "2", "is_latest_version": "yes/no" } ] } ] } }
Response Schema
{} studyCatalogdatastudyCatalogDef(optional){} studyCatalogDefstudyCatalogarray[studyCatalogDesc](optional){} studyCatalogDescpdc_study_idstring(optional)versionsarray[versionDesc](optional){} versionDescstudy_idstring(optional)study_submitter_idstring(optional)submitter_id_namestring(optional)study_shortnamestring(optional)study_versionstring(optional)is_latest_versionstring(optional)
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Gets Studies with version information for a specific pdc_study_id
get ?query={ studyCatalog (pdc_study_id: "{pdc_study_id}" acceptDUA: {acceptDUA}) { pdc_study_id versions { study_id study_submitter_id submitter_id_name study_shortname study_version is_latest_version } } }
Gets Studies with version information for a specific pdc_study_id.
Fields:- pdc_study_id
- versions
Response Sample
{ "data": { "studyCatalog": [ { "pdc_study_id": "PDC000121", "versions": [ { "study_id": "b91a0e5f-f3a0-11ea-b1fd-0aad30af8a83", "study_submitter_id": "Prospective Breast BI Phosphoproteome v2", "submitter_id_name": "Prospective Breast BI Phosphoproteome", "study_shortname": "Prospective BRCA Phosphoproteome S039-2", "study_version": "2", "is_latest_version": "yes/no" } ] } ] } }
Response Schema
{} studyCatalogdatastudyCatalogDef(optional){} studyCatalogDefstudyCatalogarray[studyCatalogDesc](optional){} studyCatalogDescpdc_study_idstring(optional)versionsarray[versionDesc](optional){} versionDescstudy_idstring(optional)study_submitter_idstring(optional)submitter_id_namestring(optional)study_shortnamestring(optional)study_versionstring(optional)is_latest_versionstring(optional)
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Get workflow metadata
get ?query={workflowMetadata (acceptDUA: {acceptDUA}) { workflow_metadata_id study_id protocol_id workflow_metadata_submitter_id pdc_study_id study_submitter_id protocol_submitter_id cptac_study_id submitter_id_name study_submitter_name analytical_fraction experiment_type instrument refseq_database_version uniport_database_version hgnc_version raw_data_processing raw_data_conversion sequence_database_search search_database_parameters phosphosite_localization ms1_data_analysis psm_report_generation cptac_dcc_mzidentml mzidentml_refseq mzidentml_uniprot gene_to_prot cptac_galaxy_workflows cptac_galaxy_tools cdap_reports cptac_dcc_tools }}
Returns a list of workflow metadata. This API can also be used with multiple input parameters.
Fields:- workflow_metadata_id
- study_id
- protocol_id
- workflow_metadata_submitter_id
- pdc_study_id
- study_submitter_id
- protocol_submitter_id
- cptac_study_id
- submitter_id_name
- study_submitter_name
- analytical_fraction
- experiment_type
- instrument
- refseq_database_version
- uniport_database_version
- hgnc_version
- raw_data_processing
- raw_data_conversion
- sequence_database_search
- search_database_parameters
- phosphosite_localization
- ms1_data_analysis
- psm_report_generation
- cptac_dcc_mzidentml
- mzidentml_refseq
- mzidentml_uniprot
- gene_to_prot
- cptac_galaxy_workflows
- cptac_galaxy_tools
- cdap_reports
- cptac_dcc_tools
Response Sample
{ "data": { "workflowMetadata": [ { "workflow_metadata_id": "b67c62e9-5766-11e8-b664-00a098d917f8", "study_id": "b9f2ccc5-57b8-11e8-b07a-00a098d917f8", "protocol_id": "05a47af4-571e-11e8-b664-00a098d917f8", "workflow_metadata_submitter_id": "TCGA_Breast_Cancer_Proteome", "pdc_study_id": "PDC000173", "study_submitter_id": "S015-1", "protocol_submitter_id": "P-S015-1", "cptac_study_id": "S015", "submitter_id_name": "MSGF+ iTRAQ 4-plex (Thermo Q-Exactive HCD)", "study_submitter_name": "TCGA_Breast_Cancer_Proteome", "analytical_fraction": "Proteome", "experiment_type": "iTRAQ4", "instrument": "Thermo Q Exactive", "refseq_database_version": "RefSeq human build 37", "uniport_database_version": "N/A", "hgnc_version": "string", "raw_data_processing": "ReAdw4Mascot2.exe version 1.2 ConvVer 20130604a", "raw_data_conversion": "msconvert 3.0.3827", "sequence_database_search": "MSGF+ v9733", "search_database_parameters": "java –Xmx3500M –jar MSGFPlus.jar -d <file>.fasta -t 20ppm -e 1 -m (3 for QExactive, 1 for Orbitrap) -inst (1 for QExactive, 1 for Orbitrap) -ntt 1 -thread 2 -tda 1 -ti 0,1 -n 1 -maxLength 50 -mod <file>.txt", "phosphosite_localization": "string", "ms1_data_analysis": "ProMS", "psm_report_generation": "single_file_report.exe", "cptac_dcc_mzidentml": "1.2.2", "mzidentml_refseq": "r82", "mzidentml_uniprot": "2017_06", "gene_to_prot": "2017-07-20", "cptac_galaxy_workflows": "N/A", "cptac_galaxy_tools": "N/A", "cdap_reports": "N/A", "cptac_dcc_tools": "N/A" } ] } }
Response Schema
{} workflowMetadatadataworkflowMetadataDef(optional){} workflowMetadataDefworkflowMetadataarray[workflowMetadataDesc](optional){} workflowMetadataDescworkflow_metadata_idstring(optional)study_idstring(optional)protocol_idstring(optional)workflow_metadata_submitter_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)protocol_submitter_idstring(optional)cptac_study_idstring(optional)submitter_id_namestring(optional)study_submitter_namestring(optional)analytical_fractionstring(optional)experiment_typestring(optional)instrumentstring(optional)refseq_database_versionstring(optional)uniport_database_versionstring(optional)hgnc_versionstring(optional)raw_data_processingstring(optional)raw_data_conversionstring(optional)sequence_database_searchstring(optional)search_database_parametersstring(optional)phosphosite_localizationstring(optional)ms1_data_analysisstring(optional)psm_report_generationstring(optional)cptac_dcc_mzidentmlstring(optional)mzidentml_refseqstring(optional)mzidentml_uniprotstring(optional)gene_to_protstring(optional)cptac_galaxy_workflowsstring(optional)cptac_galaxy_toolsstring(optional)cdap_reportsstring(optional)cptac_dcc_toolsstring(optional)
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Get workflow metadata for a Study ID
get ?query={workflowMetadata(study_id: "{study_id}" acceptDUA: {acceptDUA}) { workflow_metadata_id study_id protocol_id workflow_metadata_submitter_id pdc_study_id study_submitter_id protocol_submitter_id cptac_study_id submitter_id_name study_submitter_name analytical_fraction experiment_type instrument refseq_database_version uniport_database_version hgnc_version raw_data_processing raw_data_conversion sequence_database_search search_database_parameters phosphosite_localization ms1_data_analysis psm_report_generation cptac_dcc_mzidentml mzidentml_refseq mzidentml_uniprot gene_to_prot cptac_galaxy_workflows cptac_galaxy_tools cdap_reports cptac_dcc_tools }}
Returns a list of workflow metadata. This API can also be used with multiple input parameters.
Fields:- workflow_metadata_id
- study_id
- protocol_id
- workflow_metadata_submitter_id
- pdc_study_id
- study_submitter_id
- protocol_submitter_id
- cptac_study_id
- submitter_id_name
- study_submitter_name
- analytical_fraction
- experiment_type
- instrument
- refseq_database_version
- uniport_database_version
- hgnc_version
- raw_data_processing
- raw_data_conversion
- sequence_database_search
- search_database_parameters
- phosphosite_localization
- ms1_data_analysis
- psm_report_generation
- cptac_dcc_mzidentml
- mzidentml_refseq
- mzidentml_uniprot
- gene_to_prot
- cptac_galaxy_workflows
- cptac_galaxy_tools
- cdap_reports
- cptac_dcc_tools
Response Sample
{ "data": { "workflowMetadata": [ { "workflow_metadata_id": "b67c62e9-5766-11e8-b664-00a098d917f8", "study_id": "b9f2ccc5-57b8-11e8-b07a-00a098d917f8", "protocol_id": "05a47af4-571e-11e8-b664-00a098d917f8", "workflow_metadata_submitter_id": "TCGA_Breast_Cancer_Proteome", "pdc_study_id": "PDC000173", "study_submitter_id": "S015-1", "protocol_submitter_id": "P-S015-1", "cptac_study_id": "S015", "submitter_id_name": "MSGF+ iTRAQ 4-plex (Thermo Q-Exactive HCD)", "study_submitter_name": "TCGA_Breast_Cancer_Proteome", "analytical_fraction": "Proteome", "experiment_type": "iTRAQ4", "instrument": "Thermo Q Exactive", "refseq_database_version": "RefSeq human build 37", "uniport_database_version": "N/A", "hgnc_version": "string", "raw_data_processing": "ReAdw4Mascot2.exe version 1.2 ConvVer 20130604a", "raw_data_conversion": "msconvert 3.0.3827", "sequence_database_search": "MSGF+ v9733", "search_database_parameters": "java –Xmx3500M –jar MSGFPlus.jar -d <file>.fasta -t 20ppm -e 1 -m (3 for QExactive, 1 for Orbitrap) -inst (1 for QExactive, 1 for Orbitrap) -ntt 1 -thread 2 -tda 1 -ti 0,1 -n 1 -maxLength 50 -mod <file>.txt", "phosphosite_localization": "string", "ms1_data_analysis": "ProMS", "psm_report_generation": "single_file_report.exe", "cptac_dcc_mzidentml": "1.2.2", "mzidentml_refseq": "r82", "mzidentml_uniprot": "2017_06", "gene_to_prot": "2017-07-20", "cptac_galaxy_workflows": "N/A", "cptac_galaxy_tools": "N/A", "cdap_reports": "N/A", "cptac_dcc_tools": "N/A" } ] } }
Response Schema
{} workflowMetadatadataworkflowMetadataDef(optional){} workflowMetadataDefworkflowMetadataarray[workflowMetadataDesc](optional){} workflowMetadataDescworkflow_metadata_idstring(optional)study_idstring(optional)protocol_idstring(optional)workflow_metadata_submitter_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)protocol_submitter_idstring(optional)cptac_study_idstring(optional)submitter_id_namestring(optional)study_submitter_namestring(optional)analytical_fractionstring(optional)experiment_typestring(optional)instrumentstring(optional)refseq_database_versionstring(optional)uniport_database_versionstring(optional)hgnc_versionstring(optional)raw_data_processingstring(optional)raw_data_conversionstring(optional)sequence_database_searchstring(optional)search_database_parametersstring(optional)phosphosite_localizationstring(optional)ms1_data_analysisstring(optional)psm_report_generationstring(optional)cptac_dcc_mzidentmlstring(optional)mzidentml_refseqstring(optional)mzidentml_uniprotstring(optional)gene_to_protstring(optional)cptac_galaxy_workflowsstring(optional)cptac_galaxy_toolsstring(optional)cdap_reportsstring(optional)cptac_dcc_toolsstring(optional)
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Get workflow metadata for a PDC Study ID
get ?query={workflowMetadata(pdc_study_id: "{pdc_study_id}" acceptDUA: {acceptDUA}) { workflow_metadata_id study_id protocol_id workflow_metadata_submitter_id pdc_study_id study_submitter_id protocol_submitter_id cptac_study_id submitter_id_name study_submitter_name analytical_fraction experiment_type instrument refseq_database_version uniport_database_version hgnc_version raw_data_processing raw_data_conversion sequence_database_search search_database_parameters phosphosite_localization ms1_data_analysis psm_report_generation cptac_dcc_mzidentml mzidentml_refseq mzidentml_uniprot gene_to_prot cptac_galaxy_workflows cptac_galaxy_tools cdap_reports cptac_dcc_tools }}
Returns a list of workflow metadata. This API can also be used with multiple input parameters.
Fields:- workflow_metadata_id
- study_id
- protocol_id
- workflow_metadata_submitter_id
- pdc_study_id
- study_submitter_id
- protocol_submitter_id
- cptac_study_id
- submitter_id_name
- study_submitter_name
- analytical_fraction
- experiment_type
- instrument
- refseq_database_version
- uniport_database_version
- hgnc_version
- raw_data_processing
- raw_data_conversion
- sequence_database_search
- search_database_parameters
- phosphosite_localization
- ms1_data_analysis
- psm_report_generation
- cptac_dcc_mzidentml
- mzidentml_refseq
- mzidentml_uniprot
- gene_to_prot
- cptac_galaxy_workflows
- cptac_galaxy_tools
- cdap_reports
- cptac_dcc_tools
Response Sample
{ "data": { "workflowMetadata": [ { "workflow_metadata_id": "b67c62e9-5766-11e8-b664-00a098d917f8", "study_id": "b9f2ccc5-57b8-11e8-b07a-00a098d917f8", "protocol_id": "05a47af4-571e-11e8-b664-00a098d917f8", "workflow_metadata_submitter_id": "TCGA_Breast_Cancer_Proteome", "pdc_study_id": "PDC000173", "study_submitter_id": "S015-1", "protocol_submitter_id": "P-S015-1", "cptac_study_id": "S015", "submitter_id_name": "MSGF+ iTRAQ 4-plex (Thermo Q-Exactive HCD)", "study_submitter_name": "TCGA_Breast_Cancer_Proteome", "analytical_fraction": "Proteome", "experiment_type": "iTRAQ4", "instrument": "Thermo Q Exactive", "refseq_database_version": "RefSeq human build 37", "uniport_database_version": "N/A", "hgnc_version": "string", "raw_data_processing": "ReAdw4Mascot2.exe version 1.2 ConvVer 20130604a", "raw_data_conversion": "msconvert 3.0.3827", "sequence_database_search": "MSGF+ v9733", "search_database_parameters": "java –Xmx3500M –jar MSGFPlus.jar -d <file>.fasta -t 20ppm -e 1 -m (3 for QExactive, 1 for Orbitrap) -inst (1 for QExactive, 1 for Orbitrap) -ntt 1 -thread 2 -tda 1 -ti 0,1 -n 1 -maxLength 50 -mod <file>.txt", "phosphosite_localization": "string", "ms1_data_analysis": "ProMS", "psm_report_generation": "single_file_report.exe", "cptac_dcc_mzidentml": "1.2.2", "mzidentml_refseq": "r82", "mzidentml_uniprot": "2017_06", "gene_to_prot": "2017-07-20", "cptac_galaxy_workflows": "N/A", "cptac_galaxy_tools": "N/A", "cdap_reports": "N/A", "cptac_dcc_tools": "N/A" } ] } }
Response Schema
{} workflowMetadatadataworkflowMetadataDef(optional){} workflowMetadataDefworkflowMetadataarray[workflowMetadataDesc](optional){} workflowMetadataDescworkflow_metadata_idstring(optional)study_idstring(optional)protocol_idstring(optional)workflow_metadata_submitter_idstring(optional)pdc_study_idstring(optional)study_submitter_idstring(optional)protocol_submitter_idstring(optional)cptac_study_idstring(optional)submitter_id_namestring(optional)study_submitter_namestring(optional)analytical_fractionstring(optional)experiment_typestring(optional)instrumentstring(optional)refseq_database_versionstring(optional)uniport_database_versionstring(optional)hgnc_versionstring(optional)raw_data_processingstring(optional)raw_data_conversionstring(optional)sequence_database_searchstring(optional)search_database_parametersstring(optional)phosphosite_localizationstring(optional)ms1_data_analysisstring(optional)psm_report_generationstring(optional)cptac_dcc_mzidentmlstring(optional)mzidentml_refseqstring(optional)mzidentml_uniprotstring(optional)gene_to_protstring(optional)cptac_galaxy_workflowsstring(optional)cptac_galaxy_toolsstring(optional)cdap_reportsstring(optional)cptac_dcc_toolsstring(optional)
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