From 0a6f48d44824c0cd62b224a80fda65eeabff4381 Mon Sep 17 00:00:00 2001 From: Micky Byrnes <68259544+BenX00@users.noreply.github.com> Date: Tue, 11 Oct 2022 13:55:07 -0500 Subject: [PATCH] DEV-1267: Add missing fields to case centric model (#176) * DEV-1267: Add missing case centric fields * DEV-1267: Make samples nested --- .../case_centric/case_centric.mapping.yaml | 491 ++++++++++++++++++ 1 file changed, 491 insertions(+) diff --git a/es-models/case_centric/case_centric.mapping.yaml b/es-models/case_centric/case_centric.mapping.yaml index 4a8c834..087bc8c 100644 --- a/es-models/case_centric/case_centric.mapping.yaml +++ b/es-models/case_centric/case_centric.mapping.yaml @@ -30,6 +30,8 @@ properties: type: long days_to_index: type: long + days_to_lost_to_followup: + type: long demographic: properties: age_at_index: @@ -90,6 +92,8 @@ properties: type: keyword ann_arbor_pathologic_stage: type: keyword + best_overall_response: + type: keyword burkitt_lymphoma_clinical_variant: type: keyword cause_of_death: @@ -100,8 +104,12 @@ properties: type: keyword cog_renal_stage: type: keyword + cog_rhabdomyosarcoma_risk_group: + type: keyword colon_polyps_history: type: keyword + days_to_best_overall_response: + type: long days_to_diagnosis: type: long days_to_hiv_diagnosis: @@ -116,6 +124,8 @@ properties: type: double diagnosis_id: type: keyword + eln_risk_classification: + type: keyword esophageal_columnar_dysplasia_degree: type: keyword esophageal_columnar_metaplasia_present: @@ -142,6 +152,8 @@ properties: type: keyword international_prognostic_index: type: keyword + irs_group: + type: keyword iss_stage: type: keyword last_known_disease_status: @@ -216,6 +228,8 @@ properties: type: keyword morphologic_architectural_pattern: type: keyword + necrosis_present: + type: keyword non_nodal_regional_disease: type: keyword non_nodal_tumor_deposits: @@ -271,6 +285,8 @@ properties: type: keyword residual_disease: type: keyword + satellite_nodule_present: + type: keyword secondary_gleason_grade: type: keyword site_of_resection_or_biopsy: @@ -295,6 +311,8 @@ properties: type: keyword number_of_cycles: type: long + reason_treatment_ended: + type: keyword regimen_or_line_of_therapy: type: keyword state: @@ -320,6 +338,10 @@ properties: treatment_type: type: keyword type: nested + tumor_confined_to_organ_of_origin: + type: keyword + tumor_focality: + type: keyword tumor_grade: type: keyword tumor_largest_dimension_diameter: @@ -330,6 +352,8 @@ properties: type: keyword vascular_invasion_type: type: keyword + wilms_tumor_histologic_subtype: + type: keyword year_of_diagnosis: type: long type: nested @@ -341,6 +365,8 @@ properties: properties: alcohol_days_per_week: type: double + alcohol_drinks_per_day: + type: double alcohol_history: type: keyword alcohol_intensity: @@ -353,12 +379,18 @@ properties: type: double exposure_id: type: keyword + exposure_type: + type: keyword height: type: double pack_years_smoked: type: double + parent_with_radiation_exposure: + type: keyword radon_exposure: type: keyword + secondhand_smoke_as_child: + type: keyword state: type: keyword submitter_id: @@ -369,6 +401,10 @@ properties: type: long tobacco_smoking_status: type: keyword + type_of_smoke_exposure: + type: keyword + type_of_tobacco_used: + type: keyword weight: type: double years_smoked: @@ -388,10 +424,236 @@ properties: type: keyword relative_with_cancer_history: type: keyword + relatives_with_cancer_history_count: + type: long + submitter_id: + type: keyword + type: nested + follow_ups: + properties: + adverse_event: + type: keyword + adverse_event_grade: + type: keyword + aids_risk_factors: + type: keyword + barretts_esophagus_goblet_cells_present: + type: keyword + bmi: + type: double + body_surface_area: + type: double + cause_of_response: + type: keyword + cd4_count: + type: double + cdc_hiv_risk_factors: + type: keyword + comorbidity: + type: keyword + comorbidity_method_of_diagnosis: + type: keyword + days_to_adverse_event: + type: long + days_to_comorbidity: + type: long + days_to_follow_up: + type: long + days_to_imaging: + type: long + days_to_progression: + type: long + days_to_progression_free: + type: long + days_to_recurrence: + type: long + diabetes_treatment_type: + type: keyword + disease_response: + type: keyword + dlco_ref_predictive_percent: + type: double + ecog_performance_status: + type: keyword + evidence_of_recurrence_type: + type: keyword + eye_color: + type: keyword + fev1_fvc_post_bronch_percent: + type: double + fev1_fvc_pre_bronch_percent: + type: double + fev1_ref_post_bronch_percent: + type: double + fev1_ref_pre_bronch_percent: + type: double + follow_up_id: + type: keyword + haart_treatment_indicator: + type: keyword + height: + type: double + hepatitis_sustained_virological_response: + type: keyword + history_of_tumor: + type: keyword + history_of_tumor_type: + type: keyword + hiv_viral_load: + type: double + hormonal_contraceptive_type: + type: keyword + hormonal_contraceptive_use: + type: keyword + hormone_replacement_therapy_type: + type: keyword + hpv_positive_type: + type: keyword + hysterectomy_margins_involved: + type: keyword + hysterectomy_type: + type: keyword + imaging_result: + type: keyword + imaging_type: + type: keyword + immunosuppressive_treatment_type: + type: keyword + karnofsky_performance_status: + type: keyword + menopause_status: + type: keyword + molecular_tests: + properties: + aa_change: + type: keyword + antigen: + type: keyword + biospecimen_type: + type: keyword + biospecimen_volume: + type: double + blood_test_normal_range_lower: + type: double + blood_test_normal_range_upper: + type: double + cell_count: + type: long + chromosome: + type: keyword + clonality: + type: keyword + copy_number: + type: double + cytoband: + type: keyword + days_to_test: + type: long + exon: + type: keyword + gene_symbol: + type: keyword + histone_family: + type: keyword + histone_variant: + type: keyword + intron: + type: keyword + laboratory_test: + type: keyword + loci_abnormal_count: + type: long + loci_count: + type: long + locus: + type: keyword + mismatch_repair_mutation: + type: keyword + mitotic_count: + type: double + mitotic_total_area: + type: double + molecular_analysis_method: + type: keyword + molecular_consequence: + type: keyword + molecular_test_id: + type: keyword + pathogenicity: + type: keyword + ploidy: + type: keyword + second_exon: + type: keyword + second_gene_symbol: + type: keyword + specialized_molecular_test: + type: keyword + submitter_id: + type: keyword + test_analyte_type: + type: keyword + test_result: + type: keyword + test_units: + type: keyword + test_value: + type: double + transcript: + type: keyword + variant_origin: + type: keyword + variant_type: + type: keyword + zygosity: + type: keyword + type: nested + nadir_cd4_count: + type: double + pancreatitis_onset_year: + type: long + pregnancy_outcome: + type: keyword + procedures_performed: + type: keyword + progression_or_recurrence: + type: keyword + progression_or_recurrence_anatomic_site: + type: keyword + progression_or_recurrence_type: + type: keyword + recist_targeted_regions_number: + type: long + recist_targeted_regions_sum: + type: double + reflux_treatment_type: + type: keyword + risk_factor: + type: keyword + risk_factor_treatment: + type: keyword + scan_tracer_used: + type: keyword state: type: keyword submitter_id: type: keyword + undescended_testis_corrected: + type: keyword + undescended_testis_corrected_age: + type: long + undescended_testis_corrected_laterality: + type: keyword + undescended_testis_corrected_method: + type: keyword + undescended_testis_history: + type: keyword + undescended_testis_history_laterality: + type: keyword + viral_hepatitis_serologies: + type: keyword + weight: + type: double type: nested gene: properties: @@ -647,8 +909,237 @@ properties: type: keyword samples: properties: + biospecimen_anatomic_site: + type: keyword + biospecimen_laterality: + type: keyword + catalog_reference: + type: keyword + composition: + type: keyword + current_weight: + type: double + days_to_collection: + type: long + days_to_sample_procurement: + type: long + diagnosis_pathologically_confirmed: + type: keyword + distance_normal_to_tumor: + type: keyword + distributor_reference: + type: keyword + freezing_method: + type: keyword + growth_rate: + type: long + initial_weight: + type: double + intermediate_dimension: + type: double + is_ffpe: + type: keyword + longest_dimension: + type: double + method_of_sample_procurement: + type: keyword + oct_embedded: + type: keyword + passage_count: + type: long + pathology_report_uuid: + type: keyword + portions: + properties: + analytes: + properties: + a260_a280_ratio: + type: double + aliquots: + properties: + aliquot_id: + type: keyword + aliquot_quantity: + type: double + aliquot_volume: + type: double + amount: + type: double + analyte_type: + type: keyword + analyte_type_id: + type: keyword + center: + properties: + center_id: + type: keyword + center_type: + type: keyword + code: + type: keyword + name: + type: keyword + namespace: + type: keyword + short_name: + type: keyword + concentration: + type: double + no_matched_normal_low_pass_wgs: + type: keyword + no_matched_normal_targeted_sequencing: + type: keyword + no_matched_normal_wgs: + type: keyword + no_matched_normal_wxs: + type: keyword + selected_normal_low_pass_wgs: + type: keyword + selected_normal_targeted_sequencing: + type: keyword + selected_normal_wgs: + type: keyword + selected_normal_wxs: + type: keyword + source_center: + type: keyword + submitter_id: + type: keyword + type: nested + amount: + type: double + analyte_id: + type: keyword + analyte_quantity: + type: double + analyte_type: + type: keyword + analyte_type_id: + type: keyword + analyte_volume: + type: double + concentration: + type: double + experimental_protocol_type: + type: keyword + normal_tumor_genotype_snp_match: + type: keyword + ribosomal_rna_28s_16s_ratio: + type: double + rna_integrity_number: + type: double + spectrophotometer_method: + type: keyword + submitter_id: + type: keyword + well_number: + type: keyword + type: nested + center: + properties: + center_id: + type: keyword + center_type: + type: keyword + code: + type: keyword + name: + type: keyword + namespace: + type: keyword + short_name: + type: keyword + creation_datetime: + type: double + is_ffpe: + type: keyword + portion_id: + type: keyword + portion_number: + type: keyword + slides: + properties: + bone_marrow_malignant_cells: + type: keyword + number_proliferating_cells: + type: long + percent_eosinophil_infiltration: + type: double + percent_follicular_component: + type: double + percent_granulocyte_infiltration: + type: double + percent_inflam_infiltration: + type: double + percent_lymphocyte_infiltration: + type: double + percent_monocyte_infiltration: + type: double + percent_necrosis: + type: double + percent_neutrophil_infiltration: + type: double + percent_normal_cells: + type: double + percent_rhabdoid_features: + type: double + percent_sarcomatoid_features: + type: double + percent_stromal_cells: + type: double + percent_tumor_cells: + type: double + percent_tumor_nuclei: + type: double + prostatic_chips_positive_count: + type: double + prostatic_chips_total_count: + type: double + prostatic_involvement_percent: + type: double + section_location: + type: keyword + slide_id: + type: keyword + submitter_id: + type: keyword + tissue_microarray_coordinates: + type: keyword + type: nested + submitter_id: + type: keyword + weight: + type: double + type: nested + preservation_method: + type: keyword + sample_id: + type: keyword + sample_ordinal: + type: long sample_type: type: keyword + sample_type_id: + type: keyword + shortest_dimension: + type: double + submitter_id: + type: keyword + time_between_clamping_and_freezing: + type: double + time_between_excision_and_freezing: + type: double + tissue_collection_type: + type: keyword + tissue_type: + type: keyword + tumor_code: + type: keyword + tumor_code_id: + type: keyword + tumor_descriptor: + type: keyword + type: nested state: type: keyword submitter_id: