diff --git a/es-models/case_centric/case_centric.mapping.yaml b/es-models/case_centric/case_centric.mapping.yaml index fba1d6c..20f1e1c 100644 --- a/es-models/case_centric/case_centric.mapping.yaml +++ b/es-models/case_centric/case_centric.mapping.yaml @@ -6,6 +6,47 @@ _source: - gene.biotype - gene.is_cancer_gene_census properties: + aliquot_ids: + type: keyword + analyte_ids: + type: keyword + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested available_variation_data: type: keyword case_autocomplete: @@ -28,6 +69,8 @@ properties: type: keyword consent_type: type: keyword + created_datetime: + type: keyword days_to_consent: type: long days_to_index: @@ -42,6 +85,12 @@ properties: type: keyword cause_of_death: type: keyword + cause_of_death_source: + type: keyword + country_of_residence_at_enrollment: + type: keyword + created_datetime: + type: keyword days_to_birth: type: long days_to_death: @@ -52,20 +101,30 @@ properties: type: keyword gender: type: keyword + occupation_duration_years: + type: long + premature_at_birth: + type: keyword race: type: keyword state: type: keyword submitter_id: type: keyword + updated_datetime: + type: keyword vital_status: type: keyword + weeks_gestation_at_birth: + type: double year_of_birth: type: long year_of_death: type: long diagnoses: properties: + adrenal_hormone: + type: keyword age_at_diagnosis: type: long ajcc_clinical_m: @@ -86,30 +145,83 @@ properties: type: keyword ajcc_staging_system_edition: type: keyword + anaplasia_present: + type: keyword + anaplasia_present_type: + type: keyword ann_arbor_b_symptoms: type: keyword + ann_arbor_b_symptoms_described: + type: keyword ann_arbor_clinical_stage: type: keyword ann_arbor_extranodal_involvement: type: keyword ann_arbor_pathologic_stage: type: keyword + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested best_overall_response: type: keyword + breslow_thickness: + type: double burkitt_lymphoma_clinical_variant: type: keyword cause_of_death: type: keyword + child_pugh_classification: + type: keyword circumferential_resection_margin: type: double classification_of_tumor: type: keyword + cog_liver_stage: + type: keyword + cog_neuroblastoma_risk_group: + type: keyword cog_renal_stage: type: keyword cog_rhabdomyosarcoma_risk_group: type: keyword colon_polyps_history: type: keyword + created_datetime: + type: keyword days_to_best_overall_response: type: long days_to_diagnosis: @@ -128,6 +240,14 @@ properties: type: keyword eln_risk_classification: type: keyword + enneking_msts_grade: + type: keyword + enneking_msts_metastasis: + type: keyword + enneking_msts_stage: + type: keyword + enneking_msts_tumor_site: + type: keyword esophageal_columnar_dysplasia_degree: type: keyword esophageal_columnar_metaplasia_present: @@ -136,10 +256,22 @@ properties: type: keyword figo_staging_edition_year: type: keyword + first_symptom_prior_to_diagnosis: + type: keyword gastric_esophageal_junction_involvement: type: keyword + gleason_grade_group: + type: keyword + gleason_grade_tertiary: + type: keyword + gleason_patterns_percent: + type: long goblet_cells_columnar_mucosa_present: type: keyword + greatest_tumor_dimension: + type: long + gross_tumor_weight: + type: double hiv_positive: type: keyword hpv_positive_type: @@ -150,14 +282,26 @@ properties: type: keyword igcccg_stage: type: keyword + inpc_grade: + type: keyword + inpc_histologic_group: + type: keyword + inrg_stage: + type: keyword inss_stage: type: keyword international_prognostic_index: type: keyword irs_group: type: keyword + irs_stage: + type: keyword + ishak_fibrosis_score: + type: keyword iss_stage: type: keyword + largest_extrapelvic_peritoneal_focus: + type: keyword last_known_disease_status: type: keyword laterality: @@ -174,8 +318,14 @@ properties: type: long lymphatic_invasion_present: type: keyword + margin_distance: + type: double + margins_involved_site: + type: keyword masaoka_stage: type: keyword + medulloblastoma_molecular_classification: + type: keyword metastasis_at_diagnosis: type: keyword metastasis_at_diagnosis_site: @@ -184,14 +334,30 @@ properties: type: keyword micropapillary_features: type: keyword + mitosis_karyorrhexis_index: + type: keyword + mitotic_count: + type: long morphology: type: keyword new_event_anatomic_site: type: keyword new_event_type: type: keyword + non_nodal_regional_disease: + type: keyword + non_nodal_tumor_deposits: + type: keyword + ovarian_specimen_status: + type: keyword + ovarian_surface_involvement: + type: keyword + papillary_renal_cell_type: + type: keyword pathology_details: properties: + additional_pathology_findings: + type: keyword anaplasia_present: type: keyword anaplasia_present_type: @@ -204,6 +370,10 @@ properties: type: double columnar_mucosa_present: type: keyword + consistent_pathology_review: + type: keyword + created_datetime: + type: keyword dysplasia_degree: type: keyword dysplasia_type: @@ -230,6 +400,8 @@ properties: type: keyword morphologic_architectural_pattern: type: keyword + necrosis_percent: + type: double necrosis_present: type: keyword non_nodal_regional_disease: @@ -254,6 +426,18 @@ properties: type: double prostatic_involvement_percent: type: double + residual_tumor: + type: keyword + rhabdoid_percent: + type: double + rhabdoid_present: + type: keyword + sarcomatoid_percent: + type: double + sarcomatoid_present: + type: keyword + size_extraocular_nodule: + type: double state: type: keyword submitter_id: @@ -262,21 +446,31 @@ properties: type: keyword tumor_largest_dimension_diameter: type: double + tumor_thickness: + type: double + updated_datetime: + type: keyword vascular_invasion_present: type: keyword vascular_invasion_type: type: keyword type: nested + percent_tumor_invasion: + type: double perineural_invasion_present: type: keyword peripancreatic_lymph_nodes_positive: type: keyword peripancreatic_lymph_nodes_tested: type: double + peritoneal_fluid_cytological_status: + type: keyword pregnant_at_diagnosis: type: keyword primary_diagnosis: type: keyword + primary_disease: + type: keyword primary_gleason_grade: type: keyword prior_malignancy: @@ -293,142 +487,892 @@ properties: type: keyword site_of_resection_or_biopsy: type: keyword + sites_of_involvement: + type: keyword state: type: keyword submitter_id: type: keyword + supratentorial_localization: + type: keyword synchronous_malignancy: type: keyword tissue_or_organ_of_origin: type: keyword + transglottic_extension: + type: keyword treatments: properties: chemo_concurrent_to_radiation: type: keyword + created_datetime: + type: keyword days_to_treatment_end: type: long days_to_treatment_start: type: long initial_disease_status: type: keyword - number_of_cycles: + number_of_cycles: + type: long + reason_treatment_ended: + type: keyword + regimen_or_line_of_therapy: + type: keyword + route_of_administration: + type: keyword + state: + type: keyword + submitter_id: + type: keyword + therapeutic_agents: + type: keyword + treatment_anatomic_site: + type: keyword + treatment_arm: + type: keyword + treatment_dose: + type: long + treatment_dose_units: + type: keyword + treatment_effect: + type: keyword + treatment_effect_indicator: + type: keyword + treatment_frequency: + type: keyword + treatment_id: + type: keyword + treatment_intent_type: + type: keyword + treatment_or_therapy: + type: keyword + treatment_outcome: + type: keyword + treatment_type: + type: keyword + updated_datetime: + type: keyword + type: nested + tumor_confined_to_organ_of_origin: + type: keyword + tumor_depth: + type: double + tumor_focality: + type: keyword + tumor_grade: + type: keyword + tumor_largest_dimension_diameter: + type: double + tumor_regression_grade: + type: keyword + tumor_stage: + type: keyword + updated_datetime: + type: keyword + vascular_invasion_present: + type: keyword + vascular_invasion_type: + type: keyword + weiss_assessment_score: + type: keyword + who_cns_grade: + type: keyword + who_nte_grade: + type: keyword + wilms_tumor_histologic_subtype: + type: keyword + year_of_diagnosis: + type: long + type: nested + diagnosis_ids: + type: keyword + disease_type: + copy_to: + - case_autocomplete + type: keyword + exposures: + properties: + age_at_onset: + type: long + alcohol_days_per_week: + type: double + alcohol_drinks_per_day: + type: double + alcohol_history: + type: keyword + alcohol_intensity: + type: keyword + alcohol_type: + type: keyword + asbestos_exposure: + type: keyword + bmi: + type: double + cigarettes_per_day: + type: double + coal_dust_exposure: + type: keyword + created_datetime: + type: keyword + environmental_tobacco_smoke_exposure: + type: keyword + exposure_duration: + type: keyword + exposure_duration_years: + type: long + exposure_id: + type: keyword + exposure_type: + type: keyword + height: + type: double + marijuana_use_per_week: + type: double + pack_years_smoked: + type: double + parent_with_radiation_exposure: + type: keyword + radon_exposure: + type: keyword + respirable_crystalline_silica_exposure: + type: keyword + secondhand_smoke_as_child: + type: keyword + smokeless_tobacco_quit_age: + type: long + smoking_frequency: + type: keyword + state: + type: keyword + submitter_id: + type: keyword + time_between_waking_and_first_smoke: + type: keyword + tobacco_smoking_onset_year: + type: long + tobacco_smoking_quit_year: + type: long + tobacco_smoking_status: + type: keyword + tobacco_use_per_day: + type: double + type_of_smoke_exposure: + type: keyword + type_of_tobacco_used: + type: keyword + updated_datetime: + type: keyword + weight: + type: double + years_smoked: + type: double + type: nested + family_histories: + properties: + created_datetime: + type: keyword + family_history_id: + type: keyword + relationship_age_at_diagnosis: + type: double + relationship_gender: + type: keyword + relationship_primary_diagnosis: + type: keyword + relationship_type: + type: keyword + relative_with_cancer_history: + type: keyword + relatives_with_cancer_history_count: + type: long + state: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested + files: + properties: + access: + type: keyword + acl: + type: keyword + analysis: + properties: + analysis_id: + type: keyword + analysis_type: + type: keyword + created_datetime: + type: keyword + input_files: + properties: + access: + type: keyword + average_base_quality: + type: double + average_insert_size: + type: long + average_read_length: + type: long + channel: + type: keyword + chip_id: + type: keyword + chip_position: + type: keyword + contamination: + type: double + contamination_error: + type: double + created_datetime: + type: keyword + data_category: + type: keyword + data_format: + type: keyword + data_type: + type: keyword + error_type: + type: keyword + experimental_strategy: + type: keyword + file_id: + type: keyword + file_name: + type: keyword + file_size: + type: long + imaging_date: + type: keyword + magnification: + type: double + md5sum: + type: keyword + mean_coverage: + type: double + msi_score: + type: double + msi_status: + type: keyword + pairs_on_diff_chr: + type: long + plate_name: + type: keyword + plate_well: + type: keyword + platform: + type: keyword + proc_internal: + type: keyword + proportion_base_mismatch: + type: double + proportion_coverage_10X: + type: double + proportion_coverage_10x: + type: double + proportion_coverage_30X: + type: double + proportion_coverage_30x: + type: double + proportion_reads_duplicated: + type: double + proportion_reads_mapped: + type: double + proportion_targets_no_coverage: + type: double + read_pair_number: + type: keyword + revision: + type: double + stain_type: + type: keyword + state: + type: keyword + state_comment: + type: keyword + submitter_id: + type: keyword + total_reads: + type: long + tumor_ploidy: + type: double + tumor_purity: + type: double + updated_datetime: + type: keyword + type: nested + metadata: + properties: + read_groups: + properties: + RIN: + type: double + adapter_name: + type: keyword + adapter_sequence: + type: keyword + base_caller_name: + type: keyword + base_caller_version: + type: keyword + chipseq_antibody: + type: keyword + chipseq_target: + type: keyword + created_datetime: + type: keyword + days_to_sequencing: + type: long + experiment_name: + type: keyword + flow_cell_barcode: + type: keyword + fragment_maximum_length: + type: long + fragment_mean_length: + type: double + fragment_minimum_length: + type: long + fragment_standard_deviation_length: + type: double + fragmentation_enzyme: + type: keyword + includes_spike_ins: + type: keyword + instrument_model: + type: keyword + is_paired_end: + type: keyword + lane_number: + type: long + library_name: + type: keyword + library_preparation_kit_catalog_number: + type: keyword + library_preparation_kit_name: + type: keyword + library_preparation_kit_vendor: + type: keyword + library_preparation_kit_version: + type: keyword + library_selection: + type: keyword + library_strand: + type: keyword + library_strategy: + type: keyword + multiplex_barcode: + type: keyword + number_expect_cells: + type: long + platform: + type: keyword + read_group_id: + type: keyword + read_group_name: + type: keyword + read_group_qcs: + properties: + adapter_content: + type: keyword + basic_statistics: + type: keyword + created_datetime: + type: keyword + encoding: + type: keyword + fastq_name: + type: keyword + kmer_content: + type: keyword + overrepresented_sequences: + type: keyword + per_base_n_content: + type: keyword + per_base_sequence_content: + type: keyword + per_base_sequence_quality: + type: keyword + per_sequence_gc_content: + type: keyword + per_sequence_quality_score: + type: keyword + per_tile_sequence_quality: + type: keyword + percent_gc_content: + type: long + read_group_qc_id: + type: keyword + sequence_duplication_levels: + type: keyword + sequence_length_distribution: + type: keyword + state: + type: keyword + submitter_id: + type: keyword + total_sequences: + type: long + updated_datetime: + type: keyword + workflow_end_datetime: + type: keyword + workflow_link: + type: keyword + workflow_start_datetime: + type: keyword + workflow_type: + type: keyword + workflow_version: + type: keyword + type: nested + read_length: + type: long + rin: + type: double + sequencing_center: + type: keyword + sequencing_date: + type: keyword + single_cell_library: + type: keyword + size_selection_range: + type: keyword + spike_ins_concentration: + type: keyword + spike_ins_fasta: + type: keyword + state: + type: keyword + submitter_id: + type: keyword + target_capture_kit: + type: keyword + target_capture_kit_catalog_number: + type: keyword + target_capture_kit_name: + type: keyword + target_capture_kit_target_region: + type: keyword + target_capture_kit_vendor: + type: keyword + target_capture_kit_version: + type: keyword + to_trim_adapter_sequence: + type: keyword + updated_datetime: + type: keyword + type: nested + state: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + workflow_end_datetime: + type: keyword + workflow_link: + type: keyword + workflow_start_datetime: + type: keyword + workflow_type: + type: keyword + workflow_version: + type: keyword + archive: + properties: + archive_id: + type: keyword + created_datetime: + type: keyword + data_category: + type: keyword + data_format: + type: keyword + data_type: + type: keyword + error_type: + type: keyword + file_name: + type: keyword + file_size: + type: long + md5sum: + type: keyword + revision: + type: double + state: + type: keyword + state_comment: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + average_base_quality: + type: double + average_insert_size: + type: long + average_read_length: + type: long + center: + properties: + center_id: + type: keyword + center_type: + type: keyword + code: + type: keyword + name: + type: keyword + namespace: + type: keyword + short_name: + type: keyword + channel: + type: keyword + chip_id: + type: keyword + chip_position: + type: keyword + contamination: + type: double + contamination_error: + type: double + created_datetime: + type: keyword + data_category: + type: keyword + data_format: + type: keyword + data_type: + type: keyword + downstream_analyses: + properties: + analysis_id: + type: keyword + analysis_type: + type: keyword + created_datetime: + type: keyword + output_files: + properties: + access: + type: keyword + average_base_quality: + type: double + average_insert_size: + type: long + average_read_length: + type: long + channel: + type: keyword + chip_id: + type: keyword + chip_position: + type: keyword + contamination: + type: double + contamination_error: + type: double + created_datetime: + type: keyword + data_category: + type: keyword + data_format: + type: keyword + data_type: + type: keyword + error_type: + type: keyword + experimental_strategy: + type: keyword + file_id: + type: keyword + file_name: + type: keyword + file_size: + type: long + imaging_date: + type: keyword + magnification: + type: double + md5sum: + type: keyword + mean_coverage: + type: double + msi_score: + type: double + msi_status: + type: keyword + pairs_on_diff_chr: + type: long + plate_name: + type: keyword + plate_well: + type: keyword + platform: + type: keyword + proc_internal: + type: keyword + proportion_base_mismatch: + type: double + proportion_coverage_10X: + type: double + proportion_coverage_10x: + type: double + proportion_coverage_30X: + type: double + proportion_coverage_30x: + type: double + proportion_reads_duplicated: + type: double + proportion_reads_mapped: + type: double + proportion_targets_no_coverage: + type: double + read_pair_number: + type: keyword + revision: + type: double + stain_type: + type: keyword + state: + type: keyword + state_comment: + type: keyword + submitter_id: + type: keyword + total_reads: + type: long + tumor_ploidy: + type: double + tumor_purity: + type: double + updated_datetime: + type: keyword + type: nested + state: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + workflow_end_datetime: + type: keyword + workflow_link: + type: keyword + workflow_start_datetime: + type: keyword + workflow_type: + type: keyword + workflow_version: + type: keyword + type: nested + error_type: + type: keyword + experimental_strategy: + type: keyword + file_id: + type: keyword + file_name: + type: keyword + file_size: + type: long + imaging_date: + type: keyword + index_files: + properties: + access: + type: keyword + average_base_quality: + type: double + average_insert_size: + type: long + average_read_length: + type: long + channel: + type: keyword + chip_id: + type: keyword + chip_position: + type: keyword + contamination: + type: double + contamination_error: + type: double + created_datetime: + type: keyword + data_category: + type: keyword + data_format: + type: keyword + data_type: + type: keyword + error_type: + type: keyword + experimental_strategy: + type: keyword + file_id: + type: keyword + file_name: + type: keyword + file_size: + type: long + imaging_date: + type: keyword + magnification: + type: double + md5sum: + type: keyword + mean_coverage: + type: double + msi_score: + type: double + msi_status: + type: keyword + pairs_on_diff_chr: type: long - reason_treatment_ended: + plate_name: type: keyword - regimen_or_line_of_therapy: + plate_well: + type: keyword + platform: + type: keyword + proc_internal: + type: keyword + proportion_base_mismatch: + type: double + proportion_coverage_10X: + type: double + proportion_coverage_10x: + type: double + proportion_coverage_30X: + type: double + proportion_coverage_30x: + type: double + proportion_reads_duplicated: + type: double + proportion_reads_mapped: + type: double + proportion_targets_no_coverage: + type: double + read_pair_number: + type: keyword + revision: + type: double + stain_type: type: keyword state: type: keyword + state_comment: + type: keyword submitter_id: type: keyword - therapeutic_agents: + total_reads: + type: long + tumor_ploidy: + type: double + tumor_purity: + type: double + updated_datetime: type: keyword - treatment_anatomic_site: + type: nested + magnification: + type: double + md5sum: + type: keyword + mean_coverage: + type: double + metadata_files: + properties: + access: type: keyword - treatment_dose: + created_datetime: + type: keyword + data_category: + type: keyword + data_format: + type: keyword + data_type: + type: keyword + error_type: + type: keyword + file_id: + type: keyword + file_name: + type: keyword + file_size: type: long - treatment_frequency: + md5sum: type: keyword - treatment_id: + state: type: keyword - treatment_intent_type: + state_comment: type: keyword - treatment_or_therapy: + submitter_id: type: keyword - treatment_outcome: + type: type: keyword - treatment_type: + updated_datetime: type: keyword type: nested - tumor_confined_to_organ_of_origin: - type: keyword - tumor_focality: - type: keyword - tumor_grade: - type: keyword - tumor_largest_dimension_diameter: + msi_score: type: double - tumor_stage: + msi_status: type: keyword - vascular_invasion_present: + pairs_on_diff_chr: + type: long + plate_name: type: keyword - vascular_invasion_type: + plate_well: type: keyword - wilms_tumor_histologic_subtype: + platform: type: keyword - year_of_diagnosis: - type: long - type: nested - disease_type: - copy_to: - - case_autocomplete - type: keyword - exposures: - properties: - alcohol_days_per_week: + proc_internal: + type: keyword + proportion_base_mismatch: type: double - alcohol_drinks_per_day: + proportion_coverage_10X: type: double - alcohol_history: - type: keyword - alcohol_intensity: - type: keyword - asbestos_exposure: - type: keyword - bmi: + proportion_coverage_10x: type: double - cigarettes_per_day: + proportion_coverage_30X: type: double - exposure_id: - type: keyword - exposure_type: - type: keyword - height: + proportion_coverage_30x: type: double - pack_years_smoked: + proportion_reads_duplicated: type: double - parent_with_radiation_exposure: - type: keyword - radon_exposure: + proportion_reads_mapped: + type: double + proportion_targets_no_coverage: + type: double + read_pair_number: type: keyword - secondhand_smoke_as_child: + revision: + type: double + stain_type: type: keyword state: type: keyword - submitter_id: - type: keyword - tobacco_smoking_onset_year: - type: long - tobacco_smoking_quit_year: - type: long - tobacco_smoking_status: + state_comment: type: keyword - type_of_smoke_exposure: + submitter_id: type: keyword - type_of_tobacco_used: + tags: type: keyword - weight: - type: double - years_smoked: + total_reads: + type: long + tumor_ploidy: type: double - type: nested - family_histories: - properties: - family_history_id: - type: keyword - relationship_age_at_diagnosis: + tumor_purity: type: double - relationship_gender: - type: keyword - relationship_primary_diagnosis: - type: keyword - relationship_type: - type: keyword - relative_with_cancer_history: + type: type: keyword - relatives_with_cancer_history_count: - type: long - submitter_id: + updated_datetime: type: keyword type: nested follow_ups: @@ -455,6 +1399,8 @@ properties: type: keyword comorbidity_method_of_diagnosis: type: keyword + created_datetime: + type: keyword days_to_adverse_event: type: long days_to_comorbidity: @@ -547,6 +1493,8 @@ properties: type: keyword copy_number: type: double + created_datetime: + type: keyword cytoband: type: keyword days_to_test: @@ -591,6 +1539,8 @@ properties: type: keyword specialized_molecular_test: type: keyword + state: + type: keyword submitter_id: type: keyword test_analyte_type: @@ -603,6 +1553,8 @@ properties: type: double transcript: type: keyword + updated_datetime: + type: keyword variant_origin: type: keyword variant_type: @@ -652,6 +1604,8 @@ properties: type: keyword undescended_testis_history_laterality: type: keyword + updated_datetime: + type: keyword viral_hepatitis_serologies: type: keyword weight: @@ -875,6 +1829,8 @@ properties: type: keyword lost_to_followup: type: keyword + portion_ids: + type: keyword primary_site: copy_to: - case_autocomplete @@ -909,8 +1865,53 @@ properties: copy_to: - case_autocomplete type: keyword + releasable: + type: keyword + released: + type: keyword + state: + type: keyword + sample_ids: + type: keyword samples: properties: + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested biospecimen_anatomic_site: type: keyword biospecimen_laterality: @@ -919,6 +1920,8 @@ properties: type: keyword composition: type: keyword + created_datetime: + type: keyword current_weight: type: double days_to_collection: @@ -971,6 +1974,43 @@ properties: type: keyword analyte_type_id: type: keyword + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested center: properties: center_id: @@ -987,6 +2027,8 @@ properties: type: keyword concentration: type: double + created_datetime: + type: keyword no_matched_normal_low_pass_wgs: type: keyword no_matched_normal_targeted_sequencing: @@ -1005,8 +2047,12 @@ properties: type: keyword source_center: type: keyword + state: + type: keyword submitter_id: type: keyword + updated_datetime: + type: keyword type: nested amount: type: double @@ -1020,8 +2066,47 @@ properties: type: keyword analyte_volume: type: double + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested concentration: type: double + created_datetime: + type: keyword experimental_protocol_type: type: keyword normal_tumor_genotype_snp_match: @@ -1032,11 +2117,52 @@ properties: type: double spectrophotometer_method: type: keyword + state: + type: keyword submitter_id: type: keyword + updated_datetime: + type: keyword well_number: type: keyword type: nested + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested center: properties: center_id: @@ -1051,6 +2177,8 @@ properties: type: keyword short_name: type: keyword + created_datetime: + type: keyword creation_datetime: type: double is_ffpe: @@ -1061,8 +2189,47 @@ properties: type: keyword slides: properties: + annotations: + properties: + annotation_id: + type: keyword + case_id: + type: keyword + case_submitter_id: + type: keyword + category: + type: keyword + classification: + type: keyword + created_datetime: + type: keyword + creator: + type: keyword + entity_id: + type: keyword + entity_submitter_id: + type: keyword + entity_type: + type: keyword + legacy_created_datetime: + type: keyword + legacy_updated_datetime: + type: keyword + notes: + type: keyword + state: + type: keyword + status: + type: keyword + submitter_id: + type: keyword + updated_datetime: + type: keyword + type: nested bone_marrow_malignant_cells: type: keyword + created_datetime: + type: keyword number_proliferating_cells: type: long percent_eosinophil_infiltration: @@ -1103,13 +2270,21 @@ properties: type: keyword slide_id: type: keyword + state: + type: keyword submitter_id: type: keyword tissue_microarray_coordinates: type: keyword + updated_datetime: + type: keyword type: nested + state: + type: keyword submitter_id: type: keyword + updated_datetime: + type: keyword weight: type: double type: nested @@ -1125,6 +2300,8 @@ properties: type: keyword shortest_dimension: type: double + state: + type: keyword submitter_id: type: keyword time_between_clamping_and_freezing: @@ -1141,13 +2318,29 @@ properties: type: keyword tumor_descriptor: type: keyword + updated_datetime: + type: keyword type: nested + slide_ids: + type: keyword state: type: keyword + submitter_aliquot_ids: + type: keyword + submitter_analyte_ids: + type: keyword + submitter_diagnosis_ids: + type: keyword submitter_id: copy_to: - case_autocomplete type: keyword + submitter_portion_ids: + type: keyword + submitter_sample_ids: + type: keyword + submitter_slide_ids: + type: keyword summary: properties: data_categories: @@ -1180,3 +2373,5 @@ properties: type: keyword tissue_source_site_id: type: keyword + updated_datetime: + type: keyword diff --git a/es-models/case_centric/settings.yaml b/es-models/case_centric/settings.yaml index e4c741f..727bdae 100644 --- a/es-models/case_centric/settings.yaml +++ b/es-models/case_centric/settings.yaml @@ -22,4 +22,5 @@ analysis: type: edge_ngram index.mapping.nested_fields.limit: 100 index.mapping.nested_objects.limit: 100000000 +index.mapping.total_fields.limit: 2000 index.max_result_window: 100000000