case_centric.mapping.yaml

_size:
  enabled: true
_source:
  excludes:
  - gene.*
properties:
  available_variation_data:
    type: keyword
  case_autocomplete:
    fields:
      analyzed:
        analyzer: autocomplete_analyzed
        search_analyzer: lowercase_keyword
        type: text
      lowercase:
        analyzer: lowercase_keyword
        type: text
      prefix:
        analyzer: autocomplete_prefix
        search_analyzer: lowercase_keyword
        type: text
    type: keyword
  case_id:
    copy_to:
    - case_autocomplete
    type: keyword
  consent_type:
    type: keyword
  days_to_consent:
    type: long
  days_to_index:
    type: long
  demographic:
    properties:
      age_at_index:
        type: long
      age_is_obfuscated:
        type: keyword
      cause_of_death:
        type: keyword
      days_to_birth:
        type: long
      days_to_death:
        type: long
      demographic_id:
        type: keyword
      ethnicity:
        type: keyword
      gender:
        type: keyword
      race:
        type: keyword
      state:
        type: keyword
      submitter_id:
        type: keyword
      vital_status:
        type: keyword
      year_of_birth:
        type: long
      year_of_death:
        type: long
  diagnoses:
    properties:
      age_at_diagnosis:
        type: long
      ajcc_clinical_m:
        type: keyword
      ajcc_clinical_n:
        type: keyword
      ajcc_clinical_stage:
        type: keyword
      ajcc_clinical_t:
        type: keyword
      ajcc_pathologic_m:
        type: keyword
      ajcc_pathologic_n:
        type: keyword
      ajcc_pathologic_stage:
        type: keyword
      ajcc_pathologic_t:
        type: keyword
      ajcc_staging_system_edition:
        type: keyword
      ann_arbor_b_symptoms:
        type: keyword
      ann_arbor_clinical_stage:
        type: keyword
      ann_arbor_extranodal_involvement:
        type: keyword
      ann_arbor_pathologic_stage:
        type: keyword
      burkitt_lymphoma_clinical_variant:
        type: keyword
      cause_of_death:
        type: keyword
      circumferential_resection_margin:
        type: double
      classification_of_tumor:
        type: keyword
      cog_renal_stage:
        type: keyword
      colon_polyps_history:
        type: keyword
      days_to_diagnosis:
        type: long
      days_to_hiv_diagnosis:
        type: long
      days_to_last_follow_up:
        type: double
      days_to_last_known_disease_status:
        type: double
      days_to_new_event:
        type: long
      days_to_recurrence:
        type: double
      diagnosis_id:
        type: keyword
      esophageal_columnar_dysplasia_degree:
        type: keyword
      esophageal_columnar_metaplasia_present:
        type: keyword
      figo_stage:
        type: keyword
      figo_staging_edition_year:
        type: keyword
      gastric_esophageal_junction_involvement:
        type: keyword
      goblet_cells_columnar_mucosa_present:
        type: keyword
      hiv_positive:
        type: keyword
      hpv_positive_type:
        type: keyword
      hpv_status:
        type: keyword
      icd_10_code:
        type: keyword
      igcccg_stage:
        type: keyword
      inss_stage:
        type: keyword
      international_prognostic_index:
        type: keyword
      iss_stage:
        type: keyword
      last_known_disease_status:
        type: keyword
      laterality:
        type: keyword
      ldh_level_at_diagnosis:
        type: long
      ldh_normal_range_upper:
        type: long
      lymph_node_involved_site:
        type: keyword
      lymph_nodes_positive:
        type: long
      lymph_nodes_tested:
        type: long
      lymphatic_invasion_present:
        type: keyword
      masaoka_stage:
        type: keyword
      metastasis_at_diagnosis:
        type: keyword
      metastasis_at_diagnosis_site:
        type: keyword
      method_of_diagnosis:
        type: keyword
      micropapillary_features:
        type: keyword
      morphology:
        type: keyword
      new_event_anatomic_site:
        type: keyword
      new_event_type:
        type: keyword
      pathology_details:
        properties:
          anaplasia_present:
            type: keyword
          anaplasia_present_type:
            type: keyword
          bone_marrow_malignant_cells:
            type: keyword
          breslow_thickness:
            type: double
          circumferential_resection_margin:
            type: double
          columnar_mucosa_present:
            type: keyword
          dysplasia_degree:
            type: keyword
          dysplasia_type:
            type: keyword
          greatest_tumor_dimension:
            type: double
          gross_tumor_weight:
            type: double
          largest_extrapelvic_peritoneal_focus:
            type: keyword
          lymph_node_involved_site:
            type: keyword
          lymph_node_involvement:
            type: keyword
          lymph_nodes_positive:
            type: long
          lymph_nodes_tested:
            type: long
          lymphatic_invasion_present:
            type: keyword
          margin_status:
            type: keyword
          metaplasia_present:
            type: keyword
          morphologic_architectural_pattern:
            type: keyword
          non_nodal_regional_disease:
            type: keyword
          non_nodal_tumor_deposits:
            type: keyword
          number_proliferating_cells:
            type: long
          pathology_detail_id:
            type: keyword
          percent_tumor_invasion:
            type: double
          perineural_invasion_present:
            type: keyword
          peripancreatic_lymph_nodes_positive:
            type: keyword
          peripancreatic_lymph_nodes_tested:
            type: long
          prostatic_chips_positive_count:
            type: double
          prostatic_chips_total_count:
            type: double
          prostatic_involvement_percent:
            type: double
          state:
            type: keyword
          submitter_id:
            type: keyword
          transglottic_extension:
            type: keyword
          tumor_largest_dimension_diameter:
            type: double
          vascular_invasion_present:
            type: keyword
          vascular_invasion_type:
            type: keyword
        type: nested
      perineural_invasion_present:
        type: keyword
      peripancreatic_lymph_nodes_positive:
        type: keyword
      peripancreatic_lymph_nodes_tested:
        type: double
      pregnant_at_diagnosis:
        type: keyword
      primary_diagnosis:
        type: keyword
      primary_gleason_grade:
        type: keyword
      prior_malignancy:
        type: keyword
      prior_treatment:
        type: keyword
      progression_or_recurrence:
        type: keyword
      residual_disease:
        type: keyword
      secondary_gleason_grade:
        type: keyword
      site_of_resection_or_biopsy:
        type: keyword
      state:
        type: keyword
      submitter_id:
        type: keyword
      synchronous_malignancy:
        type: keyword
      tissue_or_organ_of_origin:
        type: keyword
      treatments:
        properties:
          chemo_concurrent_to_radiation:
            type: keyword
          days_to_treatment_end:
            type: long
          days_to_treatment_start:
            type: long
          initial_disease_status:
            type: keyword
          number_of_cycles:
            type: long
          regimen_or_line_of_therapy:
            type: keyword
          state:
            type: keyword
          submitter_id:
            type: keyword
          therapeutic_agents:
            type: keyword
          treatment_anatomic_site:
            type: keyword
          treatment_dose:
            type: long
          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
        type: nested
      tumor_grade:
        type: keyword
      tumor_largest_dimension_diameter:
        type: double
      tumor_stage:
        type: keyword
      vascular_invasion_present:
        type: keyword
      vascular_invasion_type:
        type: keyword
      year_of_diagnosis:
        type: long
    type: nested
  disease_type:
    copy_to:
    - case_autocomplete
    type: keyword
  exposures:
    properties:
      alcohol_days_per_week:
        type: double
      alcohol_history:
        type: keyword
      alcohol_intensity:
        type: keyword
      asbestos_exposure:
        type: keyword
      bmi:
        type: double
      cigarettes_per_day:
        type: double
      exposure_id:
        type: keyword
      height:
        type: double
      pack_years_smoked:
        type: double
      radon_exposure:
        type: keyword
      state:
        type: keyword
      submitter_id:
        type: keyword
      tobacco_smoking_onset_year:
        type: long
      tobacco_smoking_quit_year:
        type: long
      tobacco_smoking_status:
        type: keyword
      weight:
        type: double
      years_smoked:
        type: double
    type: nested
  family_histories:
    properties:
      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
      state:
        type: keyword
      submitter_id:
        type: keyword
    type: nested
  gene:
    properties:
      biotype:
        type: keyword
      cnv:
        properties:
          chromosome:
            type: keyword
          cnv_change:
            type: keyword
          cnv_id:
            type: keyword
          end_position:
            type: long
          gene_level_cn:
            type: boolean
          ncbi_build:
            type: keyword
          observation:
            properties:
              observation_id:
                type: keyword
              sample:
                properties:
                  tumor_sample_barcode:
                    type: keyword
                  tumor_sample_uuid:
                    type: keyword
              src_file_id:
                type: keyword
              variant_calling:
                properties:
                  variant_caller:
                    type: keyword
              variant_status:
                type: keyword
            type: nested
          start_position:
            type: long
        type: nested
      gene_id:
        type: keyword
      is_cancer_gene_census:
        type: boolean
      ssm:
        properties:
          chromosome:
            type: keyword
          clinical_annotations:
            properties:
              civic:
                properties:
                  gene_id:
                    type: keyword
                  variant_id:
                    type: keyword
          consequence:
            properties:
              consequence_id:
                type: keyword
              transcript:
                properties:
                  aa_change:
                    type: keyword
                  annotation:
                    properties:
                      amino_acids:
                        type: keyword
                      ccds:
                        type: keyword
                      cdna_position:
                        type: keyword
                      cds_end:
                        type: long
                      cds_length:
                        type: long
                      cds_position:
                        type: keyword
                      cds_start:
                        type: long
                      clin_sig:
                        type: keyword
                      codons:
                        type: keyword
                      dbsnp_rs:
                        type: keyword
                      dbsnp_val_status:
                        type: keyword
                      domains:
                        type: keyword
                      ensp:
                        type: keyword
                      existing_variation:
                        type: keyword
                      hgvsc:
                        type: keyword
                      hgvsp:
                        type: keyword
                      hgvsp_short:
                        type: keyword
                      polyphen_impact:
                        type: keyword
                      polyphen_score:
                        type: float
                      protein_position:
                        type: keyword
                      pubmed:
                        type: keyword
                      sift_impact:
                        type: keyword
                      sift_score:
                        type: float
                      swissprot:
                        type: keyword
                      transcript_id:
                        type: keyword
                      trembl:
                        type: keyword
                      uniparc:
                        type: keyword
                      vep_impact:
                        type: keyword
                  consequence_type:
                    type: keyword
                  ref_seq_accession:
                    type: keyword
                  transcript_id:
                    type: keyword
            type: nested
          cosmic_id:
            type: keyword
          end_position:
            type: long
          genomic_dna_change:
            type: keyword
          mutation_subtype:
            type: keyword
          mutation_type:
            type: keyword
          ncbi_build:
            type: keyword
          observation:
            properties:
              center:
                type: keyword
              input_bam_file:
                properties:
                  normal_bam_uuid:
                    type: keyword
                  tumor_bam_uuid:
                    type: keyword
              mutation_status:
                type: keyword
              normal_genotype:
                properties:
                  match_norm_seq_allele1:
                    type: keyword
                  match_norm_seq_allele2:
                    type: keyword
              observation_id:
                type: keyword
              read_depth:
                properties:
                  n_depth:
                    type: long
                  t_alt_count:
                    type: long
                  t_depth:
                    type: long
                  t_ref_count:
                    type: long
              sample:
                properties:
                  matched_norm_sample_barcode:
                    type: keyword
                  matched_norm_sample_uuid:
                    type: keyword
                  tumor_sample_barcode:
                    type: keyword
                  tumor_sample_uuid:
                    type: keyword
              tumor_genotype:
                properties:
                  tumor_seq_allele1:
                    type: keyword
                  tumor_seq_allele2:
                    type: keyword
              validation:
                properties:
                  tumor_validation_allele1:
                    type: keyword
                  tumor_validation_allele2:
                    type: keyword
                  validation_method:
                    type: keyword
              variant_calling:
                properties:
                  variant_caller:
                    type: keyword
                  variant_process:
                    type: keyword
            type: nested
          reference_allele:
            type: keyword
          ssm_id:
            type: keyword
          start_position:
            type: long
          tumor_allele:
            type: keyword
        type: nested
      symbol:
        type: keyword
    type: nested
  index_date:
    type: keyword
  lost_to_followup:
    type: keyword
  primary_site:
    copy_to:
    - case_autocomplete
    type: keyword
  project:
    properties:
      dbgap_accession_number:
        type: keyword
      disease_type:
        copy_to:
        - case_autocomplete
        type: keyword
      intended_release_date:
        type: keyword
      name:
        copy_to:
        - case_autocomplete
        type: keyword
      primary_site:
        copy_to:
        - case_autocomplete
        type: keyword
      program:
        properties:
          dbgap_accession_number:
            type: keyword
          name:
            type: keyword
          program_id:
            type: keyword
      project_id:
        copy_to:
        - case_autocomplete
        type: keyword
  samples:
    properties:
      sample_type:
        type: keyword
  state:
    type: keyword
  submitter_id:
    copy_to:
    - case_autocomplete
    type: keyword
  summary:
    properties:
      data_categories:
        properties:
          data_category:
            type: keyword
          file_count:
            type: long
        type: nested
      experimental_strategies:
        properties:
          experimental_strategy:
            type: keyword
          file_count:
            type: long
        type: nested
      file_count:
        type: long
      file_size:
        type: long
  tissue_source_site:
    properties:
      bcr_id:
        type: keyword
      code:
        type: keyword
      name:
        type: keyword
      project:
        type: keyword
      tissue_source_site_id:
        type: keyword