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bento-model

A general data model for the Bento framework

Bento General Data Model

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Additional model files

Perl exposure exposure alcohol_intensity bmi cigarettes_per_day tobacco_smoking_onset_year coal_dust_exposure asbestos_exposure time_between_waking_and_first_smoke alcohol_days_per_week radon_exposure respirable_crystalline_silica_exposure tobacco_smoking_status type_of_smoke_exposure alcohol_drinks_per_day type_of_tobacco_used years_smoked exposure_node_id smoking_frequency tobacco_smoking_quit_year alcohol_history environmental_tobacco_smoke_exposure pack_years_smoked study_subject study_subject study_subject_id index_date study_subject_is_ref consent_type status pool primary_site disease_type lost_to_followup days_to_consent days_to_lost_to_followup taxon study_subject_source_id study_subject_first_name exposure->study_subject of_study_subject fraction fraction weight creation_datetime fraction_type fraction_id fraction_number sample sample necropsy_sample sample_type_id analysis_area catalog_reference tumor_tissue_area sample_anatomic_site tumor_descriptor analysis_area_percentage_glass tumor_code total_tissue_area current_weight time_between_clamping_and_freezing percentage_tumor analysis_area_percentage_stroma percentage_stroma tissue_type composition analysis_area_percentage_pigmented_tumor width_of_tumor preservation_method passage_count method_of_sample_procurement comment date_of_sample_collection days_to_sample_procurement tumor_code_id analysis_area_percentage_tumor growth_rate non_tumor_tissue_area time_between_excision_and_freezing shortest_dimension initial_weight intermediate_dimension diagnosis_pathologically_confirmed pool longest_dimension sample_id sample_is_ref sample_laterality distributor_reference days_to_collection distance_normal_to_tumor sample_type fraction->sample of_sample laboratory_procedure laboratory_procedure laboratory_procedure_target_type instrument_version laboratory_procedure_type instrument_model laboratory_procedure_id software_version software_name instrument_name reagent_description fraction->laboratory_procedure processed_by analyte analyte spectrophotometer_method normal_tumor_genotype_snp_match analyte_type analyte_type_id analyte_id well_number ribosomal_rna_28s_16s_ratio analyte_concentration analyte_quantity analyte_volume a260_a280_ratio analyte->fraction of_fraction analyte->sample of_sample analyte->laboratory_procedure processed_by file file file_name md5sum file_size file_description file_status file_type file_location file_id file_format diagnosis diagnosis perineural_invasion_present days_to_best_overall_response goblet_cells_columnar_mucosa_present anaplasia_present percent_tumor_invasion peripancreatic_lymph_nodes_tested supratentorial_localization medulloblastoma_molecular_classification ajcc_clinical_t enneking_msts_tumor_site new_event_type days_to_recurrence gross_tumor_weight largest_extrapelvic_peritoneal_focus site_of_resection_or_biopsy irs_stage esophageal_columnar_dysplasia_degree progression_free_survival_event prior_malignancy metastasis_at_diagnosis_site ajcc_pathologic_stage progression_free_survival colon_polyps_history days_to_last_follow_up inpc_grade cog_rhabdomyosarcoma_risk_group days_to_hiv_diagnosis days_to_new_event tumor_grade metastasis_at_diagnosis synchronous_malignancy residual_disease weiss_assessment_score year_of_diagnosis irs_group morphology circumferential_resection_margin micropapillary_features inss_stage classification_of_tumor cog_liver_stage concurrent_disease_type ldh_level_at_diagnosis diagnosis_id iss_stage igcccg_stage ajcc_pathologic_t cog_renal_stage treatment_data hpv_status wilms_tumor_histologic_subtype tumor_focality secondary_gleason_grade primary_gleason_grade enneking_msts_metastasis gastric_esophageal_junction_involvement ajcc_pathologic_n new_event_anatomic_site non_nodal_tumor_deposits tumor_stage primary_diagnosis ajcc_pathologic_m lymph_nodes_tested lymphatic_invasion_present vascular_invasion_present enneking_msts_stage inrg_stage mitotic_count hpv_positive_type days_to_diagnosis first_symptom_prior_to_diagnosis ldh_normal_range_upper anaplasia_present_type age_at_diagnosis ajcc_clinical_n peritoneal_fluid_cytological_status ann_arbor_pathologic_stage tumor_regression_grade international_prognostic_index ann_arbor_extranodal_involvement ovarian_specimen_status breslow_thickness ajcc_clinical_stage vascular_invasion_type lymph_nodes_positive last_known_disease_status date_of_histology_confirmation ann_arbor_b_symptoms enneking_msts_grade ishak_fibrosis_score days_to_birth pathology_report ajcc_staging_system_edition ovarian_surface_involvement ajcc_clinical_m hiv_positive tumor_confined_to_organ_of_origin esophageal_columnar_metaplasia_present prior_treatment date_of_diagnosis mitosis_karyorrhexis_index concurrent_disease child_pugh_classification peripancreatic_lymph_nodes_positive method_of_diagnosis icd_10_code follow_up_data days_to_death gleason_grade_group days_to_last_known_disease_status cog_neuroblastoma_risk_group burkitt_lymphoma_clinical_variant tumor_largest_dimension_diameter laterality tissue_or_organ_of_origin progression_or_recurrence masaoka_stage best_overall_response inpc_histologic_group figo_stage cause_of_death overall_survival non_nodal_regional_disease ann_arbor_clinical_stage file->diagnosis of_diagnosis file->sample of_sample study study index_date submission_enabled release_requested study_id state request_submission in_review primary_site end_date intended_release_date analytical_fraction study_external_url study_name date_of_approval study_type dbgap_accession_number study_short_description study_manager releasable is_legacy study_full_description embargo_date acquisition_type released study_sort_order study_acronym start_date file->study of_study file->laboratory_procedure of_laboratory_procedure project project request_submission in_review state project_short_description project_id primary_site submission_enabled release_requested index_date project_type project_sort_order date_of_approval project_manager project_full_description analytical_fraction intended_release_date end_date project_acronym dbgap_accession_number project_external_url project_name embargo_date start_date released acquisition_type is_legacy releasable file->project of_project file->study_subject of_study_subject program program program_manager date_of_approval end_date intended_release_date request_submission in_review state program_acronym program_sort_order program_full_description submission_enabled release_requested index_date released program_name start_date embargo_date sponsor program_short_description releasable is_legacy program_id program_external_url dbgap_accession_number file->program of_program diagnosis->study_subject of_study_subject institution institution institution_url institution_id institution_name therapeutic_procedure therapeutic_procedure days_to_treatment_start treatment_anatomic_site treatment_or_therapy therapeutic_procedure_id therapeutic_agents treatment_effect treatment_type treatment_outcome initial_disease_status treatment_intent_type regimen_or_line_of_therapy days_to_treatment_end therapeutic_procedure->diagnosis of_diagnosis sample->laboratory_procedure processed_by sample->study_subject of_study_subject aliquot aliquot aliquot_is_ref no_matched_normal_wxs aliquot_id no_matched_normal_wgs no_matched_normal_low_pass_wgs selected_normal_targeted_sequencing selected_normal_wgs selected_normal_low_pass_wgs selected_normal_wxs no_matched_normal_targeted_sequencing aliquot_concentration aliquot_quantity status aliquot_volume pool aliquot->analyte of_analyte aliquot->laboratory_procedure processed_by cross_reference_database cross_reference_database cross_reference_database_url cross_reference_database_name cross_reference_database_id family_medical_history family_medical_history relationship_gender relationship_primary_diagnosis relationship_age_at_diagnosis family_history_id relationship_type relative_with_cancer_history relatives_with_cancer_history_count family_medical_history->study_subject of_study_subject study->program of_program laboratory_procedure->program of_program follow_up follow_up height karnofsky_performance_status diabetes_treatment_type document_number physical_exam_performed hepatitis_sustained_virological_response fev1_fvc_pre_bronch_percent follow_up_id progression_or_recurrence fev1_fvc_post_bronch_percent days_to_progression_free contact_type viral_hepatitis_serologies treatment_since_last_contact ecog_performance_status comorbidity_method_of_diagnosis days_to_follow_up days_to_adverse_event progression_or_recurrence_anatomic_site days_to_comorbidity risk_factor_treatment adverse_event fev1_ref_post_bronch_percent reflux_treatment_type dlco_ref_predictive_percent fev1_ref_pre_bronch_percent date_of_last_contact patient_status explain_unknown_status menopause_status comorbidity weight cause_of_response progression_or_recurrence_type physical_exam_changes bmi disease_response hpv_positive_type days_to_progression pancreatitis_onset_year barretts_esophagus_goblet_cells_present days_to_recurrence risk_factor follow_up->diagnosis of_diagnosis follow_up->study_subject of_study_subject demographic_data demographic_data premature_at_birth days_to_death height gender age_is_obfuscated vital_status neutered_indicator ethnicity days_to_birth weight cause_of_death_source cause_of_death race weeks_gestation_at_birth date_of_birth breed demographic_data_id year_of_death occupation_duration_years year_of_birth age_at_index demographic_data->study_subject of_study_subject project->program of_program study_subject->cross_reference_database cross_referenced_at study_subject->study of_study study_subject->project of_project study_subject->program of_program program->institution of_institution report report report_name md5sum report_id report_format report_size report_type report_location report_description report->fraction of_fraction report->analyte of_analyte report->sample of_sample report->aliquot of_aliquot report->laboratory_procedure of_laboratory_procedure