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ctn-model

Location for Clinical Trial Node model description files and related artifacts

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ctn-model

Location for CRDC Clinical Trial Node model description files and related artifacts

Description

This repo is a workspace for development of the data model for the Cancer Research Data Commons Clinical Trial Node.

The files are created in Model Description Format and can be visualized using model-tool.

Perl genomic_report genomic_report surgical_event_id variant_report_received_date molecular_id variant_report_type total_confirmed_amois cellularity status total_amois total_confirmed_mois total_mois status_date total_variants assay assay genomic_report->assay of_assay stratification stratification planned_radiotherapy planned_chemotherapy_stratification grouped_recurrence_score tumor_size_stratification menopausal_status_stratification combined_stratification_variable case case patient_id included_in_analysis on_study_crf_submitted case_id ineligible stratification->case of_case prior_therapy prior_therapy best_response total_number_of_doses_any_therapy any_therapy date_of_last_dose agent_name agent_units_of_measure date_of_last_dose_any_therapy number_of_prior_regimens_any_therapy total_dose therapy_type date_of_first_dose treatment_performed_at_site prior_therapy_type treatment_performed_in_minimal_residual dose_schedule nonresponse_therapy_type prior_therapy->prior_therapy next enrollment enrollment date_of_registration patient_subgroup cohort_description date_of_informed_consent site_short_name registering_institution prior_therapy->enrollment at_enrollment file file file_size file_type file_locations uuid file_description file_format md5sum file_name file_status file->assay of_assay diagnosis diagnosis histological_grade date_of_diagnosis date_of_histology_confirmation tumor_size_group estrogen_receptor_status histology_cytopathology follow_up_data concurrent_disease stage_of_disease treatment_data concurrent_disease_type pathology_report tumor_size diagnosis_code recurrence_score progesterone_receptor_status nuclear_grade primary_disease_site disease_term file->diagnosis from_diagnosis sample sample analysis_area_percentage_tumor surgical_event_id analysis_area_percentage_glass general_sample_pathology analysis_area total_tissue_area sample_id percentage_stroma percentage_tumor pathology_status_date tumor_tissue_area analysis_area_percentage_stroma width_of_tumor date_of_sample_collection non_tumor_tissue_area length_of_tumor necropsy_sample sample_type analysis_area_percentage_pigmented_tumor file->sample of_sample assay->sample of_sample survival survival type_of_first_recurrence type_of_first_dfs_event disease_free_survival_interval consent_withdrawn survival_status disease_free_event_indicator recurrence_free_interval lost_to_follow_up recurrence_indicator cause_of_death distant_recurrence_indicator distant_recurrence_interval length_of_survival survival->case of_case diagnosis->case of_case study study date_of_iacuc_approval clinical_study_type ctep_su_category clinical_study_id clinical_study_designation ctep_term dates_of_conduct clinical_study_name ctep_category clinical_study_description case->study member_of adverse_event adverse_event ae_agent_name unexpected_adverse_event adverse_event_attribution adverse_event_description date_resolved adverse_event_grade ae_other adverse_event_term adverse_event_grade_description ae_dose case->adverse_event had_adverse_event study_arm study_arm ctep_treatment_assignment_code treatment_arm_version arm case->study_arm member_of cohort cohort cohort_description cohort_dose case->cohort member_of sample->case of_case sample->sample next prior_surgery prior_surgery date_of_surgery therapeutic_indicator surgical_finding procedure residual_disease anatomical_site_of_surgery prior_surgery->prior_surgery next prior_surgery->enrollment at_enrollment agent_administration agent_administration stop_time route_of_administration medication_duration medication medication_vial_id date_of_missed_dose medication_actual_units_of_measure start_time medication_lot_number missed_dose_units_of_measure dose_units_of_measure medication_units_of_measure medication_actual_dose medication_missed_dose medication_course_number dose_level missed_dose_amount agent agent medication agent_administration->agent of_agent evaluation evaluation date_of_evaluation follow_up follow_up explain_unknown_status patient_status treatment_since_last_contact contact_type date_of_last_contact follow_up->case of_case agent->study_arm of_study_arm demographic demographic race menopausal_status weight sex patient_age_at_enrollment date_of_birth ethnicity demographic->case of_case program program program_external_url name short_name program_short_description program_acronym program_name program_sort_order program_full_description study->program member_of variant variant hgvs alternative_allele ref_copy_number confirmed gene_name copy_number read_depth raw_copy_number allele_frequency confidence_interval_05percent status arm_specific strand ocp_alt chromosome genome_reference exon transcript cds_alt position confidence_interval_95percent aMOI molecular_id_analysis_id function status_date variant_type ocp_ref protein cds_ref variant->genomic_report of_report enrollment->case of_case adverse_event->agent of_agent adverse_event->adverse_event next study_arm->study member_of study_arm->study of_study image image image->assay of_assay treatment treatment duration_of_endocrine_therapy type_of_chemotherapy_regimen_received endocrine_therapy_discontinued type_of_endocrine_therapy_received specific_chemotherapy_regimen_received time_to_first_endocrine_therapy received_chemotherapy primary_surgical_procedure time_to_last_endocrine_therapy treatment->case of_case cohort->study member_of cohort->study_arm member_of visit visit visit_number visit_date visit->visit next