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MUSIC

MUSIC Main DataFrame Columns

Python
[
  "study_id",
  "redcap_event_name",
  "age",
  "sex",
  "study_group",
  "diagnosis_comments",
  "date_of_diagnosis",
  "age_at_diagnosis",
  "cucq_date",
  "cucq_1",
  "cucq_2",
  "cucq_3",
  "cucq_4",
  "cucq_5",
  "cucq_6",
  "cucq_7",
  "cucq_8",
  "cucq_9",
  "cucq_10",
  "cucq_11",
  "cucq_12",
  "cucq_13",
  "cucq_14",
  "cucq_15",
  "cucq_16",
  "cucq_17",
  "cucq_18",
  "cucq_19",
  "cucq_20",
  "cucq_21",
  "cucq_22",
  "cucq_23",
  "cucq_24",
  "cucq_25",
  "cucq_26",
  "cucq_27",
  "cucq_28",
  "cucq_29",
  "cucq_30",
  "cucq_31",
  "cucq_32",
  "proms_comments",
  "smoking_status",
  "when_smoking_stopped",
  "when_smoking_stopped_units",
  "height",
  "weight",
  "bmi",
  "has_active_symptoms",
  "visit_date",
  "physician_global_assessment",
  "disease_activity",
  "symptoms_description",
  "cucq_total",
  "change_in_montreal",
  "disease_activity_score_date",
  "hbi_general_well_being",
  "hbi_abdominal_pain",
  "hbi_abdominal_mass",
  "hbi_liquid_stools_present",
  "hbi_liquid_stools",
  "hbi_no_complications",
  "hbi_arthralgia",
  "hbi_uveitis",
  "hbi_erythema_nodosum",
  "hbi_apthous_ulcers",
  "hbi_pyoderma",
  "hbi_anal_fissures",
  "hbi_new_fistula",
  "hbi_abscess",
  "sccai_bowel_frequency_day",
  "sccai_bowel_frequency_night",
  "sccai_urgency",
  "sccai_blood_in_stool",
  "sccai_general_well_being",
  "sccai_no_complications",
  "sccai_erythema_nodosum",
  "sccai_pyoderma",
  "sccai_arthralgia",
  "sccai_uveitis",
  "sccai_total",
  "hbi_total",
  "disease_activity_score_comments",
  "mayo_stool_frequency",
  "mayo_rectal_bleeding",
  "mayo_physician_global_assessment",
  "mayo_total",
  "unplanned_hospital_admission",
  "new_flare_up",
  "flare_up_1_date",
  "flare_up_1_description",
  "flare_up_1_management_community",
  "flare_up_1_management_inpatient",
  "flare_up_1_management_oral_steroids",
  "flare_up_1_management_asa",
  "flare_up_1_management_dietetics",
  "flare_up_1_management_other",
  "flare_up_1_management_other_text",
  "flare_up_2_date",
  "flare_up_2_description",
  "flare_up_2_management_community",
  "flare_up_2_management_inpatient",
  "flare_up_2_management_oral_steroids",
  "flare_up_2_management_asa",
  "flare_up_2_management_dietetics",
  "flare_up_2_management_other",
  "flare_up_2_management_other_text",
  "flare_up_comments",
  "steroid_use_1_reason",
  "steroid_use_1_reason_text",
  "steroid_use_1_drug",
  "steroid_use_1_dose",
  "steroid_use_1_frequency",
  "steroid_use_1_frequency_text",
  "steroid_use_1_start_date",
  "steroid_use_1_still_taking",
  "steroid_use_1_end_date",
  "steroid_use_1_reason_stopped",
  "steroid_use_1_reason_changed_text",
  "steroid_use_2_reason",
  "steroid_use_2_drug",
  "steroid_use_2_dose",
  "steroid_use_2_frequency",
  "steroid_use_2_frequency_text",
  "steroid_use_2_start_date",
  "steroid_use_2_still_taking",
  "steroid_use_2_end_date",
  "steroid_use_2_reason_stopped",
  "steroid_use_2_reason_changed_text",
  "hospital_admission_1_for_acute_severe_colitis",
  "hospital_admission_1_for_ibd_flare_not_asc",
  "hospital_admission_1_for_perianal_disease",
  "hospital_admission_1_for_surgery",
  "hospital_admission_1_for_investigation_not_meeting_other_criteria",
  "hospital_admission_1_for_other",
  "hospital_admission_1_for_other_text",
  "hospital_admission_2_for_other_text",
  "hospital_admission_2_for_acute_severe_colitis",
  "hospital_admission_2_for_ibd_flare_not_asc",
  "hospital_admission_2_for_perianal_disease",
  "hospital_admission_2_for_surgery",
  "hospital_admission_2_for_investigation_not_meeting_other_criteria",
  "hospital_admission_2_for_other",
  "hospital_admission_1_admission_date",
  "hospital_admission_2_admission_date",
  "hospital_admission_1_discharge_date",
  "hospital_admission_2_discharge_date",
  "hospital_admission_comments",
  "new_oral_steroids_since_last_visit",
  "montreal_classification_date",
  "montreal_cd_location",
  "montreal_cd_behaviour",
  "montreal_perianal",
  "montreal_upper_gi",
  "montreal_uc_extent",
  "montreal_uc_severity",
  "montreal_classification_comments",
  "baseline_previous_ibd_treatment",
  "baseline_eims_arthralgia",
  "baseline_eims_ank_spon",
  "baseline_eims_erythema_nodosum",
  "baseline_eims_pyoderma",
  "baseline_eims_uveitis",
  "baseline_eims_episcleritis",
  "baseline_eims_none",
  "baseline_eims_iritis_scleritis",
  "baseline_eims_sacroileitis",
  "baseline_eims_conjunctivitis",
  "baseline_eims_angular_cheilitis",
  "baseline_eims_other",
  "baseline_eims_other_text",
  "baseline_surgical_history",
  "endoscopy_prior_to_recruitment_date",
  "endoscopy_prior_to_recruitment_colonoscopy",
  "endoscopy_prior_to_recruitment_flexible_sigmoidoscopy",
  "endoscopy_prior_to_recruitment_report",
  "endoscopy_prior_to_recruitment_mayo_score",
  "endoscopy_prior_to_recruitment_uceis_score",
  "radiology_prior_to_recruitment_date",
  "radiology_prior_to_recruitment_ctap",
  "radiology_prior_to_recruitment_mri_sb",
  "radiology_prior_to_recruitment_mri_pelvis",
  "radiology_prior_to_recruitment_report",
  "histology_prior_to_recruitment_date",
  "histology_prior_to_recruitment_report",
  "surgical_history_number",
  "surgical_history_1_date",
  "surgical_history_1_report",
  "surgical_history_2_date",
  "surgical_history_2_report",
  "surgical_history_3_date",
  "surgical_history_3_report",
  "phenotyping_comments",
  "previous_appendicectomy",
  "previous_tonsillectomy",
  "appendicectomy_age",
  "tonsillectomy_age",
  "pmh_1_start_date",
  "pmh_1_end_date",
  "pmh_1_diagnosis",
  "pmh_2_start_date",
  "pmh_2_end_date",
  "pmh_2_diagnosis",
  "pmh_3_start_date",
  "pmh_3_end_date",
  "pmh_3_diagnosis",
  "pmh_4_start_date",
  "pmh_4_end_date",
  "pmh_4_diagnosis",
  "pmh_5_start_date",
  "pmh_5_end_date",
  "pmh_5_diagnosis",
  "pmh_comments",
  "fh_number_brothers",
  "fh_number_sisters",
  "fh_number_siblings",
  "fh_number_daughters",
  "fh_number_sons",
  "fh_number_children",
  "fh_of_ibd_present",
  "fh_of_ibd_number_affected",
  "fh_1_relationship",
  "fh_1_age_at_diagnosis",
  "fh_1_diagnosis",
  "fh_1_diagnosis_other",
  "fh_2_relationship",
  "fh_2_age_at_diagnosis",
  "fh_2_diagnosis",
  "fh_2_diagnosis_other",
  "fh_2_diagnosis_other_text",
  "fh_3_relationship",
  "fh_3_age_at_diagnosis",
  "fh_3_diagnosis",
  "fh_3_diagnosis_other",
  "fh_4_relationship",
  "fh_4_age_at_diagnosis",
  "fh_4_diagnosis",
  "fh_comments",
  "endoscopy_date",
  "endoscopy_type_colonoscopy",
  "endoscopy_type_flexible_sigmoidoscopy",
  "upload_endoscopic_image",
  "endoscopy_report",
  "pathology_report",
  "mayo_endoscopic_score",
  "uceis",
  "sescd",
  "physician_endoscopic_severity",
  "endoscopy_comments",
  "endoscopic_mucosal_healing",
  "complete_mucosal_healing",
  "radiology_test_date",
  "ct_abdomen_pelvis",
  "axr",
  "uss_abdomen",
  "mri_small_bowel",
  "mri_pelvis",
  "ct_abdomen_pelvis_report",
  "axr_report",
  "uss_abdomen_report",
  "mri_small_bowel_report",
  "mri_pelvis_report",
  "radiology_report_summary",
  "ibd_surgery_performed",
  "ibd_surgery_date",
  "ibd_surgery_procedure",
  "ibd_surgery_procedure_other",
  "ibd_surgery_procedure_other_text",
  "ibd_surgery_comments",
  "ibd_surgery_histology_report",
  "saliva_sample_complete",
  "sampling_imm",
  "sampling_tnf",
  "sampling_jaki",
  "sampling_steroids",
  "sampling_abx",
  "sampling_asa",
  "sampling_ppi",
  "sampling_steroid_details",
  "sampling_aza",
  "sampling_mp",
  "sampling_ifx",
  "sampling_ada",
  "sampling_vedo",
  "sampling_uste",
  "sampling_tofa",
  "sampling_mtx",
  "sampling_ciclosporin",
  "sampling_filgo",
  "sampling_upa",
  "sampling_risa",
  "baseline_asa",
  "baseline_mtx",
  "baseline_ifx",
  "baseline_ada",
  "baseline_aza",
  "baseline_mp",
  "baseline_uste",
  "baseline_vedo",
  "baseline_goli",
  "baseline_tofa",
  "baseline_filgo",
  "baseline_risa",
  "qfit_result",
  "qfit_result_date",
  "albumin",
  "crp",
  "nhs_bloods_date",
  "haemoglobin",
  "red_cell_count",
  "haematocrit",
  "white_cell_count",
  "neutrophils",
  "lymphocytes",
  "monocytes",
  "eosinophils",
  "basophils",
  "platelets",
  "egfr",
  "qfit_comment",
  "urea",
  "creatinine",
  "sodium",
  "potassium",
  "bilirubin",
  "calprotectin_date",
  "calprotectin",
  "drug_level_date",
  "ada_level",
  "ada_antibody",
  "ifx_level",
  "ifx_antibody",
  "lab_tests_comments",
  "saliva_rev_date",
  "saliva_sample",
  "saliva_setting",
  "sample_date",
  "saliva_eim",
  "eims_details",
  "saliva_abx",
  "abx_detail",
  "saliva_abx3m",
  "abx3m_detail",
  "saliva_piercing",
  "saliva_brushing",
  "saliva_brush_tongue",
  "saliva_dietibd",
  "diet_details",
  "saliva_cs",
  "saliva_denture",
  "dentures_details",
  "comments_saliva",
  "surgical_history_1_procedure",
  "surgical_history_2_procedure",
  "surgical_history_3_procedure",
  "study_center",
  "endoscopic_mucosal_healing_at_3_6_months",
  "complete_mucosal_healing_at_3_6_months",
  "endoscopic_mucosal_healing_at_12_months",
  "complete_mucosal_healing_at_12_months"
]

MUSIC Demographics DataFrame Columns

This is a subset of the main music dataframe, keeping only timepoint_1 and reducing the number of columns retrieved.

Python
[
  "study_id",
  "redcap_event_name",
  "age",
  "sex",
  "study_group",
  "diagnosis_comments",
  "date_of_diagnosis",
  "age_at_diagnosis",
  "smoking_status",
  "when_smoking_stopped",
  "when_smoking_stopped_units",
  "height",
  "weight",
  "bmi",
  "has_active_symptoms",
  "visit_date",
  "physician_global_assessment",
  "disease_activity",
  "symptoms_description",
  "cucq_total",
  "change_in_montreal",
  "disease_activity_score_date",
  "sccai_total",
  "hbi_total",
  "disease_activity_score_comments",
  "mayo_total",
  "montreal_classification_date",
  "montreal_cd_location",
  "montreal_cd_behaviour",
  "montreal_perianal",
  "montreal_upper_gi",
  "montreal_uc_extent",
  "montreal_uc_severity",
  "montreal_classification_comments",
  "baseline_previous_ibd_treatment",
  "baseline_eims_arthralgia",
  "baseline_eims_ank_spon",
  "baseline_eims_erythema_nodosum",
  "baseline_eims_pyoderma",
  "baseline_eims_uveitis",
  "baseline_eims_episcleritis",
  "baseline_eims_none",
  "baseline_eims_iritis_scleritis",
  "baseline_eims_sacroileitis",
  "baseline_eims_conjunctivitis",
  "baseline_eims_angular_cheilitis",
  "baseline_eims_other",
  "baseline_eims_other_text",
  "baseline_surgical_history",
  "endoscopy_prior_to_recruitment_date",
  "endoscopy_prior_to_recruitment_colonoscopy",
  "endoscopy_prior_to_recruitment_flexible_sigmoidoscopy",
  "endoscopy_prior_to_recruitment_report",
  "endoscopy_prior_to_recruitment_mayo_score",
  "endoscopy_prior_to_recruitment_uceis_score",
  "radiology_prior_to_recruitment_date",
  "radiology_prior_to_recruitment_ctap",
  "radiology_prior_to_recruitment_mri_sb",
  "radiology_prior_to_recruitment_mri_pelvis",
  "radiology_prior_to_recruitment_report",
  "histology_prior_to_recruitment_date",
  "histology_prior_to_recruitment_report",
  "surgical_history_number",
  "surgical_history_1_date",
  "surgical_history_1_report",
  "surgical_history_2_date",
  "surgical_history_2_report",
  "surgical_history_3_date",
  "surgical_history_3_report",
  "phenotyping_comments",
  "previous_appendicectomy",
  "previous_tonsillectomy",
  "appendicectomy_age",
  "tonsillectomy_age",
  "pmh_1_start_date",
  "pmh_1_end_date",
  "pmh_1_diagnosis",
  "pmh_2_start_date",
  "pmh_2_end_date",
  "pmh_2_diagnosis",
  "pmh_3_start_date",
  "pmh_3_end_date",
  "pmh_3_diagnosis",
  "pmh_4_start_date",
  "pmh_4_end_date",
  "pmh_4_diagnosis",
  "pmh_5_start_date",
  "pmh_5_end_date",
  "pmh_5_diagnosis",
  "pmh_comments",
  "fh_number_brothers",
  "fh_number_sisters",
  "fh_number_siblings",
  "fh_number_daughters",
  "fh_number_sons",
  "fh_number_children",
  "fh_of_ibd_present",
  "fh_of_ibd_number_affected",
  "fh_1_relationship",
  "fh_1_age_at_diagnosis",
  "fh_1_diagnosis",
  "fh_2_relationship",
  "fh_2_age_at_diagnosis",
  "fh_2_diagnosis",
  "fh_2_diagnosis_other",
  "fh_2_diagnosis_other_text",
  "fh_3_relationship",
  "fh_3_age_at_diagnosis",
  "fh_3_diagnosis",
  "fh_3_diagnosis_other",
  "fh_4_relationship",
  "fh_4_age_at_diagnosis",
  "fh_4_diagnosis",
  "fh_comments",
  "baseline_asa",
  "baseline_mtx",
  "baseline_ifx",
  "baseline_ada",
  "baseline_aza",
  "baseline_mp",
  "baseline_uste",
  "baseline_vedo",
  "baseline_goli",
  "baseline_tofa",
  "baseline_filgo",
  "baseline_risa",
  "surgical_history_1_procedure",
  "surgical_history_2_procedure",
  "surgical_history_3_procedure",
  "sescd",
  "uceis",
  "mayo_endoscopic_score",
  "physician_endoscopic_severity",
  "endoscopic_mucosal_healing_at_3_6_months",
  "complete_mucosal_healing_at_3_6_months",
  "endoscopic_mucosal_healing_at_12_months",
  "complete_mucosal_healing_at_12_months"
  "cd_pro2_raw",
  "cd_pro2_weighted",
  "uc_pro2",
  "ibdresponse_criteria_cd_met",
  "ibdresponse_criteria_uc_met",
]

Column Construction Comments

Mucosal Healing Definitions

  1. Endoscopic Mucosal Healing: SES-CD or UCEIS score of 0. yes or no.
  2. Complete Mucosal Healing: Endoscopic Mucosal Healing + Normal Pathology. yes/no/partial.

Mucosal Healing Columns

  • sescd was created by merging sescd_noncalc into sescd_calc and renamed.
  • uceis was created by merging uceis_noncalc and uceis_calc and renamed.
  • endo_healing was renamed to endoscopic_mucosal_healing
  • cmh was renamed to complete_mucosal_healing
  • endoscopic_mucosal_healing_at_3_6_months was created by taking the endoscopic_mucosal_healing value at timepoint_2 and populating it to timepoint_1 to timepoint_5.
  • complete_mucosal_healing_at_3_6_months was created by taking the complete_mucosal_healing value at timepoint_2 and populating it to timepoint_1 to timepoint_5.
  • endoscopic_mucosal_healing_at_12_months was created by taking the endoscopic_mucosal_healing value at timepoint_5 and populating it to timepoint_1 to timepoint_5.
  • complete_mucosal_healing_at_12_months was created by taking the complete_mucosal_healing value at timepoint_5 and populating it to timepoint_1 to timepoint_5.

PRO2 Columns

  • cd_pro2_raw is the raw PRO2 score for Crohn's disease calculated by hbi_liquid_stools + hbi_abdominal_pain where pain is scored 0-3 corresponding to none, mild, moderate, severe.
  • cd_pro2_weighted is the weighted PRO2 score for Crohn's disease calculated by hbi_liquid_stools + (hbi_abdominal_pain * 2) where pain is scored 0-3 corresponding to none, mild, moderate, severe and multiplied by 5.
  • uc_pro2 is the PRO2 score for Ulcerative Colitis calculated by scoring mayo_stool_frequency 0-3 based on the categories + mayo_rectal_bleeding 0-3.
  • ibdresponse_criteria_cd_met is a boolean indicating if the PRO2 score meets the IBD Response Study Criteria, where hbi_liquid_stools >= 4 and hbi_abdominal_pain >= 2.
  • ibdresponse_criteria_uc_met is a boolean indicating if the PRO2 score meets the IBD Response Study Criteria, where mayo_stool_frequency = 3 and mayo_rectal_bleeding > 0.