dict.yaml

SUBJECT:
    ID: string
    DOB: date
    GENDER: category
    MRN: string
    CONSENT: date
        Registry_Consent: bool
        Sample_Collection: category
            Biorepository: bool
            CHIMP: bool
            Oral_Microbiome: bool
            Grand_Lee_Genetics: bool
            Bousvaros_Immunoregulation: bool
            Further_Contact: bool
            Reg_Blood: bool
            Reg_Fecal: bool
            Reg_Biopsy: bool
            Reg_Oral: bool
            Reg_Tissue: bool
            Reg_Saliva: bool
            Reg_Urine: bool
            Reg_Other: bool
                other_sample: string
    DEMOGRAPHIC:
        Race: category
        Hispanic or Latino: bool
        Jewish: bool
           Sephardic: bool
           Ashkenazi: bool
           Unknown: bool
        NonUS: string
            date_arrived: date
    ONSET:
       VEOIBD: category
       Diagnosis: category
       Date_of_Dx: date
       Age_at_Dx: int
       Date_of_Sx: date
    HISTORY:
       Hx_Obtained:
           patient: bool
           parent: bool
           other: bool
                other: string
       Base_Surgery: category
       Base_Hospitalizations: category
       Base_Medications: category
       Base_Questionnaire: category
       Consanguinity: category
       Family_Dx: bool
           ibd:
                cd_father: bool
                cd_mother: bool
                cd_son: bool
                cd_daughter: bool
                cd_2nd_degree: bool
                cd_brother: bool
                cd_sister: bool
                cd_twin: bool
                uc_father: bool
                uc_mother: bool
                uc_son: bool
                uc_daughter: bool
                uc_2nd_degree: bool
                uc_brother: bool
                uc_sister: bool
                uc_twin: bool
                uibd_father: bool
                uibd_mother: bool
                uibd_son: bool
                uibd_daughter: bool
                uibd_2nd_degree: bool
                uibd_brother: bool
                uibd_sister: bool
                uibd_twin: bool
           1st_degree_autoimmune: category
                inflammatory_arthritis: bool
                diabetes_Type_1: bool
                thyroiditis: bool
                psoriasis: bool
                systemic_lupus_erythematosus: bool
                vasculitis: bool
                other: bool
                    what: string
           1st_degree_immunodeficiency: category
                cgd: bool
                il10r_deficiency: bool
                ipex: bool
                nemo: bool
                was: bool
                xla: bool
                other: bool
                    what: string
           1st_degree_crc: category
       Breastfed: category
                apprx_duration: int
                apprx_exclusive: str
       Caesarean: category
       Tobacco_Use: bool
           tobacco_recent: bool
           no_of_years: bool
           packs_per_day: bool
           smoker_6mo+: category
           smoker_6mo-: category
           mother_smoke: category
       Alcohol_Use: category
           alcohol_recent: category
           years_of_use: int
           drinks_per_day: int
       Antibiotic_Use: category
           duration: string
       Steroid_Use: category
           duration: string
       Perianal_Oral:
            perianal: category
            oral: category
            neither: category
       NSAIDS: category
            freq: category
       GI_Infection: category
    VISITS:
        Visit_ID: string (?)
        Date: date
        Age_at_Visit: int
        Event_Name: string
        Type: category
        RC_Entered: string
        Reviewed: string
        Date_Entered: date
        Weight: float
            date: date
            previous: float
            previous_date: date
        Height: float
            date: date
            previous: float
            previous_date: date
        Liver_Complications_Developed: category
            drug_induced_hepatitis: bool
            steatohepatitis: bool
            psc: bool
            autoimmune_hepatitis: bool
            other: bool
                what:string
        Extraintestinal_Developed: category
            arthralgias: bool
            arthritis: bool
            erythema_nodosum: bool
            pyoderma_gangrenosum: bool
            uveitis: bool
            fever: bool
            other: bool
                other: string
        Autoimmune_Developed: category
            psoriasis: bool
            diabetes: bool
            celiac: bool
            thyroiditis: bool
            systemic_lupus_erythematosus: bool
            other: bool
                what: string
        Immunodeficiency_Developed:
                which: category
                    other: string
        Is_Baseline: string
            time_passed: string
        Radiology: bool
        EGD: bool
        Colonoscopy: bool
        Capsule: bool
          Not_done: bool
        Other: bool
          what: string
        CD_Esophagus_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Stomach_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Duodenum_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Jejunum_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Ileum_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Cecum_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Transverse_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Descending_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Sigmoid_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Rectum_Active: string
             endoscopy: bool
             histology: bool
             radiology: bool
        CD_Oropharyngeal: category
        CD_Perianal: category
        CD_Skin_Tags: category
        CD_Fissure: category
        CD_Fistula_or_abscess: category
        CD_Stricture: category
        CD_Mucosal_inflammatory: category
        CD_Stenosing: category
        CD_Fistulizing: category
            internal: category
            fistula_to_skin: category
            vaginal_or_scrotal: category
            fistula_to_bladder: category
        CD_Abdominal_Abscess: category
        CD_Paris_Classification: string
            l1: bool
            l2: bool
            l3: bool
            l4a: bool
            l4b: bool
            behavior: string
            growth: string
        PCDAI:
            pcdai_score: int
            pcdai_severity: category
            pcdai_date: date
            in_person: bool
            phone: bool
            mrr: bool
            abdominal_pain: string
            stool_per_day: string
            functional_limitations: string
            weight_gain: string
            tenderness: string
            perirectal: string
            extraintestinal: category (?)
        HBAI:
            hbai_score: int
            hbai_date: date
            in_person: bool
            phone: bool
            mrr: bool
            wellbeing: category
            abdominal_pain: category
            liquid_stool: int
            abdominal_mass: category
            complications: category
                arthralgia: bool
                uveitis: bool
                erythma_nodosum: bool
                aphthous_ulcers: bool
                pyoderma_gangrenosum: bool
                anal_fissure: bool
                new_fistula: bool
                abscess: bool
        UC_Proctits: category
            endoscopy: bool
            histology: bool
            radiology: bool
        UC_Left_Sided:  category
            endoscopy: bool
            histology: bool
            radiology: bool
        UC_Pancolitis: category
            endoscopy: bool
            histology: bool
            radiology: bool
        UC_Paris_Classification:
            extent: category
            severity: category
        PUCAI:
            pucai_score: int
            pucai_severity: category
            pucai_date: date
            in_person: bool
            phone: bool
            mrr: bool
            abdominal_pain: category
            stool_consistency: category
            stool_freq: category
            nocturnal_stool: category
            activity_level: category
        Hx_of_CRC: category
        Hx_of_polyps: category
        Hx_of_dysplasia: category
            type: category
            grade: category
        Abdominal_Pain: category
        Diarrhea: category
        Growth_Failure: category
        Malaise: category
        Rectal_Bleeding: category
        Weight_Loss: category
        Medication:
            info_source:
                patient_or_family: bool
                limited_chart_review: bool
                provider: bool
                other: bool
                    other: string
                dis_patient_or_family: bool
                dis_limited_chart_review: bool
                dis_provider: bool
                dis_other: bool
                    dis_what: string
            aminosalicylates: category
                mesalamine: category
                    discontinued: category
                    adverse_effect: category
                sulfasalazine: category
                    discontinued: category
                    adverse_effect: category
                balsalazide: category
                    discontinued: category
                    adverse_effect: category
                olsalazine: category
                    discontinued: category
                    adverse_effect: category
            non_biologics: category
                6mp: category
                    discontinued: category
                    adverse_effect: category
                azathoprine: category
                    discontinued: category
                    adverse_effect: category
                methotrexate: category
                    discontinued: category
                    adverse_effect: category
                fk506: category
                    discontinued: category
                    adverse_effect: category
                cyclosporine_a: category
                    discontinued: category
                    adverse_effect: category
                thalidomide: category
                    discontinued: category
                    adverse_effect: category
                lenalidomide: category
                    discontinued: category
                    adverse_effect: category
            antitnf: category
                infliximab: category
                    discontinued: category
                    adverse_effect: category
                adalimumab: category
                    discontinued: category
                    adverse_effect: category
                certolizumab: category
                    discontinued: category
                    adverse_effect: category
                golimumab: category
                    discontinued: category
                    adverse_effect: category
            other_biologic: category
                natalizumab: category
                    discontinued: category
                    adverse_effect: category
                tocilizumab: category
                    discontinued: category
                    adverse_effect: category
                vedolizumab: category
                    discontinued: category
                    adverse_effect: category
                ustekinumab: category
                    discontinued: category
                    adverse_effect: category
            glucocoricords: category
                oral_enteric: category
                    discontinued: category
                    adverse_effect: category
                rectal: category
                    discontinued: category
                    adverse_effect: category
                oral: category
                    discontinued: category
                    adverse_effect: category
                intravenous: category
                    discontinued: category
                    adverse_effect: category
                courses: int
            antibiotics: category
                metronidazole: category
                    discontinued: category
                    adverse_effect: category
                ciprofloxacin: category
                    discontinued: category
                    adverse_effect: category
                trimethoprim_sulfamethoxazole: category
                    discontinued: category
                    adverse_effect: category
                amoxicillin: category
                    discontinued: category
                    adverse_effect: category
                vancomycin: category
                    discontinued: category
                    adverse_effect: category
            psc_medications: category
                ursodiol: category
                    discontinued: category
                    adverse_effect: category
                cholestyra: category
                    discontinued: category
                    adverse_effect: category
                rifampin: category
                    discontinued: category
                    adverse_effect: category
            enteral_feeding: category
                suppement: category
                omega_three: category
                probiotic: category
            fecal_transplant: category
        Labs:
            date: date
            alb: float
            alk: int
            ast: int
            bun: int
            creatinine: float
            crp: string
            esr: int
            ggt: int
            hct: float
            hemoglobin: float
            plt: int
            wbc: float
    SURGERY:
        Date: date
        Type:
            jejunum: bool
            ileum: bool
            cecum: bool
            segmental_colonic: bool
            stricturoplasty: bool
            stomy_creation: bool
            stomy_closure: bool
            perianal: bool
            abscess_drainage: bool
            apendctomy: bool
            colectomy_ileostomy: bool
            jpouch: bool
            jpouch_closure: bool
    HOSPITALIZATIONS:
        Date: date
        Type: category
        Reason: category
    SAMPLES:
        Record_ID: string
        Sample_ID: string
        Label: string
        Date: date
        Type: category
        Freq: category
        Stored:
            biorepo: bool
            camilla: bool
            netherlands:  bool
            pfizer: bool
            il10: bool
            other: bool
                what: string
        Blood:
            dna: bool
            pax: bool
            pbmcs: bool
            serum: bool
            plasma: bool
            heparin: bool
            whole: blool
        Stool:
            time_to_minus_twenty: category
            time_to_minus_eighty: category
            freeze: bool
            rna_later: bool
            ethanol: bool
            dna_genotek: bool
            dna_isolated: category
        Biopsy:
            obtained: category
                antrum_in: bool
                antrum_un: bool
                corpus_in: bool
                corpus_un: bool
                duo_in: bool
                duo_un: bool
                ti_in: bool
                ti_un: bool
                cecum_in: bool
                cecum_un: bool
                right_in: bool
                right_un: bool
                hepa_in: bool
                hepa_un: bool
                trans_in: bool
                trans_un: bool
                splen_in: bool
                splen_un: bool
                left_in: bool
                left_un: bool
                sig_in: bool
                sig_un: bool
                rectum_in: bool
                rectum_un: bool
                pouch_in: bool
                pouch_un: bool
                freeze: bool
                organoid: bool
                rna_later: bool
                snap: bool
                formalin: bool
            Medication:
                aminosalicylate_2_wks: category
                    mesalamine: bool
                    balsalazide: bool
                    sulfasalazine: bool
                    olsalazine: bool
                antibiotic_2_wks: category
                    amoxicillin: bool
                    ciproflaxcin: bool
                    metronidazole: bool
                    rifaximin: bool
                    sulfamethoxazole: bool
                    vancomycin: bool
                    other: bool
                        what: string
                probiotic_1_mo: category
                    vsl3: bool
                    lgg: bool
                    florastor: bool
                    other: bool
                        what: string
                steroid_2_wks: category
                    budesonide: bool
                    hydrocortisone_enema: bool
                    methylprednisolone: bool
                    prednisone: bool
                immunomodulator:  category
                    6mp: bool
                    azathioprine: bool
                    methotrexate: bool
                antitnf_3_mo: category
                    infliximab: bool
                    adalimumab: bool
                    certolizumab: bool
                    golimumab: bool
                calcinerin_inhibitor_3_mo:
                    cyclosporine: bool
                    tacrolimus: bool
                biologic_3_mo: category
                    natalizumab: bool
                    ustekinumab: bool
                    vedolizumab: bool
                    abatacept: bool
                fecal_transplant: category
                other_meds_2_wks: category
                    thalidomide: bool
                    other: bool
                        what: string