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states indicated only on questioning. + + + + + These feeling states spontaneously reported verbally. + + + + + Communicates feeling states non-verbally, i.e. through facial expression, posture, voice and tendency to weep. + + + + + Patient reports virtually only these feeling states in his/her spontaneous verbal and non-verbal communication. + + + + + + + + + + + + + + Absent. + + + + + Self reproach, feels he/she has let people down. + + + + + Ideas of guilt or rumination over past errors or sinful deeds. + + + + + Present illness is a punishment. Delusions of guilt. + + + + + Hears accusatory or denunciatory voices and/or experiences threatening visual hallucinations. + + + + + + + + + + + + + + Absent. + + + + + Feels life is not worth living. + + + + + Wishes he/she were dead or any thoughts of possible death to self. + + + + + Ideas or gestures of suicide. + + + + + Attempts at suicide (any serious attempt rate 4). + + + + + + + + + + + + No difficulty falling asleep. + + + + + Complains of occasional difficulty falling asleep, i.e. more than 1/2 hour + + + + + Complains of nightly difficulty falling asleep. + + + + + + + + + + + + No difficulty. + + + + + Patient complains of being restless and disturbed during the night. + + + + + Waking during the night - any getting out of bed rates 2 (except for purposes of voiding). + + + + + + + + + + + + No difficulty. + + + + + Waking in early hours of the morning but goes back to sleep. + + + + + Unable to fall asleep again if he/she gets out of bed. + + + + + + + + + + + + + + No difficulty. + + + + + Thoughts and feelings of incapacity, fatigue or weakness related to activities, work or hobbies. + + + + + Loss of interest in activity, hobbies or work - either directly reported by the patient or indirect in listlessness, indecision and vacillation (feels he/she has to push self to work or activities). + + + + + Decrease in actual time spent in activities or decrease in productivity. Rate 3 if the patient does not spend at least three hours a day in activities (job or hobbies) excluding routine chores. + + + + + Stopped working because of present illness. Rate 4 if patient engages in no activities except routine chores, or if patient fails to perform routine chores unassisted. + + + + + + + + + + + + + + Normal speech and thought. + + + + + Slight retardation during the interview. + + + + + Obvious retardation during the interview. + + + + + Interview difficult. + + + + + Complete stupor. + + + + + + + + + + + + + + None. + + + + + Fidgetiness. + + + + + Playing with hands, hair, etc. + + + + + Moving about, cannot sit still. + + + + + Hand wringing, nail biting, hair-pulling, biting of lips. + + + + + + + + + + + + + + No difficulty. + + + + + Subjective tension and irritability. + + + + + Worrying about minor matters. + + + + + Apprehensive attitude apparent in face or speech. + + + + + Fears expressed without questioning. + + + + + + + + + + + + + + Absent. + + + + + Mild. + + + + + Moderate. + + + + + Severe. + + + + + Incapacitating. + + + + + + + + + + + + None. + + + + + Loss of appetite but eating without staff encouragement. Heavy feelings in abdomen. + + + + + Difficulty eating without staff urging. Requests or requires laxatives or medication for bowels or medication for gastro-intestinal symptoms. + + + + + + + + + + + + None. + + + + + Heaviness in limbs, back or head. Backaches, headaches, muscle aches. Loss of energy and fatigability. + + + + + Any clear-cut symptom rates 2. + + + + + + + + + + + + Absent. + + + + + Mild. + + + + + Severe. + + + + + + + + + + + + + + Not present. + + + + + Self-absorption (bodily). + + + + + Preoccupation with health. + + + + + Frequent complaints, requests for help, etc. + + + + + Hypochondriacal delusions. + + + + + + + + + + + + + No weight loss. + + + + + Probable weight loss associated with present illness. + + + + + Definite (according to patient) weight loss. + + + + + Not assessed. + + + + + + + + + + + + + Less than 1 lb weight loss in week. + + + + + Greater than 1 lb weight loss within week. + + + + + Greater than 2 lb weight loss in week. + + + + + Not assessed. + + + + + + + + + + + + Acknowledges being depressed and ill. + + + + + Acknowledges illness but attributes cause to bad food, climate, overwork, virus, need for rest, etc. + + + + + Denies being ill at all. + + + + + + + HAMD1-Depressed Mood + + + + + + HAMD1-Feelings of Guilt + + + + + + HAMD1-Suicide + + + + + + HAMD1-Insomnia Early - Early Night + + + + + + HAMD1-Insomnia Middle - Middle Night + + + + + + HAMD1-Insomnia Early Hours - Morning + + + + + + HAMD1-Work and Activities + + + + + + HAMD1-Retardation + + + + + + HAMD1-Agitation + + + + + + HAMD1-Anxiety Psychic + + + + + + HAMD1-Anxiety Somatic + + + + + + HAMD1-Somatic Symptoms GI + + + + + + HAMD1-General Somatic Symptoms + + + + + + HAMD1-Genital Symptoms + + + + + + HAMD1-Hypochondriasis + + + + + + HAMD1-Loss of WT According to Patient + + + + + + HAMD1-Loss of WT According to WK Meas + + + + + + HAMD1-Insight + + + + + + HAMD1-Total Score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Exclusion + + + + + + Inclusion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Males and postmenopausal females at least 50 years of age. + + + + + Diagnosis of probable AD as defined by NINCDS and the ADRDA guidelines. + + + + + MMSE score of 10 to 23. + + + + + Modified Hachinski Ischemic Scale score of <= 4. + + + + + CNS imaging (CT scan or MRI of brain) compatible with AD within past 1 year. (See Protocol for incompatible findings.) + + + + + Investigator has obtained informed consent signed by the patient (and/or legal representative) and by the caregiver. + + + + + Geographic proximity to investigator's site that allows adequate follow-up. + + + + + Caregiver will monitor administration of prescribed medications, and will be responsible for the overall care of the patient at home. + + + + + Persons who have previously completed or withdrawn from this study or any other investigating xanomeline TTS or the oral formulation of Zanomaline. + + + + + Use of any investigational agent or approved Alzheimer's therapeutic medication within 30 days prior to enrollment into the study. + + + + + Serious illness which required hospitalization within 3 months of screening. + + + + + Diagnosis of serious neurological conditions + + + + + Episode of depression meeting DSM-IV criteria within 3 months of screening. + + + + + A history within the last 5 years of the following: a) Schizophrenia b) Bipolar Disease c) Ethanol or psychoactive drug abuse or dependence. + + + + + A history of syncope within the last 5 years. + + + + + Evidence from ECG recording at screening of any of the following conditions: a) Left bundle branch block b) Bradycardia <50 beats per minute c) Sinus pauses >2 seconds (See Protocol for Remainder) + + + + + A history within the last 5 years of a serious cardiovascular disorder, including a) Clinically significant arrhythmia (See Protocol for Remainder) + + + + + A history within the last 5 years of a serious gastrointestinal disorder, including +a) Chronic peptic/duodenal/gastric/esophageal ulcer that are untreated or refractory to treatment(See Protocol) + + + + + A history within the last 5 years of a serious endocrine disorder, including +a) Uncontrolled Insulin Dependent Diabetes Mellitus (IDDM) (See Protocol for other excluded disorders) + + + + + A history within the last 5 years of a serious respiratory disorder, including a) Asthma with bronchospasm refractory to treatment b) Decompensated chronic obstructive pulmonary disease. + + + + + A history within the last 5 years of a serious genitourinary disorder, including a) Renal failure b) Uncontrolled urinary retention + + + + + A history within the last 5 years of a serious rheumatologic disorder, including a) Lupus b) Temporal arteritis c) Severe rheumatoid arthritis + + + + + A known history of human immunodeficiency virus (HIV) within the last 5 years. + + + + + A history within the last 5 years of a serious infectious disease including a) Neurosyphilis b) Meningitis c) Encephalitis + + + + + A history within the last 5 years of a primary or recurrent malignant disease (See Exceptions in Protocol). + + + + + Visual, hearing, or communication disabilities impairing the ability to participate in the study; (for example, inability to speak or understand English, illiteracy). + + + + + Laboratory test values exceeding the Reference Range III for the patient's age in any of the following analytes: creatinine, total bilirubin, SGOT, SGPT, (See Protocol for Additional Analytes) + + + + + Central laboratory test values below reference range for folate, and vitamin B12, and outside reference range for thyroid function tests. + + + + + Positive syphilis screening with confirmatory testing. + + + + + Central laboratory test value above reference range for glycosylated hemoglobin (A1C) (insulin dependent diabetes mellitus patients only). + + + + + Treatment with medications within 1 month prior to enrollment a) Anticonvulsants b) Alpha receptor blockers c) Calcium channel blockers that are CNS active + + + + + Diagnosis of serious neurological conditions (Amend 1) + + + + + Treatment with medications within 1 month prior to enrollment a) Anticonvulsants b) Alpha receptor blockers c) Calcium channel blockers that are CNS active (Amend 1) + + + + + + + Parallel + + + + + + + + + Drug + + + + + + + + + Left + + + + + + Right + + + + + + + + + Chemistry + + + + + Hematology + + + + + Urinalysis + + + + + Other + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Albumin Measurement + + + + + + Alkaline Phosphatase Measurement + + + + + + Alanine Aminotransferase Measurement + + + + + + Anisocyte Measurement + + + + + + Aspartate Aminotransferase Measurement + + + + + + Total Basophil Count + + + + + + Total Bilirubin Measurement + + + + + + Calcium Measurement + + + + + + Cholesterol Measurement + + + + + + Creatine Kinase Measurement + + + + + + Chloride Measurement + + + + + + Color Assessment + + + + + + Creatinine Measurement + + + + + + Eosinophil Count + + + + + + Gamma Glutamyl Transpeptidase Measurement + + + + + + Glucose Measurement + + + + + + Hematocrit Measurement + + + + + + Hemoglobin Measurement + + + + + + Potassium Measurement + + + + + + Ketone Measurement + + + + + + Lymphocyte Count + + + + + + Macrocyte Count + + + + + + Erythrocyte Mean Corpuscular Hemoglobin + + + + + + Erythrocyte Mean Corpuscular Hemoglobin Concentration + + + + + + Erythrocyte Mean Corpuscular Volume + + + + + + Monocyte Count + + + + + + pH + + + + + + Phosphate Measurement + + + + + + Platelet Count + + + + + + Poikilocyte Measurement + + + + + + Total Protein Measurement + + + + + + Erythrocyte Count + + + + + + Sodium Measurement + + + + + + Specific Gravity + + + + + + Thyrotropin Measurement + + + + + + Urate Measurement + + + + + + Urea Nitrogen Measurement + + + + + + Urobilinogen Measurement + + + + + + Vitamin B12 Measurement + + + + + + Leukocyte Count + + + + + + + + + + + + + + + Conjunctiva + + + + + + Eye + + + + + + Anterior Chamber of the Eye + + + + + + Iris + + + + + + Cornea + + + + + + + + + Ear + + + + + + Oral Cavity + + + + + + + + + Symptom Onset + + + + + + + + + Alzheimer's Disease + + + + + + + Adverse Event + + + + + + Completed + + + + + + Death + + + + + + Lack of Efficacy + + + + + + Lost to Follow-Up + + + + + + Other + + + + + + Physician Decision + + + + + + Pregnancy + + + + + + Protocol Deviation + + + + + + Screen Failure + + + + + + Study Terminated By Sponsor + + + + + + Withdrawal By Parent/Guardian + + + + + + Withdrawal By Subject + + + + + + + + + Not Done + + + + + + + + + Abnormal + + + + + + Normal + + + + + + + + + Abnormal + + + + + + High + + + + + + Low + + + + + + Normal + + + + + + + + + + + + + Interpretation + + + + + + + + No + + + + + + Yes + + + + + + + + + Yes + + + + + + + + + Right Eye + + + + + + Left Eye + + + + + + + + + Slit-lamp Examination + + + + + + + + + + + + + + + + Abnormality Detail + + + + + Interpretation + + + + + + + + + Fatal + + + + + + Not Recovered/Not Resolved + + + + + + Recovered/Resolved + + + + + + Recovered/Resolved With Sequelae + + + + + + Recovering/Resolving + + + + + + Unknown + + + + + + + + + PHQ01-Little Interest/Pleasure in Things + + + + + + PHQ01-Feeling Down Depressed or Hopeless + + + + + + PHQ01-Trouble Falling or Staying Asleep + + + + + + PHQ01-Feeling Tired or Little Energy + + + + + + PHQ01-Poor Appetite or Overeating + + + + + + PHQ01-Feeling Bad About Yourself + + + + + + PHQ01-Trouble Concentrating on Things + + + + + + PHQ01-Moving Slowly or Fidgety/Restless + + + + + + PHQ01-Thoughts You Be Better Off Dead + + + + + + PHQ01-Difficult to Work/Take Care Things + + + + + + PHQ01-Total Score + + + + + + + + + + + + + + + + + + + + + Not at all + + + + + Several days + + + + + More than half the days + + + + + Nearly every day + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Standing + + + + + + Supine + + + + + + + + + Informed Consent + + + + + + + + + Patient Health Questionnaire - 9 Item + + + + + + + + + Satisfaction With Life Scale Questionnaire + + + + + + + + + American Indian Or Alaska Native + + + + + + Asian + + + + + + Black Or African American + + + + + + Native Hawaiian Or Other Pacific Islander + + + + + + White + + + + + + + + + Multiple + + + + + + + Adverse Events + + + + + + Disposition + + + + + + Death Details + + + + + + Findings About Events or Interventions + + + + + + + + + Many + + + + + + One + + + + + + + + + Oral + + + + + + Topical + + + + + + Intravenous + + + + + + Nasal + + + + + + Inhalation Route of Administration + + + + + + Transdermal + + + + + + + + + Subcutaneous Route of Administration + + + + + + + + + Hamilton Depression Rating Scale 17 Item Clinical Classification + + + + + + + + + Female + + + + + + Male + + + + + + + + + + + + + + + + + Interventional + + + + + + + + + SWLS01-Have Gotten Important Things + + + + + + SWLS01-I Am Satisfied with My Life + + + + + + SWLS01-Live Life Over Change Nothing + + + + + + SWLS01-My Life Conditions are Excellent + + + + + + SWLS01-My Life is Close to Ideal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Strongly disagree + + + + + Disagree + + + + + Slightly disagree + + + + + Neither agree nor disagree + + + + + Slightly agree + + + + + Agree + + + + + Strongly agree + + + + + + + Double Blind + + + + + + + + + Placebo + + + + + + + + + Treatment + + + + + + + + + Phase II Trial + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Actual Subject Number + + + + + + Adaptive Study Design Indicator + + + + + + Test Product Added to Existing Treatment + + + + + + Planned Maximum Age of Subjects + + + + + + Planned Minimum Age of Subjects + + + + + + Data Cutoff Date Description + + + + + + Data Cutoff Date + + + + + + Dose + + + + + + Pharmaceutical Dosage Form + + + + + + Dose Frequency + + + + + + Dosage Form Unit + + + + + + Planned Country of Investigational Site + + + + + + Healthy Subject Indicator + + + + + + Trial Indication + + + + + + Intervention Model + + + + + + Intervention Type + + + + + + Trial Length + + + + + + Planned Number of Arms + + + + + + Trial Primary Objective + + + + + + Trial Secondary Objective + + + + + + Primary Outcome Measure + + + + + + Secondary Outcome Measure + + + + + + Pharmacological Class of Investigational Therapy + + + + + + Planned Subject Number + + + + + + Randomization + + + + + + Randomization Quotient + + + + + + Clinical Trial Registry Identifier + + + + + + Route of Administration + + + + + + Study Data Tabulation Model Implementation Guide Version + + + + + + Study Data Tabulation Model Version + + + + + + Clinical Study End Date + + + + + + Sex of Study Group + + + + + + Clinical Study Sponsor + + + + + + Study Start Date + + + + + + Study Stop Rule + + + + + + Study Type + + + + + + Trial Blinding Schema + + + + + + Control Type + + + + + + Diagnosis Group + + + + + + Clinical Study by Intent + + + + + + Trial Title + + + + + + Trial Phase + + + + + + Protocol Agent + + + + + + Trial Type + + + + + + + + + Efficacy + + + + + + Pharmacokinetic + + + + + + Safety + + + + + + + + + Milligram + + + + + + Nanogram + + + + + + Tablet + + + + + + + + + Milliliter + + + + + + + + + Gram per Liter + + + + + + + + + Milligram + + + + + + + + + Million per Microliter + + + + + + + + + Billion per Liter + + + + + + + + + Percentage + + + + + + + + + Unit per Liter + + + + + + + + + Femtoliter + + + + + + + + + Femtomole + + + + + + + + + Femtomole + + + + + + + + + Gram per Deciliter + + + + + + + + + Milliequivalent Per Liter + + + + + + + + + Microinternational Unit per Milliliter + + + + + + + + + Microunit per Milliliter + + + + + + + + + Milligram per Deciliter + + + + + + + + + Millimole per Liter + + + + + + + + + Nanogram per Liter + + + + + + + + + Picogram + + + + + + + + + Picomole per Liter + + + + + + + + + Micromole per Liter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Diastolic Blood Pressure + + + + + + Pulse Rate + + + + + + Height + + + + + + Systolic Blood Pressure + + + + + + Temperature + + + + + + Weight + + + + + + + + + Millimeter of Mercury + + + + + + + + + Millimeter of Mercury + + + + + + + + + Inch + + + + + + + + + Centimeter + + + + + + + + + Beats per Minute + + + + + + + + + Beats per Minute + + + + + + + + + Degree Fahrenheit + + + + + + + + + Degree Celsius + + + + + + + + + Pound + + + + + + + + + Kilogram + + + + + + + + + + + + + + + + + + + + + + + + + + If AEENRTPT is populated, AEENTPT is DM.RFPENDTC for the subject. + + + + + If CMENRTPT is populated, CMENTPT is DM.RFPENDTC for the subject. + + + + + Study day relative to RFSTDTC. Date - RFSTDTC + 1 if on or after RFSTDTC. Date - RFSTDTC if date precedes RFSTDTC. + + + + + Starts at "1" for first device identifier and increments by one for each DIPARM + + + + + If DTHDTC is populated then DTHFL='Y' + + + + + EPOCH from SE where date >= SESTDTC and date < SEENDTC + + + + + EXDOSE = ECDOSE * ECPSTRG expressed in mg. + + + + + If FTSTRESC is numeric then FTSTRESN=FTSTRESC in numeric format, else null. + + + + + If IECAT=INCLUSION then IEORRES=N, else if IECAT=EXCLUSION then IEORRES=Y + + + + + LBSTRESC is equal to LBORRES or the value in standard units if a conversion is necessary. + + + + + Set to "Y" for last record with non-null original result on or before the first dose date (RFXSTDTC). Null otherwise. + + + + + If QSORRES="Not at all" then 0 +If QSORRES="Several days" then 1 +If QSORRES="More than half the days" then 2 +If QSORRES="Nearly every day" then 3 + + + + + QSSTRESC=QSORRES + + + + + If QSORRES="Strongly disagree" then 1 +If QSORRES="Disagree" then 2 +If QSORRES="Slightly disagree" then 3 +If QSORRES="Neither agree nor disagree" then 4 +If QSORRES="Slightly agree" then 5 +If QSORRES="Agree" then 6 +If QSORRES="Strongly agree" then 7 + + + + + If QSSTRESC is numeric then QSSTRESN=QSSTRESC in numeric format, else null. + + + + + The Date of Study Completion or Early Termination. Null for screen failures. + + + + + The latest date of assessment for the subject as determined by the End of Study Form, any scheduled assessments, Adverse Events, or Concomitant Medications. + + + + + The first date/time of study drug. Null for screen failures. + + + + + The last date/time of study drug administration. Null for subjects with no treatment data. + + + + + The first date/time of study drug administration. Null for subjects with no treatment data. + + + + + RSSTRESC is the corresponding numeric value of RSORRES according the values shown on the HAMD-17 CRF page. + + + + + SEENDTC is set to the start of the next Element, or RFPENDTC for the last Element. + + + + + Unique sequence number within a subject, restarting at 1 for every subject, applied to sorted data. + + + + + SESTDTC if set to the --DTC for that subject which exists in the data for the defined start of the Element, such as DSSTDTC when DSDECOD=INFORMED CONSENT OBTAINED for Screening Elements or min(EXSTDTC) for Dosing Elements. + + + + + If --STRESC represents a numeric value then --STRESN is the numeric version of --STRESC, else null. "--" represents the domain code. + + + + + For each scheduled visit, SVENDTC = the last (max) date associated with a subject for that visit. For unplanned visits, SVENDTC is the date of the visit. + + + + + For each scheduled visit, SVSTDTC = the first (min) date associated with a subject for that visit. For unplanned visits, SVSTDTC is the date of the visit. + + + + + Unique sequence number within each TSPARM, restarting at 1 for per TSPARM, applied to sorted data. + + + + + Data collected in conventional units (i.e. F, lbs, inches) is converted using standard conversion factors to standard units (C, kg, cm). + + + + + + + + + + + Even though the variable is 'Assigned' an annotation has been added to page 23 to clarify the assignment. + + + + + Coding variables are not populated due to the proprietary coding dictionary, but the variables are included as they are Expected or Required. + + + + + Coding variables are not populated due to the proprietary coding dictionary, but the variables are included as they are Expected or Required. Note CDISC Conformance Rule CG0014 would fire for this variable due to the decision not to populate coding variables. + + + + + Subject CDISC003 had an AE of Epistaxis on 2013-09-30 with AESER set to 'Y' without any of the individual serious qualifiers set to 'Y' also. The site was queried several times but the data were not updated. Note Conformance Rule CG0041 would fire for this subject. + + + + + If the CM is not taken for a 'Primary Study Condition' then CMINDC would be 'Prophylaxis or Non-therapeutic use' + + + + + Since no collected data was subjective then QEVAL was not populated. It is an 'Expected' variable and so is included. + + + + + Since no subjects had more than 3 Races, RACE4 was not used. + + + + + Since no subjects had more than 3 Races, RACE5 was not used. + + + + + Variable is Assigned but there are annotations to help understand the data and so references to the proper pages are included + + + + + DataType is 'partialDatetime' instead of 'datetime' since datetime values are planned to be collected without seconds for this study. + + + + + All values are null as the findings are not visit based. The variable is Expected and so is included. + + + + + The FA domain contains Findings About Injection Site Reaction Adverse Events + + + + + IEDY is needed if IEDTC is included. Note RFSTDTC is not populated for not randomized subjects then IEDY could not be populated in those cases. + + + + + Please see Appendix 1 of the cSDRG for complete versions of IETESTCD and IETEST. + + + + + Standard's Conformance Notes: +1) The SDTM v1.7/SDTMIG v3.3 datasets were evaluated manually and programmatically by the CDISC SDS MSG Team. At the completion of the SDTM-MSG v2.0, the CDISC SDTM v1.7/SDTMIG v3.3 conformance rules were recently published, but not available by any validation tools to validate. +2) The Define-XML document was evaluated manually and programmatically by the CDISC SDS MSG Team. At the completion of the SDTM-MSG v2.0, the CDISC +Define-XML v2.1 conformance rules were not published, nor available by any validation tools to validate. Please ensure that any official regulatory submission of an Define-XML v2.1 document and accompanying data is done in accordance to the respective regulatory health authorities requirements/guidance. + + + + + Per protocol, electroencephalograms are only performed after such an event were to occur. No subjects within the trial had an occurrence of an electroencephalogram event. Therefore, no data exists for the NV dataset and as such was not submitted. + + + + + Per protocol, electroencephalograms are only performed after such an event were to occur. No subjects within the trial had an occurrence of an electroencephalogram event. Therefore, no data exists for the NV dataset and as such SUPPNV was not submitted. + + + + + No subjects within the trial had an ophthalmic examination of clinical significance to report. Therefore, no data exists for the SUPPOE dataset and as such was not submitted. + + + + + QSPH contains the PATIENT HEALTH QUESTIONNAIRE-9 (PHQ-9) questionnaire data. + + + + + QSSL contains the SATISFACTION WITH LIFE SURVEY (SWLS) questionnaire data. + + + + + Study Data Tabulation Model Implementation Guide: Human Clinical Trials Version 3.3 + + + + + Study Data Tabulation Model Implementation Guide for Medical Devices Version 1.0 + + + + + This was the latest release of CDISC CT available when this sample submission was completed. + + + + + This was the CDISC CT Package associated to the CDISC Define-XML Specification Version 2.1 when this sample submission was completed. + + + + + All vital signs were performed as expected, so VSSTAT was never populated. The variable is included as it was possible to populate it in this study. + + + + + + + + + + Annotated CRF + + + + Reviewers Guide + + + + + + + + + + diff --git a/docs/files/unit-test-ruleid-sdtmigexample-negative.xlsx b/docs/files/unit-test-ruleid-sdtmigexample-negative.xlsx new file mode 100644 index 0000000..d2a9816 Binary files /dev/null and b/docs/files/unit-test-ruleid-sdtmigexample-negative.xlsx differ diff --git a/docs/files/unit-test-coreid-12345-positive.xlsx b/docs/files/unit-test-ruleid-sdtmigexample-positive.xlsx similarity index 69% rename from docs/files/unit-test-coreid-12345-positive.xlsx rename to docs/files/unit-test-ruleid-sdtmigexample-positive.xlsx index a560bb0..9b89e54 100644 Binary files a/docs/files/unit-test-coreid-12345-positive.xlsx and b/docs/files/unit-test-ruleid-sdtmigexample-positive.xlsx differ diff --git a/docs/files/unit-test-sdtmig-sendig-template.xlsx b/docs/files/unit-test-sdtmig-sendig-template.xlsx new file mode 100644 index 0000000..414f75b Binary files /dev/null and b/docs/files/unit-test-sdtmig-sendig-template.xlsx differ diff --git a/docs/screenshots/TIGexample_library_worksheet.jpg b/docs/screenshots/TIGexample_library_worksheet.jpg new file mode 100644 index 0000000..3497ecb Binary files /dev/null and b/docs/screenshots/TIGexample_library_worksheet.jpg differ diff --git a/docs/screenshots/TestDataTemplate_datasets_worksheet.jpg b/docs/screenshots/TestDataTemplate_datasets_worksheet.jpg new file mode 100644 index 0000000..5efef9a Binary files /dev/null and b/docs/screenshots/TestDataTemplate_datasets_worksheet.jpg differ diff --git a/docs/screenshots/TestDataTemplate_domains_worksheet.jpg b/docs/screenshots/TestDataTemplate_domains_worksheet.jpg new file mode 100644 index 0000000..efecaa9 Binary files /dev/null and b/docs/screenshots/TestDataTemplate_domains_worksheet.jpg differ diff --git a/docs/screenshots/TestDataTemplate_library_worksheet.jpg b/docs/screenshots/TestDataTemplate_library_worksheet.jpg new file mode 100644 index 0000000..ba8ce7a Binary files /dev/null and b/docs/screenshots/TestDataTemplate_library_worksheet.jpg differ diff --git a/docs/screenshots/TestDataTemplate_worksheets.jpg b/docs/screenshots/TestDataTemplate_worksheets.jpg new file mode 100644 index 0000000..eb55c15 Binary files /dev/null and b/docs/screenshots/TestDataTemplate_worksheets.jpg differ diff --git a/docs/screenshots/TestData_Highlighting.jpg b/docs/screenshots/TestData_Highlighting.jpg new file mode 100644 index 0000000..f21e42a Binary files /dev/null and b/docs/screenshots/TestData_Highlighting.jpg differ diff --git a/docs/screenshots/TestData_Validation_Sheet.jpg b/docs/screenshots/TestData_Validation_Sheet.jpg new file mode 100644 index 0000000..76b2749 Binary files /dev/null and b/docs/screenshots/TestData_Validation_Sheet.jpg differ diff --git a/docs/test_data.md b/docs/test_data.md index 46ba3ed..42ff1f3 100644 --- a/docs/test_data.md +++ b/docs/test_data.md @@ -1,48 +1,121 @@ # Test Data -## Preparation +## Preparing Test Data for Unit Testing ### Assumptions -- CORE MVP 1.0 must support SAS V5 XPT data sets. Other formats such as CSV, Dataset-XML, etc. are a nice-to-haves. -- Many volunteer contributors do not have the ability to create SAS V5 XPT files, easily and quickly. -- An Excel approach is very similar to creating data examples in the wiki. +- CORE MVP 1.0 must support SAS V5 XPT and Dataset-JSON data file formats for validation. Other formats such as CSV, Dataset-XML, etc. are a nice-to-haves. +- Many volunteer contributors do not have the ability to create SAS V5 XPT files, easily and quickly for creation of test data for unit testing. +- An Excel format approach is very similar to creating data examples in the wiki. - A well-templated Excel adds consistency and reduces fatigue. +- Test data in Excel are to be used for unit testing = checking whether the rule logic works correctly and output matches with what is expected. - Volunteer contributors could also use unit testing for debugging rule logic. -- Unit test includes both positive and negative tests. -- Unit test will be conducted per CORE rule. Test data will be relatively small, just enough data points to assert correctness. -- Existing mock studies in SDTM format are a valuable resource. -- Volunteer contributors will receive a report for each run of unit test. + +- Unit testing includes testing rule logic on both positive and negative test data. + - Positive test data: Test data is in compliance with the conformance rule and will not result in output. All test data passes. + - Negative test data: Test data is not in compliance with the conformance rule and will result in output. Not all test data passes. +- Unit testing will be conducted per CDISC Open Rule. If more than one conformance rule (e.g. conformance rules from 2 different standards like SDTMIG and SENDIG use exactly the same rule logic and scope) is included in 1 CDISC Open Rule, then unit testing should only be done once. The standard used to create test data can be chosen by the volunteer contributor. +- Test data should be kept relatively small, just enough data points to assert correctness and full functionality of the rule. +- Existing mock studies in are available to the volunteer contributors as a valuable resource +- Volunteer contributors will receive a report (= results file) for each run of unit testing. ### Not Covered -This proposal does not cover these topics: +This Test Data section does not cover unit test execution. -- Define-XML generation. -- Unit test execution. +### Test Data Format -### Proposal +- Volunteer contributors will use Excel workbooks to create test data, such that there will be: + - At least one file for positive test data. + - At least one file for negative test data. + - Positive and negative test data will be created in separate Excel workbooks. +- Multiple domains can be added in 1 Excel workbook. +- Because we want to simulate SAS V5 XPT, the Excel workbook contain different worksheets. +- Test Data templates are available and will ensure consistency in test data creation among the volunteer contributors but also help them in generating test data in the most efficient way. + +#### SDTMIG & SENDIG + +**Worksheets:** + - A worksheet for library details, called '**Library**' where 'Product' and 'Version' need to be defined (e.g. Product = sdtmig, Version = 3-4) + - A worksheet for Dataset metadata, called '**Datasets**' where 'Filename' and 'Label' need to be defined. + - One worksheet **for each dataset** needed for the unit testing, with both variable metadata and data (e.g. ae.xpt for AE dataset, dm.xpt for DM dataset,...). + + ![Test Data Template - worksheets](./screenshots/TestDataTemplate_worksheets.jpg) -- Volunteer contributors will use Excel to create test data, such that: - - There will be at least one set for positive test. - - At least another for negative test will be created. - - One Excel workbook will be created per set. -- Because we want to simulate SAS V5 XPT, the Excel workbook will contain: - - A worksheet for dataset metadata. - - One worksheet for each dataset, with both variable metadata and data. -- To ensure consistency and reduce fatigue, volunteer contributors will have access to a well-templated Excel workbook to jumpstart: - - The Dataset worksheet will contain all domains modeled in SDTMIG v3.4, with: +**Worksheet Completion based on Template:** +To ensure consistency and reduce fatigue, the templates are already prepopulated with standard data that can be adapted based on the need per rule. Adaptations should be done to only serve the rule testing purpose. All additional domains, worksheets,... should be removed. + +- **Library**: + - The Library worksheet will contain a list of different IGs (name and version) and also CDISC controlled terminology versions (e.g. sdtmct-2024-03-29) + - Based on the rule that is going to be tested and the IG scope, the applicable 'product' and 'version' should be completed. Example: CG0100 is applicable for SDTMIG 3.3 so Product= sdtmig and Version = 3-3 + - If a rule is applicable for multiple versions of an IG, then only 1 IG should be tested unless there is a clear distinction in rule logic between IG versions. + - If a rule needs to use CDISC CT, then also the CT version needs to be specified in a new record under 'Product'. + + ![Test Data Template - library worksheet](./screenshots/TestDataTemplate_library_worksheet.jpg) + +- **Datasets** + - The Dataset worksheet will contain all domains modeled in the included IGs - Dataset filename (e.g., ae.xpt) - Dataset label (e.g., Adverse Events) - - There will be one worksheet per SDTMIG v3.4 domain, fitted with: + - Based on the rule that is going to be tested and the scope (Class, Domain), the dataset filename and dataset label of the domains that are used to perform the unit testing (= test data created), need to be completed in the Datasets worksheet. If AE is used to test the rule logic, then ae.xpt should be specified in the Datasets worksheet. All datasets that are created should be specified. + - This worksheet should not list datasets that are not created. + + ![Test Data Template - datasets worksheet](./screenshots/TestDataTemplate_datasets_worksheet.jpg) + +- **\*.xpt** + - There will be one worksheet per domain, fitted with: - Variable name (e.g., AETERM) - Variable label (e.g., Reported Term for the Adverse Event) - Data type (i.e., Char or Num) - Default variable length (i.e., 50 for Char, 8 for Num) - - These will also be included to maximize customization: + - The templates also include additional data for further customization. - A list of Identifiers and Timing variables from SDTM v2.0. - A list of Events, Interventions, and Findings class variables from SDTM v2.0. -- Volunteer contributors will use the information available to instantiate test data, such that: + + ![Test Data Template - domains worksheets](./screenshots/TestDataTemplate_domains_worksheet.jpg) + + #### ADaMIG + + under construction + + #### Define-XML + + - In case a CDISC Open Rule is using metadata captured in a define.xml to execute rule logic, then a test define.xml needs to be created (negative and positive) and uploaded for unit testing. + - To create this test define.xml, the templates created for the Metadata Submission Guidelines for SDTM and ADaM can be used and adapted accordingly. + + #### TIG + + - Test data creation for TIG is similar to creation of test data for SDTMIG, SENDIG or ADaMIG. + - There are 2 additional parameters in the library worksheet that need to be specified for TIG. + - Substandard: sdtm, send, adam + - Use_Case: PROD, INDH, NONCLIN, ANALYSIS + - The applicability of these 2 parameters is indicated in the TIG conformance rules spreadsheet published on the CDISC website: https://www.cdisc.org/system/files/members/standard/foundational/TIG%20Conformance%20Rules%20v1.0%20%281%29.xlsx + + ![TIG Example - library worksheet](./screenshots/TIGexample_library_worksheet.jpg) + + #### USDM + + under construction + +### Creating Correct Test Data + +**Best Practices** + +Creating solid, qualitative test data is a skill on its own and needs to be done with care. Below best practices will help you during this process. +- Test data should test **all** functionalities of the rule logic. +- Test data should test both **condition** (if appplicable) and **rule**. +- If more than 1 domain is in scope, test data should be created for more than 1 domain. + - Scope = EVENTS, then for example test data can be made for AE and MH. + - Scope = ALL then for example test data for 1 EVENTS domain and 1 FINDINGS domain can be made. + - If a domain is excluded from the scope, then this domain should be included in the test data as positive test data. +- Generating too many rows in test data should be avoided. Only what is necessary to test the rule logic should be created. +- If the rule logic is testing >, = , < or something similar, then test data should be created that is testing the treshold values. +- Positive test data should not generate output in unit testing. +- Negative test data should generate output in unit testing. + +- If the rule that is being testing is referencing CDISC CT, then the correct name and version should be added under 'Product' in the 'Library' worksheet. + +- Volunteer contributors should use the information available to create the test data, such that: - A test dataset can be a copied from a templated worksheet. - Worksheet can be renamed to match the dataset metadata. - Test data can be inserted as data rows to the copied worksheet. @@ -51,33 +124,76 @@ This proposal does not cover these topics: - Dataset metadata can be modified in accordance to test purpose of the associated rule logic. - Mock study data will be available to volunteer contributors to easily borrow (i.e., copy and paste) as test data. -### Templates +- The Test Data Files should follow the naming conventions. + - Positive Test Data + - unit-test--positive1.xlsx + - unit-test--positive2.xlsx (only if applicable) + - ... + - Negative Test Data + - unit-test--negative1.xlsx + - unit-test--negative2.xlsx (only if applicable) + - ... + + - Examples + - unit-test-CG0288-positive1.xlsx + - unit-test-CG0288-negative1.xlsx + +### Adding Predefined Discrepancies +- Prior to unit testing, expected output should be marked in the negative test data file. Cells expected to generate output should be highlighted in 'yellow'. +- In addition to the highlights, an additional validation sheet should be completed to list the expected output so that during unit testing this can be compared automatically with the output of the unit testing. +- Completion of the **Validation** worksheet. + - **Error Group**: + - Add each error as a new validation group (note that this might not be only a single row - for example if you highlight two cells that will cause a single error, and be outputted as a single error, then you should create TWO rows in the same validation group (ie both in group '1')). + - Create groups using sequential numbers for the validation group column. + - **Sheet**: Name of the data sheet with the error e.g. cm.xpt + - **Error Level**: + - Add 'Record' if it is a normal row error + - 'Variable' if it is an error related to an entire column, + - 'Dataset' if it is an error related to a whole dataset (ie missing ae.xpt sheet or similar). + - **Row num**: Provide the row number (Note that any variable names will be row 1 and the first row starts from row 5 due to the metadata rows in the sheets). + - **Variable**: Provide the variable name (found in the first row of the column) - with the row number this fully identifies the error cell. + - **Error Value**: + - Copy the error value from the highlighted cell into the 'Error value'. + - If the highlighted cell has no value, use '[ABSENT]' to indicate this (including the square brackets). + +![Negative Test Data - yellow highlighting](./screenshots/TestData_Highlighting.jpg) + +![Negative Test Data - Validation Sheet](./screenshots/TestData_Validation_Sheet.jpg) -With the information given above, attached here is a mock of the well-templated Excel workbook. It contains all class variables and domains and, such that: +### Templates - Examples - Sample Data -- The Dataset worksheet contains a list of datasets can be used for unit testing. -- The Identifier, Events, Interventions, Findings, Timing, and Associated Persons worksheets are variables from SDTM v2.0. -- The \*.xpt worksheets contain domain metadata from SDTMIG v3.4, as well as AC, APRELSUB, DI, and TX from SDTM v2.0. +This section contains links to the different Test Data Templates, Test Data Examples and Sample Data. Together with the instructions given above, this should give the volunteer contributors sufficient information to create consistent, qualitative test data that should ensure correct unit testing of the rule. -[unit-test-sdtmig-3-4-template.xlsx](files/unit-test-sdtmig-3-4-template.xlsx ":ignore") + #### Template #### -Also, here is a mock Excel workbook for positive testing against a fictitious CORE rule Id 12345, using: + - The Dataset worksheet contains a list of datasets can be used for unit testing. + - The Identifier, Events, Interventions, Findings, Timing, and Associated Persons worksheets are variables from SDTM v2.0. + - The \*.xpt worksheets contain domain metadata from SDTMIG v3.4, as well as AC, APRELSUB, DI, and TX from SDTM v2.0. -- dm.xpt and ae.xpt. -- Both with variable metadata adjusted, unused columns removed, data rows added. + [unit-test-sdtmig-sendig-template.xlsx](files/unit-test-sdtmig-sendig-template.xlsx ":ignore") -[unit-test-coreid-12345-positive.xlsx](files/unit-test-coreid-12345-positive.xlsx ":ignore") + #### Examples #### -CDISC has 2 sets of mock study in SDTM format. They have been converted into Excel format, which can be tailored for unit test data. + Also, here is a mock Excel workbook for positive and negative testing against which contains: -- [CDISCTestData-sdtm-xpt-xlsx.zip](files/CDISCTestData-sdtm-xpt-xlsx.zip ":ignore") A set of test data files transformed from the CDISCTestData Github repo, sourced from /SDTM/XPT. Per Read Me, this mock study implements "SDTM IG Version 3.2." -- [sdtm-msg-2-0-m5-datasets-xlsx.zip](files/sdtm-msg-2-0-m5-datasets-xlsx.zip ":ignore") A set of test data files transformed from the example submission bundled in the SDTM MSG v2.0, sourced from /m5/datasets/cdiscpilot01/tabulations/sdtm, as well as the split subdirectory. Per documentation, this example submission implements "SDTM v1.7/SDTMIG v3.3, and SDTM Terminology 2020-03-27." + - dm.xpt and ae.xpt. + - Both with variable metadata adjusted, unused columns removed, data rows added. + + [unit-test-ruleid-sdtmigexample-positive.xlsx](files/unit-test-sdtmigexample-positive.xlsx ":ignore") + [unit-test-ruleid-sdtmigexample-negative.xlsx](files/unit-test-sdtmigexample-negative.xlsx ":ignore") + + #### Sample Data #### + + CDISC has 2 sets of mock study in SDTM format. They have been converted into Excel format, which can be tailored for unit test data. + + - [CDISCTestData-sdtm-xpt-xlsx.zip](files/CDISCTestData-sdtm-xpt-xlsx.zip ":ignore") A set of test data files transformed from the CDISCTestData Github repo, sourced from /SDTM/XPT. Per Read Me, this mock study implements "SDTM IG Version 3.2. + - [sdtm-msg-2-0-m5-datasets-xlsx.zip](files/sdtm-msg-2-0-m5-datasets-xlsx.zip ":ignore") A set of test data files transformed from the example submission bundled in the SDTM MSG v2.0, sourced from /m5/datasets/cdiscpilot01/tabulations/sdtm, as well as the split subdirectory. Per documentation, this example submission implements "SDTM v1.7/SDTMIG v3.3, and SDTM Terminology 2020-03-27. ## Storage ### Assumptions -- 1000 is an estimate of # of rules volunteer contributors will create. +- 1500 is an estimate of # of rules volunteer contributors will create. - Each rule will have file artifacts, such as SAS, Excel, and XML files. - Main purpose for these file artifacts is to support unit testing. Secondary purpose is to support regression test. - Unit testing will need both data for positive test & negative test, which each volunteer contributors is responsible to create & maintain. @@ -88,28 +204,21 @@ CDISC has 2 sets of mock study in SDTM format. They have been converted into Exc ### Proposal -CDISC SharePoint will be used for storage: +GitHub will be used for storage: -- Has precedent use case, e.g., CDISC Interchange speakers from different organizations to add & update presentation materials. - Supports drag-and-drops. - File versioning is a built-in functionality, behind the scene, without user interventions. -- For occasional permissioning issues when SharePoint is confused due to crossing organizations, volunteer contributors can receive support from either CDISC I.T. or Jira project for CORE. - -Other platforms considered: - -- CDISC Confluence wiki: Could be unwieldy given the anticipating volume of test artifacts; folder structure not supported. -- Github or Azure DevOps: Could be very intimating for volunteer contributors who are not familiar with git repos; yet another tool to learn. +- Test data storage is directly linked to the rule YAML file and the results file generated via automated unit testing, allowing clear traceability and version control. ### Sharepoint Site -[CORE Rules test data (permission required)](https://cdisc.sharepoint.com/sites/CORERules/Shared%20Documents/Forms/AllItems.aspx) +SharePoint will be used to store the source data catalogs, templates etc. for volunteer contributors to use whenever needed. -### Local OneDrive Access +[CORE Rules SharePoint (permission required)](https://cdisc.sharepoint.com/sites/CORERules/Shared%20Documents/Forms/AllItems.aspx) -It is recommended that you use OneDrive for the CORE Rules test data. This will allow you the ability to: +### Local OneDrive Access -- edit test files on your local desktop without the need to upload or edit within the browser -- load test files in the CORE Editor by browsing to the Excel files without the need to download files from Sharepoint +It is recommended that you use OneDrive for access to the CORE Rules SharePoint. This will allow you the ability to consult files on your local desktop without the need to upload or edit within the browser. There are two options for accessing the Sharepoint files from OneDrive. The choice is personal preference, but Sharepoint allows you to only do one or the other.