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The document provides an overview of the standard lab system in Oracle Clinical. It discusses how to establish and maintain laboratories, lab units and questions, conversions between lab units, and assignment of normal ranges for questions based on age and sex. The basic process flow includes creating lab questions, units, assigning units to questions, defining conversions, assigning ranges manually or via load, and setting up criteria for assignment of labs to clinical data. It also covers creating textbook ranges, preferred copy groups, and electronic loading of lab ranges.

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OC Labs Module Presenter:Priya Gehlawat
Lab System Overview ā€¢ Oracle Clinical provides a lab system to facilitate the collection and reporting of laboratory data ā€¢ The lab system allows the user to establish and maintain ā€¢ Laboratories ā€¢ Lab units and assignment to lab test questions ā€¢ Conversions between lab units by lab test question ā€¢ Ranges for questions based on age and sex ā€¢ Assignment of labs to received DCMs ā€¢ Creation of lab extract views in oracle and SAS 2
Lab System Overview ā€¢ The standard lab system allows ranges to be assigned to any question that is of type LAB TEST and data type NUMBER ā€¢ After a response is entered/loaded, the value can be compared against lab normal ranges and identified as Hi, Lo, or Normal ā€¢ Lab data however is often non-numeric (>3, 5-8, +++, etc.) ā€¢ These values cannot be handled by the standard lab system and require the use of the NORMLAB2 module ā€¢ In this training, we will cover the standard lab system followed by the set-up and use of NORMLAB2; throughout the practice we will set up the objects required for both 3
Lab System Basic Lab System Process Flow 4 Create Lab Questions in Glib Create Lab Units Assign Lab Units to Lab Questions Define Lab Unit Conversion Formula Assign ranges to Lab Questions for each Lab/Lab Subset manually or via batch load Set-up Criteria for assignment of labs to DCMs Conduct Data Entry Reassign Labs to RDCMs Create Lab Data Extracts Create Lab
Lab System Lab Test Questions 5 Menu: Glib ļƒ° Questions ļƒ° QuestionsCreate lab questions in Glib
Lab System Lab Units 6 Define Lab Units Assign Lab Units to Lab Questions Define Lab Unit Conversion Formula Define Preferred Conversion Units
Lab System Lab Units ā€¢ Lab units are the expected measurement units for lab questions ā€¢ Lab units are created using the menu ā€¢ Labs ļƒŖļ€ Lab Units ļƒŖ Lab Units Ā© 2008, Cognizant Technology Solutions. Confidential 7 Unique code and name is required for each lab unit Representative lab unit code can be used to group lab units that can be used interchangeably
Lab System Lab Test Question Units ā€¢ Any question from the Global Library of type LAB TEST and data type NUMBER can be assigned lab units ā€¢ Lab units are assigned to questions via the menu ā€¢ Labs ļƒŖ Lab Units ļƒŖ LTQ Units ā€¢ All units which may ever apply to the question should be assigned so that the ranges can be defined for those units ā€¢ All the lab units associated with the representative lab unit become available in setting up ranges for that lab question ā€¢ Units do not have to be defined for a range to be set up for a lab test question; some lab tests do not have units 8
Lab System Lab Test Question Units Ā© 2008, Cognizant Technology Solutions. Confidential 9 Lab units are assigned to lab test questions Each question in each domain can have one or more representative lab units assigned to it Lab units can be deactivated if they are not to be used any longer
Lab System Lab Unit Conversion ā€¢ Lab unit conversions provide a means to create a formula to convert data for a lab test from one unit to another unit ā€¢ For each lab test question, multiple conversion formulas can be created for the various lab unit combinations ā€¢ Conversion formulas are created in the menu ā€¢ Labs ļƒŖ Lab Units ļƒŖ LU Conversions ā€¢ The conversion formulas are available in reports and can be used in derivation procedures to convert responses between units ā€¢ The conversion formula are used by the NORMLAB2 process to convert lab values to standard units in the data extract view 10
Lab System Lab Unit Conversion 11 Conversion formula are created between units
Lab System Labs and Lab Subsets ā€¢ Labs define locations where data is collected or analyzed ā€¢ Each lab is identified by a code (Lab) and description (Name) which must be unique across replicated locations ā€¢ Lab questions and normal ranges are associated with each lab ā€¢ Each lab can have subsets; this allows the assignment of the same set of questions to the lab with different ranges ā€¢ A set of normal ranges for diabetic patients and one set for non- diabetic patients ā€¢ Lab are created using the menu ā€¢ Labs ļƒŖļ€ Labs ļƒŖļ€ Labs 12
Lab System Labs and Lab Subsets ā€¢ When a lab is created, a lab range subset named DEFAULT is automatically created ā€¢ Other subsets are assigned to labs by selecting a subset name from a LOV in the lab range subset window ā€¢ Lab range subset names must first be created in the installation codelist LAB RANGE SUBSET CODE ā€¢ The naming convention used to reference lab range subsets is ā€¢ LABNAME$<SUBSET NAME> for non-default subsets ā€¢ LABNAME or LABNAME$DEFAULT for default subset 13
Lab System Labs and Lab Subsets 14 Optional address and descriptive information may also be entered Physical laboratories are identified at each site with a unique lab name and description Subsets can be defined for each lab The format mask name will automatically default in the batch data load data file screen when this lab is identified with a data file
Lab System Labs and Lab Subsets 15 Each subset code must first be set up in the installation codelist LAB RANGE SUBSET CODE Subsets are assigned; DEEFAULT is automatically assigned by the system
Lab System Labs and Lab Subsets 16 ā€¢ Other subsets can be assigned to the lab at any time ā€¢ Subsets can never be removed from a lab ā€¢ Ranges may be assigned directly, copied from the DEFAULT subset, or electronically loaded ā€¢ Ranges for a question can only be assigned to other subsets once that question has been assigned to the DEFAULT subset
Lab System Lab Ranges ā€¢ Ranges represent the defined normal range of high and low values for a particular unit for each lab test question ā€¢ Different ranges can be defined for each lab subset; note that the primary lab is always the DEFAULT subset ā€¢ Every question that will have ranges in a lab subset must also have ranges in the DEFAULT subset ā€¢ Within each lab subset, multiple ranges can be defined per lab test question as long as ranges are based on a unique combination of these factors ā€¢ Gender, age, domain, and effective dates 17
Lab System Lab Ranges ā€¢ The DEFAULT lab and subsets can have lab questions and ranges ā€¢ Manually assigned ā€¢ Copied from another lab; subsets can only have ranges copied from the DEFAULT lab ā€¢ Loaded electronically from an ASCII file ā€¢ Assigned via textbook ranges; these are only available for the DEFAULT lab ā€¢ Lab ranges depend on age and sex information from the patient enrollment form 18
Lab System Lab Ranges 19 Question Domain Sex Min Max Values Units Effective Dates Age Age Lo Hi Start End Glucose Global M 18 35 2 5 mgs Glucose Global M 35 65 25 50 dgs Glucose Global F 35 60 dgs 30-06-1998 Glucose Global F 40 80 mgs 01-07-98 None of these lab ranges conflict (overlap) with each other
Lab System Lab Ranges 20 Question Domain Sex Min Max Values Units Effective Dates Age Age Lo Hi Start End Glucose Global M 18 35 2 5 mgs Glucose Global M 35 65 25 50 dgs Glucose Global F 35 60 dgs 30-06-1998 Glucose Global F 40 80 mgs 01-07-1998 Glucose Global M 18 65 2 5 dgs Conflict These ranges overlap and can not be entered
Lab System Lab Ranges 21 Lab Test Question: ā€¢ Any question identified in the Global Library of question type LAB TEST and data type NUMBER ā€¢ The question does not have to be active to have lab ranges assigned
Lab System Lab Ranges 22 Question Domain: ā€¢ The question domain from the Global Library ā€¢ Different ranges can be assigned to the lab test question with the same name in different domains, but NORMLAB2 will not work in this situation
Lab System Lab Ranges 23 Sex: ā€¢ The sex of the patient that this normal range applies to ā€¢ List of values include M, F, or B; defaults to B, for both ā€¢ The patient must be enrolled with a sex assigned for the lab range to be applied
Lab System Lab Ranges 24 Age: ā€¢ The minimum and maximum age of the patient that this range applies to ā€¢ Optional ā€¢ The patient must be enrolled with a birth date assigned for the lab range to be applied ā€¢ Ages may not overlap for the same lab test question for the same sex ļƒ¼ Use age ranges like 18-35 and 35-65 without gaps or else patients with ages like 35.5 will be excluded
Lab System Lab Ranges 25 Values: ā€¢ The low and high range values ā€¢ Lab derived values are compared against this range and identified as being H (High), L (Low), or N (Normal)
Lab System Lab Ranges 26 Lab Unit Name: ā€¢ The lab units that this lab test is collected in ā€¢ Ranges may be defined in different units for different groups if appropriate, e.g., mg/dL for M, IU/L for F ā€¢ Units are not required for a range
Lab System Lab Ranges Ā© 2008, Cognizant Technology Solutions. Confidential 27 Effective Date: ā€¢ The start and end date in which this range is effective ā€¢ Optional ā€¢ A lab question may appear multiple times with different, non-overlapping start and end dates ā€¢ These dates are optional and only need to be used if the applied ranges will change during the course of the study
Lab System Lab Ranges 28 Age Unit: ā€¢ The minimum and maximum units the age of the patient is measured in ā€¢ The default is YEARS
Lab System Lab Ranges Ā© 2008, Cognizant Technology Solutions. Confidential 29 Status: ā€¢ The status of the lab ranges ā€¢ If the high or low values or the units are missing, the system automatically sets the status to MISSING; in this case the range is not available upon extract ā€¢ If these values are entered the system defaults the value of APPROVED ā€¢ Can be changed by the user to UNAPPROVED or SUSPICIOUS to manually mark ranges which need to be checked, but this does not affect whether the ranges are actually used in the extract
Lab System Lab Ranges 30 Range Type: ā€¢ Identifies whether the range was assigned directly (LAB) or via textbook ranges (TEXTBOOK) ā€¢ This field is system set and cannot be manually changed ā€¢ TEXTBOOK range types have greater restrictions on changes than LAB range type
Lab System Lab Ranges 31 Comment: ā€¢ Optional comment about the lab range ā€¢ If the ranges were copied in, the comment will indicate it
Lab System Electronic Load of Lab Ranges ā€¢ Range data for one or more labs can be electronically loaded using a text file ā€¢ The format of the data file needs to be the following with a user specified delimiter; M indicates that a field is mandatory; excluded fields should have a null placeholder (,,) ā€¢ Lab name (M), lab range subset code, lab test question (M), sex, min. age, max. age, min. value (M), max. value (M), unit name, effective start date, effective end date, min. age unit, max. age unit, range type (M) ā€¢ HLAB1, DEFAULT, CHOL, F, 18, 65, 135, 200, MMOL/L,,,,,LAB (here the delimiter is ā€˜,ā€™) 32
Lab System Electronic Load of Lab Ranges 33 This form is used to submit the electronic file to load lab ranges Menu: Labs ļƒ°Lab Batch Data Load ļƒ°Lab Ranges Batch Data Load Identify if the file should be loaded or if this is a test Identify the full path of the file to load Identify the file delimiter Lab questions in a file must all be from the same domain N identifies that the file to load has effective dates Y identifies that the system will supply the effective start and end date for ranges
Lab System Electronic Load of Lab Ranges ā€¢ Duplicate lab ranges cannot be loaded ā€¢ Ranges cannot be loaded if the subset referenced in the file does not exist in the database ā€¢ If date ranges overlap they have to be ordered chronologically ā€¢ End date must be later than the start date and start date is mandatory if end date is provided ā€¢ A question must be assigned to the DEFAULT subset for a lab before ranges can be assigned to any other subset for this lab 34
Lab System Electronic Load of Lab Ranges ā€¢ Default ranges must be loaded before subset ranges can be loaded for a question; they can not be loaded in the same file ā€¢ Ranges that are loaded without a subset range name in the file are loaded into the DEFAULT subset ā€¢ Effective dates are required if the Default Effective Dates parameter of the batch job is set to N ā€¢ Ranges which have different units (e.g., 10 DAYS - 1 YEAR) fail when loaded electronically (Note: this is a bug) 35
Lab System Electronic Load of Lab Ranges ā€¢ Oracle Clinical provides two methods for reviewing lab electronic range loads ā€¢ The output file of the load job lists all of the errors along with the erroneous records ā€¢ The LAB RANGES BATCH LOAD DATA FILE STATUS report includes summary and status information for each lab range load ā€¢ If there are any errors in the load, the data file can be corrected and the load can be re-executed 36
Lab System Electronic Load of Lab Ranges 37 The erroneous record of data The reason the load failed
Lab System Lab Range Load Status Report 38 Menu: Labs ļƒ°Lab Batch Data Load ļƒ°Report Results of the Data Load Identify the full path of the data file under review or use pattern matching to identify a group Identify the date range the files were loaded
Lab System Lab Range Load Status Report 39 11-MAR-99 08:28 Ranges Batch Data Load Data files Status Page 2 0f 2 Data File Created On Mode of Load Status Sub Job Id Number of Errors /val100/lab01.txt 11-MAR-1999 Load and Prepare BAD PREPARE 34777 4 /val100/lab02.txt 11-MAR-1999 Load and Prepare SUCCESS 34957 0 /val100/lab01.txt 11-MAR-1999 Load and Prepare BAD PREPARE 34977 4 /val100/lab01.txt 11-MAR-1999 Load and Prepare SUCCESS 34997 0 ļ‚® This report can be executed after several files have been loaded to review which have failed ļ‚® The output files of the failed jobs can then be reviewed to determine the exact reason for the failure
Lab System Textbook Ranges/Preferred Copy Groups ā€¢ Textbook ranges provide a way to set up standard ranges for a lab test question that can also be used when the lab does not provide specific ranges ā€¢ Multiple textbook ranges can be defined for the same question for different units ā€¢ For example, for the question ALBUMIN, ranges can be defined for men 18-34 years old in both mg/dL and g/L 40
Lab System Textbook Ranges/Preferred Copy Groups ā€¢ Preferred copy groups identify for each lab test question the preferred unit of measurement ā€¢ The preferred copy group is used to copy textbook ranges to a lab ā€¢ The preferred copy group identifies which ranges for each lab test question to copy from the textbook range to the lab 41
Lab System Textbook Ranges/Preferred Copy Groups 42 Textbook ranges are identified per question in a domain Unit, sex, age, or effective dates must be unique between ranges Ranges are defined for GLUC in both g/dL and mg/dL in this example
Lab System Textbook Ranges/Preferred Copy Groups 43 The preferred copy group identifies one unit for each lab test question and only the ranges for that unit are copied to the lab when the textbook range is copied This preferred copy group identifies that textbook ranges for question GLUC that have units in g/dL should be copied to the lab
Lab System Textbook Ranges/Preferred Copy Groups 44 Identify the preferred copy group Click on the [Use Textbook Ranges] button to copy textbook ranges to a lab Optionally enter start and end dates to override the effective dates for the textbook ranges to be copied and click [OK] Optionally enter a text range date to copy older textbook ranges; leave blank to copy current ranges
Lab System Textbook Ranges/Preferred Copy Groups 45 The textbook ranges for GLUC that have the same unit as those identified in the preferred copy group (g/dL) are copied to the Lab
Lab System Textbook Ranges/Preferred Copy Groups 46 Textbook Ranges (Question Specific) Gluc, 20, 50, g/dL Gluc, 2, 5, mg/dl Grancast, 1, 5, mm Grancast, .1, .5 cm Preferred Copy Group ā€¢ Identifies Questions to copy based on unit ā€¢ Allows for multiple questions to be assigned to a lab ā€¢ Gluc (g/dL), Grancast (mm) Lab (Multiple Questions) Gluc, 20, 50, g/dL Grancast, 1, 5, mm
Lab System Assignment of Labs to RDCMs ā€¢ Lab ranges must be assigned to entered or batch loaded data for the ranges to be used in procedures or extracts ā€¢ Lab ranges are assigned to responses by assigning the lab to the received DCM in one of the following ways ā€¢ By the data entry operator during data entry ā€¢ During batch data load (identified in the data file entry) ā€¢ Manually to the RDCM using the lab module ā€¢ Automatically by the system during data entry or batch Data load based on pre-set lab assignment criteria (LAC) ā€¢ During or after data has been entered or batch loaded using the lab assignment criteria module 47
Lab System Lab Assignment Criteria ā€¢ Lab assignment criteria (LAC) allow the automatic assignment of labs to a RDCM either during log-in or after it has been received ā€¢ LAC can be created using any unique combination of the following criteria ā€¢ Study ā€¢ Start date ā€¢ End date ā€¢ Site ā€¢ Investigator 48 ļƒ¼ DCI ļƒ¼ DCM ļƒ¼ Patient ļƒ¼ Clinical planned event ļƒ¼ Actual event
Lab System Lab Assignment Criteria 49 Query for the study, then click on [Lab Assignment Criteria] Menu: Labs ļƒ°Lab Assignment Criteria
Lab System Lab Assignment Criteria 50 Enter lab assignment criteria by site, patient, DCI, etc. Data entered/loaded after the set- up of LAC will automatically have these labs assigned
Lab System LAC/Received DCMs 51 Lab Assignment Type: ā€¢ Assigned by the system based on how lab was assigned to the received DCM ā€¢ The possible values are ļƒ¼ UNKNOWN ā€“ No lab is assigned ļƒ¼ CRITERION ā€“ Lab was assigned automatically during data entry or batch data load based on lab assignment criteria ļƒ¼ LOGIN ā€“ Lab was assigned during log-in by data entry operator ļƒ¼ USER ā€“ Lab was assigned directly to received DCM in this form ā€¢ To assign a received DCM to another lab, select a different lab from the LOV Menu: Labs ļƒ°Lab Assignment Criteria ļƒ° Received DCMs
Lab System Applying LAC 52 LAC must be set up in advance for the study to use the apply lac functionality Another way to modify lab assignment after data is entered or loaded is to use the [Apply LAC] functionality
Lab System Applying LAC 53 The lab assignment type selected will determine which lab values will be changed. Select from LOV and click on [Apply] The assignment types are hierarchical and will only change ones equal to or at lower levels; if LOGIN were selected it would override lab assignments of type LOGIN, UNKNOWN and CRITERION, but not SYSTEM or USER
Lab System NORMLAB2 Overview ā€¢ The standard Oracle Clinical lab system does not allow ranges to be applied to non-numeric responses ā€¢ This excludes a large set of lab responses such as >6, 7-9, etc. ā€¢ Such responses would create data type discrepancies and would be stored as null values for the actual response ā€¢ The NORMLAB2 approach handles this type of lab data by accepting all lab test responses as character text ā€¢ The character text is converted into numeric values using a variety of algorithms built into a standard derivation procedure ā€¢ The converted numeric values can have lab ranges values applied to them from the standard lab range system 54
Lab System NORMLAB2 Overview ā€¢ The standard Oracle Clinical approach does not take into account all of the types of expected responses to lab test questions, as this chart illustrates Ā© 2008, Cognizant Technology Solutions. Confidential 55 Lab Question Response Result Hemoglobin 2.5 Lab ranges applied PSA <1 Data type discrepancy Urine_RBC 1 ā€“ 3 Data type discrepancy Urine_Color YELLOW Cannot be converted to numeric lab score
Lab System NORMLAB2 Overview ā€¢ Using the NORMLAB2 approach, all lab DCMs (HEMA, URIN, etc.) have the same structure and contain five questions Ā© 2008, Cognizant Technology Solutions. Confidential 56 Question Intent Data Type Derived? LPARM Lab Test CHAR No LVALUE Lab Value CHAR No LVALUEN Numeric Value NUMBER Yes LVALSTD Standard Value NUMBER Yes RETESTSN Retest Seq No NUMBER No
Lab System How NORMLAB2 Works ā€¢ Each response to LPARM is the name of the test (GLUCOSE) ā€¢ For each test, there must be a corresponding question in the Glib (GLUCOSE) of type LAB TEST, data type NUMBER ā€¢ The appropriate ranges are assigned to the question GLUCOSE ā€¢ A standard packaged procedure supplied with NORMLAB2 ā€¢ Matches the lab test name to the Global Library question ā€¢ Converts the character value of LVALUE into a numeric equivalent ā€¢ The NORMLAB2 data extract view includes the original data, the converted values, and comparisons to the range values 57
Lab System How NORMLAB2 Works ā€¢ The NORMLAB2 derivation procedure converts lab questions based on their medical evaluation type ā€¢ Questions of type LAB NUMBER (1.4 mg/dl, >3.4) are stripped of the extra characters ā€¢ Questions of type LAB BANDED (.42 - 54) are split into two values ā€¢ Questions of type LAB CHAR (Bright Yellow) are associated with a DVG and then converted into either the number associated with the long value (6 Bright Yellow) of the DVG or the display seq no. of the short value 58
Lab System NORMLAB2 Numeric Questions LPARM LVALUE LVALUEN LVALSTD Hemoglobin (g/dL) 2.5 2.5 2.5 (g/dL) Hemoglobin (mg/dL) 2.5 2.5 .025 (g/dL) Lymphocytes >.72 0.72 0.72 ā€¢ LVALUEN stores the numeric value with the ā€˜>ā€˜ stripped ā€¢ LVALSTD stores the numeric value converted to Standard Units based on the preferred copy group (to determine the standard units) and the lab unit conversion formula 59
Lab System NORMLAB2 Banded Questions LPARM LVALUE LVALUEN LVALSTD Urine_RBC 3-5 3 5 ā€¢ LVALUEN is used to store the lower value of the band (3) ā€¢ LVALSTD is used to store the upper value of the band (5) ā€¢ There is no conversion to standard units for banded questions ā€¢ LVALUEN is assessed against the normal range for the lab test question (e.g., 1-2) to determine the range flag; the upper part of the band is not used in range comparisons 60
Lab System NORMLAB2 Character Questions ā€¢ Create shadow questions with the same name as the lab test question concatenated with an ā€œ_Cā€, where medical evaluation type is LAB CHAR and data type is CHAR ā€¢ For example, HCG_C, URINE_COLOR_C ā€¢ Lab ranges are maintained for lab test questions HCG, URINE_COLOR which have data type NUMBER ā€¢ Assign a DVG to the shadow question ā€¢ Assign the standard lab DVG named LAB_CHAR_VALUES if all conversion values will be held in one DVG ā€¢ Alternatively, assign another DVG with the conversion values for that specific lab test question 61
Lab System NORMLAB2 Character QuestionsLPARM LVALUE LVALUEN LVALSTD HCG NEGATIVE 0 Urine_Color YELLOW 1 Urine_Protein +++ 3 ā€¢ LVALUEN is used to store a numeric code for the character text based on the standard DVG LAB_CHAR_VALUES 62 Seq Short Value Long Value Value Used 6 NEGATIVE 0 0 7 YELLOW 1 1 8 +++ 3 3 ļ‚® +++ is converted to the value 3 and is checked against the normal range for the question Urine_Protein
Lab System NORMLAB2 Set-up of Lab Differentials ā€¢ Add 2 new codes to the the installation codelist MEDICAL EVAL TYPE CODE ā€“ LAB WBC and LAB DIFF ā€¢ Change the medical evaluation type of appropriate lab questions to these types ā€¢ WBC would be type LAB WBC, and Monocytes, Eosinophils, Basophils, etc. would be type LAB DIFF ā€¢ Create a lab unit called ā€˜%ā€™, ā€˜PCTā€™, or ā€˜PERCENTā€™ ā€¢ Assign this percentage unit and the absolute units to each of the lab tests ā€¢ Identify the appropriate unit for the normal ranges for these questions for each lab 63
Lab System Lab Differential Calculations ā€¢ If the WBC value is collected before the lab differential questions in the DCM, the NORMLAB2 procedure will automatically perform the conversion ā€¢ If the preferred units for the LAB DIFF questions are set up as (ā€˜%ā€™, ā€˜PCTā€™, or ā€˜PERCENT), then the converted value for the LAB DIFF question is automatically calculated as [100 * LAB DIFF question numeric value/WBC value] ā€¢ If the preferred units for the LAB DIFF questions are set up in absolute terms, then the converted value for the LAB DIFF question is automatically calculated as [LAB DIFF question numeric value * WBC value/100] 64
Lab System NORMLAB2 Set-up ā€¢ All lab tests must have a question with that name in the Global Library (can be provisional) set up with the appropriate medical evaluation type ā€¢ Each of these questions must be assigned appropriate units in the LTQ Units menu ā€¢ Each lab question with any appropriate ranges must be assigned to the lab where the data is collected ā€¢ A standard lab DCM (e.g., HEMA) with the five questions must be created ā€¢ The data values for the lab test and lab values must be either manually entered or batch loaded into this DCM 65
Lab System NORMLAB2 Set-up ā€¢ A super DVG with the name LAB_CHAR_VALUES must contain all the character responses that will be converted to numeric values ā€¢ Alternatively, create individual DVGs with the conversion values for each specific lab test question ā€¢ For each short value, the long value should contain a number which is used to determine if the value is Lo, Hi, or Normal ā€¢ The lab test question of data type CHAR must have the DVG LAB_CHAR_VALUES or the alternative DVG assigned to it 66
Lab System NORMLAB2 Set-up ā€¢ A preferred copy group must be set up which contains all of the lab questions which may have multiple units; the unit defined in the preferred copy group is the standard unit ā€¢ The study must have a clinical objective of type LAB set up with the preferred copy group identified as the objective ā€¢ A lab unit conversion formula must be created for any lab question that has multiple units; this defines the conversion to the preferred unit, as defined by the preferred copy group not by the preferred conversion group ā€¢ A standard derivation procedure must be created for each DCM which calls the NORMLAB2 packaged procedure LAB2 67
Lab System NORMLAB2 Set-upā€¢ Add a short value of LAB to the installation codelist OBJECTIVE TYPE CODE ā€¢ Add an objective to the study in the clinical studies screen of type LAB and with an objective equal to the name of the preferred copy group name; the name must be entered in caps and there is no list of values 68
Lab System NORMLAB2 Set-upā€¢ The derivation procedure populates LVALUEN and LVALSTD ā€¢ The NORMLAB2 extract is created using the menu ā€¢ Admin ļƒŖ User Menu ļƒŖ Custom ļƒŖ Create NORMLAB2 ā€¢ The view can be generated using any of the four account types: CURRENT, TEST, STABLE, and SNAPSHOT; they must first be created using the normal view extract mechanism ā€¢ The NORMLAB2 extract contains the standard extract values, LPARM, LVALUE, LVALUEN, LVALSTD, unit, lo range and hi range (for question units and standard units), and out of range flag 69
Lab System NORMLAB2 Extract Fields 70 STUDY CHAR(6) DOCNUM VARCHAR2(20) INVSITE VARCHAR2(10) LABID VARCHAR2(10) LABSUB NUMBER INV VARCHAR2(10) PT VARCHAR2(10) PFREZFLG VARCHAR2(1) DCMNAME VARCHAR2(16) DCMSUBNM VARCHAR2(8) SUBSETSN NUMBER DCMQGNAM VARCHAR2(4) EVALTYPE VARCHAR2(15) ACCESSTS DATE LOGINTS DATE LSTCHGTS DATE LOCKFLAG VARCHAR2(1) CPEVENT VARCHAR2(20) ACTEVENT NUMBER DCMDATE VARCHAR2(8) DCMTIME VARCHAR2(6) OBSSD NUMBER SEX VARCHAR2(1) BSAGE NUMBER SASNAME VARCHAR2(8) SASLABEL VARCHAR2(40) QUALVAL VARCHAR2(70) REPEATSN NUMBER RETEST NUMBER LPARM VARCHAR2(20) LVALUE VARCHAR2(30) LVALUEN NUMBER LVALSTD NUMBER STDUNIT VARCHAR2(10) STDLORNG NUMBER STDHIRNG NUMBER STDTYPE VARCHAR2(10) LOWRANG NUMBER HIRANG NUMBER LABUNIT VARCHAR2(10) RNGFLAG VARCHAR2(1)
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Labs Module_Katalyst HLS

  • 2. Lab System Overview ā€¢ Oracle Clinical provides a lab system to facilitate the collection and reporting of laboratory data ā€¢ The lab system allows the user to establish and maintain ā€¢ Laboratories ā€¢ Lab units and assignment to lab test questions ā€¢ Conversions between lab units by lab test question ā€¢ Ranges for questions based on age and sex ā€¢ Assignment of labs to received DCMs ā€¢ Creation of lab extract views in oracle and SAS 2
  • 3. Lab System Overview ā€¢ The standard lab system allows ranges to be assigned to any question that is of type LAB TEST and data type NUMBER ā€¢ After a response is entered/loaded, the value can be compared against lab normal ranges and identified as Hi, Lo, or Normal ā€¢ Lab data however is often non-numeric (>3, 5-8, +++, etc.) ā€¢ These values cannot be handled by the standard lab system and require the use of the NORMLAB2 module ā€¢ In this training, we will cover the standard lab system followed by the set-up and use of NORMLAB2; throughout the practice we will set up the objects required for both 3
  • 4. Lab System Basic Lab System Process Flow 4 Create Lab Questions in Glib Create Lab Units Assign Lab Units to Lab Questions Define Lab Unit Conversion Formula Assign ranges to Lab Questions for each Lab/Lab Subset manually or via batch load Set-up Criteria for assignment of labs to DCMs Conduct Data Entry Reassign Labs to RDCMs Create Lab Data Extracts Create Lab
  • 5. Lab System Lab Test Questions 5 Menu: Glib ļƒ° Questions ļƒ° QuestionsCreate lab questions in Glib
  • 6. Lab System Lab Units 6 Define Lab Units Assign Lab Units to Lab Questions Define Lab Unit Conversion Formula Define Preferred Conversion Units
  • 7. Lab System Lab Units ā€¢ Lab units are the expected measurement units for lab questions ā€¢ Lab units are created using the menu ā€¢ Labs ļƒŖļ€ Lab Units ļƒŖ Lab Units Ā© 2008, Cognizant Technology Solutions. Confidential 7 Unique code and name is required for each lab unit Representative lab unit code can be used to group lab units that can be used interchangeably
  • 8. Lab System Lab Test Question Units ā€¢ Any question from the Global Library of type LAB TEST and data type NUMBER can be assigned lab units ā€¢ Lab units are assigned to questions via the menu ā€¢ Labs ļƒŖ Lab Units ļƒŖ LTQ Units ā€¢ All units which may ever apply to the question should be assigned so that the ranges can be defined for those units ā€¢ All the lab units associated with the representative lab unit become available in setting up ranges for that lab question ā€¢ Units do not have to be defined for a range to be set up for a lab test question; some lab tests do not have units 8
  • 9. Lab System Lab Test Question Units Ā© 2008, Cognizant Technology Solutions. Confidential 9 Lab units are assigned to lab test questions Each question in each domain can have one or more representative lab units assigned to it Lab units can be deactivated if they are not to be used any longer
  • 10. Lab System Lab Unit Conversion ā€¢ Lab unit conversions provide a means to create a formula to convert data for a lab test from one unit to another unit ā€¢ For each lab test question, multiple conversion formulas can be created for the various lab unit combinations ā€¢ Conversion formulas are created in the menu ā€¢ Labs ļƒŖ Lab Units ļƒŖ LU Conversions ā€¢ The conversion formulas are available in reports and can be used in derivation procedures to convert responses between units ā€¢ The conversion formula are used by the NORMLAB2 process to convert lab values to standard units in the data extract view 10
  • 11. Lab System Lab Unit Conversion 11 Conversion formula are created between units
  • 12. Lab System Labs and Lab Subsets ā€¢ Labs define locations where data is collected or analyzed ā€¢ Each lab is identified by a code (Lab) and description (Name) which must be unique across replicated locations ā€¢ Lab questions and normal ranges are associated with each lab ā€¢ Each lab can have subsets; this allows the assignment of the same set of questions to the lab with different ranges ā€¢ A set of normal ranges for diabetic patients and one set for non- diabetic patients ā€¢ Lab are created using the menu ā€¢ Labs ļƒŖļ€ Labs ļƒŖļ€ Labs 12
  • 13. Lab System Labs and Lab Subsets ā€¢ When a lab is created, a lab range subset named DEFAULT is automatically created ā€¢ Other subsets are assigned to labs by selecting a subset name from a LOV in the lab range subset window ā€¢ Lab range subset names must first be created in the installation codelist LAB RANGE SUBSET CODE ā€¢ The naming convention used to reference lab range subsets is ā€¢ LABNAME$<SUBSET NAME> for non-default subsets ā€¢ LABNAME or LABNAME$DEFAULT for default subset 13
  • 14. Lab System Labs and Lab Subsets 14 Optional address and descriptive information may also be entered Physical laboratories are identified at each site with a unique lab name and description Subsets can be defined for each lab The format mask name will automatically default in the batch data load data file screen when this lab is identified with a data file
  • 15. Lab System Labs and Lab Subsets 15 Each subset code must first be set up in the installation codelist LAB RANGE SUBSET CODE Subsets are assigned; DEEFAULT is automatically assigned by the system
  • 16. Lab System Labs and Lab Subsets 16 ā€¢ Other subsets can be assigned to the lab at any time ā€¢ Subsets can never be removed from a lab ā€¢ Ranges may be assigned directly, copied from the DEFAULT subset, or electronically loaded ā€¢ Ranges for a question can only be assigned to other subsets once that question has been assigned to the DEFAULT subset
  • 17. Lab System Lab Ranges ā€¢ Ranges represent the defined normal range of high and low values for a particular unit for each lab test question ā€¢ Different ranges can be defined for each lab subset; note that the primary lab is always the DEFAULT subset ā€¢ Every question that will have ranges in a lab subset must also have ranges in the DEFAULT subset ā€¢ Within each lab subset, multiple ranges can be defined per lab test question as long as ranges are based on a unique combination of these factors ā€¢ Gender, age, domain, and effective dates 17
  • 18. Lab System Lab Ranges ā€¢ The DEFAULT lab and subsets can have lab questions and ranges ā€¢ Manually assigned ā€¢ Copied from another lab; subsets can only have ranges copied from the DEFAULT lab ā€¢ Loaded electronically from an ASCII file ā€¢ Assigned via textbook ranges; these are only available for the DEFAULT lab ā€¢ Lab ranges depend on age and sex information from the patient enrollment form 18
  • 19. Lab System Lab Ranges 19 Question Domain Sex Min Max Values Units Effective Dates Age Age Lo Hi Start End Glucose Global M 18 35 2 5 mgs Glucose Global M 35 65 25 50 dgs Glucose Global F 35 60 dgs 30-06-1998 Glucose Global F 40 80 mgs 01-07-98 None of these lab ranges conflict (overlap) with each other
  • 20. Lab System Lab Ranges 20 Question Domain Sex Min Max Values Units Effective Dates Age Age Lo Hi Start End Glucose Global M 18 35 2 5 mgs Glucose Global M 35 65 25 50 dgs Glucose Global F 35 60 dgs 30-06-1998 Glucose Global F 40 80 mgs 01-07-1998 Glucose Global M 18 65 2 5 dgs Conflict These ranges overlap and can not be entered
  • 21. Lab System Lab Ranges 21 Lab Test Question: ā€¢ Any question identified in the Global Library of question type LAB TEST and data type NUMBER ā€¢ The question does not have to be active to have lab ranges assigned
  • 22. Lab System Lab Ranges 22 Question Domain: ā€¢ The question domain from the Global Library ā€¢ Different ranges can be assigned to the lab test question with the same name in different domains, but NORMLAB2 will not work in this situation
  • 23. Lab System Lab Ranges 23 Sex: ā€¢ The sex of the patient that this normal range applies to ā€¢ List of values include M, F, or B; defaults to B, for both ā€¢ The patient must be enrolled with a sex assigned for the lab range to be applied
  • 24. Lab System Lab Ranges 24 Age: ā€¢ The minimum and maximum age of the patient that this range applies to ā€¢ Optional ā€¢ The patient must be enrolled with a birth date assigned for the lab range to be applied ā€¢ Ages may not overlap for the same lab test question for the same sex ļƒ¼ Use age ranges like 18-35 and 35-65 without gaps or else patients with ages like 35.5 will be excluded
  • 25. Lab System Lab Ranges 25 Values: ā€¢ The low and high range values ā€¢ Lab derived values are compared against this range and identified as being H (High), L (Low), or N (Normal)
  • 26. Lab System Lab Ranges 26 Lab Unit Name: ā€¢ The lab units that this lab test is collected in ā€¢ Ranges may be defined in different units for different groups if appropriate, e.g., mg/dL for M, IU/L for F ā€¢ Units are not required for a range
  • 27. Lab System Lab Ranges Ā© 2008, Cognizant Technology Solutions. Confidential 27 Effective Date: ā€¢ The start and end date in which this range is effective ā€¢ Optional ā€¢ A lab question may appear multiple times with different, non-overlapping start and end dates ā€¢ These dates are optional and only need to be used if the applied ranges will change during the course of the study
  • 28. Lab System Lab Ranges 28 Age Unit: ā€¢ The minimum and maximum units the age of the patient is measured in ā€¢ The default is YEARS
  • 29. Lab System Lab Ranges Ā© 2008, Cognizant Technology Solutions. Confidential 29 Status: ā€¢ The status of the lab ranges ā€¢ If the high or low values or the units are missing, the system automatically sets the status to MISSING; in this case the range is not available upon extract ā€¢ If these values are entered the system defaults the value of APPROVED ā€¢ Can be changed by the user to UNAPPROVED or SUSPICIOUS to manually mark ranges which need to be checked, but this does not affect whether the ranges are actually used in the extract
  • 30. Lab System Lab Ranges 30 Range Type: ā€¢ Identifies whether the range was assigned directly (LAB) or via textbook ranges (TEXTBOOK) ā€¢ This field is system set and cannot be manually changed ā€¢ TEXTBOOK range types have greater restrictions on changes than LAB range type
  • 31. Lab System Lab Ranges 31 Comment: ā€¢ Optional comment about the lab range ā€¢ If the ranges were copied in, the comment will indicate it
  • 32. Lab System Electronic Load of Lab Ranges ā€¢ Range data for one or more labs can be electronically loaded using a text file ā€¢ The format of the data file needs to be the following with a user specified delimiter; M indicates that a field is mandatory; excluded fields should have a null placeholder (,,) ā€¢ Lab name (M), lab range subset code, lab test question (M), sex, min. age, max. age, min. value (M), max. value (M), unit name, effective start date, effective end date, min. age unit, max. age unit, range type (M) ā€¢ HLAB1, DEFAULT, CHOL, F, 18, 65, 135, 200, MMOL/L,,,,,LAB (here the delimiter is ā€˜,ā€™) 32
  • 33. Lab System Electronic Load of Lab Ranges 33 This form is used to submit the electronic file to load lab ranges Menu: Labs ļƒ°Lab Batch Data Load ļƒ°Lab Ranges Batch Data Load Identify if the file should be loaded or if this is a test Identify the full path of the file to load Identify the file delimiter Lab questions in a file must all be from the same domain N identifies that the file to load has effective dates Y identifies that the system will supply the effective start and end date for ranges
  • 34. Lab System Electronic Load of Lab Ranges ā€¢ Duplicate lab ranges cannot be loaded ā€¢ Ranges cannot be loaded if the subset referenced in the file does not exist in the database ā€¢ If date ranges overlap they have to be ordered chronologically ā€¢ End date must be later than the start date and start date is mandatory if end date is provided ā€¢ A question must be assigned to the DEFAULT subset for a lab before ranges can be assigned to any other subset for this lab 34
  • 35. Lab System Electronic Load of Lab Ranges ā€¢ Default ranges must be loaded before subset ranges can be loaded for a question; they can not be loaded in the same file ā€¢ Ranges that are loaded without a subset range name in the file are loaded into the DEFAULT subset ā€¢ Effective dates are required if the Default Effective Dates parameter of the batch job is set to N ā€¢ Ranges which have different units (e.g., 10 DAYS - 1 YEAR) fail when loaded electronically (Note: this is a bug) 35
  • 36. Lab System Electronic Load of Lab Ranges ā€¢ Oracle Clinical provides two methods for reviewing lab electronic range loads ā€¢ The output file of the load job lists all of the errors along with the erroneous records ā€¢ The LAB RANGES BATCH LOAD DATA FILE STATUS report includes summary and status information for each lab range load ā€¢ If there are any errors in the load, the data file can be corrected and the load can be re-executed 36
  • 37. Lab System Electronic Load of Lab Ranges 37 The erroneous record of data The reason the load failed
  • 38. Lab System Lab Range Load Status Report 38 Menu: Labs ļƒ°Lab Batch Data Load ļƒ°Report Results of the Data Load Identify the full path of the data file under review or use pattern matching to identify a group Identify the date range the files were loaded
  • 39. Lab System Lab Range Load Status Report 39 11-MAR-99 08:28 Ranges Batch Data Load Data files Status Page 2 0f 2 Data File Created On Mode of Load Status Sub Job Id Number of Errors /val100/lab01.txt 11-MAR-1999 Load and Prepare BAD PREPARE 34777 4 /val100/lab02.txt 11-MAR-1999 Load and Prepare SUCCESS 34957 0 /val100/lab01.txt 11-MAR-1999 Load and Prepare BAD PREPARE 34977 4 /val100/lab01.txt 11-MAR-1999 Load and Prepare SUCCESS 34997 0 ļ‚® This report can be executed after several files have been loaded to review which have failed ļ‚® The output files of the failed jobs can then be reviewed to determine the exact reason for the failure
  • 40. Lab System Textbook Ranges/Preferred Copy Groups ā€¢ Textbook ranges provide a way to set up standard ranges for a lab test question that can also be used when the lab does not provide specific ranges ā€¢ Multiple textbook ranges can be defined for the same question for different units ā€¢ For example, for the question ALBUMIN, ranges can be defined for men 18-34 years old in both mg/dL and g/L 40
  • 41. Lab System Textbook Ranges/Preferred Copy Groups ā€¢ Preferred copy groups identify for each lab test question the preferred unit of measurement ā€¢ The preferred copy group is used to copy textbook ranges to a lab ā€¢ The preferred copy group identifies which ranges for each lab test question to copy from the textbook range to the lab 41
  • 42. Lab System Textbook Ranges/Preferred Copy Groups 42 Textbook ranges are identified per question in a domain Unit, sex, age, or effective dates must be unique between ranges Ranges are defined for GLUC in both g/dL and mg/dL in this example
  • 43. Lab System Textbook Ranges/Preferred Copy Groups 43 The preferred copy group identifies one unit for each lab test question and only the ranges for that unit are copied to the lab when the textbook range is copied This preferred copy group identifies that textbook ranges for question GLUC that have units in g/dL should be copied to the lab
  • 44. Lab System Textbook Ranges/Preferred Copy Groups 44 Identify the preferred copy group Click on the [Use Textbook Ranges] button to copy textbook ranges to a lab Optionally enter start and end dates to override the effective dates for the textbook ranges to be copied and click [OK] Optionally enter a text range date to copy older textbook ranges; leave blank to copy current ranges
  • 45. Lab System Textbook Ranges/Preferred Copy Groups 45 The textbook ranges for GLUC that have the same unit as those identified in the preferred copy group (g/dL) are copied to the Lab
  • 46. Lab System Textbook Ranges/Preferred Copy Groups 46 Textbook Ranges (Question Specific) Gluc, 20, 50, g/dL Gluc, 2, 5, mg/dl Grancast, 1, 5, mm Grancast, .1, .5 cm Preferred Copy Group ā€¢ Identifies Questions to copy based on unit ā€¢ Allows for multiple questions to be assigned to a lab ā€¢ Gluc (g/dL), Grancast (mm) Lab (Multiple Questions) Gluc, 20, 50, g/dL Grancast, 1, 5, mm
  • 47. Lab System Assignment of Labs to RDCMs ā€¢ Lab ranges must be assigned to entered or batch loaded data for the ranges to be used in procedures or extracts ā€¢ Lab ranges are assigned to responses by assigning the lab to the received DCM in one of the following ways ā€¢ By the data entry operator during data entry ā€¢ During batch data load (identified in the data file entry) ā€¢ Manually to the RDCM using the lab module ā€¢ Automatically by the system during data entry or batch Data load based on pre-set lab assignment criteria (LAC) ā€¢ During or after data has been entered or batch loaded using the lab assignment criteria module 47
  • 48. Lab System Lab Assignment Criteria ā€¢ Lab assignment criteria (LAC) allow the automatic assignment of labs to a RDCM either during log-in or after it has been received ā€¢ LAC can be created using any unique combination of the following criteria ā€¢ Study ā€¢ Start date ā€¢ End date ā€¢ Site ā€¢ Investigator 48 ļƒ¼ DCI ļƒ¼ DCM ļƒ¼ Patient ļƒ¼ Clinical planned event ļƒ¼ Actual event
  • 49. Lab System Lab Assignment Criteria 49 Query for the study, then click on [Lab Assignment Criteria] Menu: Labs ļƒ°Lab Assignment Criteria
  • 50. Lab System Lab Assignment Criteria 50 Enter lab assignment criteria by site, patient, DCI, etc. Data entered/loaded after the set- up of LAC will automatically have these labs assigned
  • 51. Lab System LAC/Received DCMs 51 Lab Assignment Type: ā€¢ Assigned by the system based on how lab was assigned to the received DCM ā€¢ The possible values are ļƒ¼ UNKNOWN ā€“ No lab is assigned ļƒ¼ CRITERION ā€“ Lab was assigned automatically during data entry or batch data load based on lab assignment criteria ļƒ¼ LOGIN ā€“ Lab was assigned during log-in by data entry operator ļƒ¼ USER ā€“ Lab was assigned directly to received DCM in this form ā€¢ To assign a received DCM to another lab, select a different lab from the LOV Menu: Labs ļƒ°Lab Assignment Criteria ļƒ° Received DCMs
  • 52. Lab System Applying LAC 52 LAC must be set up in advance for the study to use the apply lac functionality Another way to modify lab assignment after data is entered or loaded is to use the [Apply LAC] functionality
  • 53. Lab System Applying LAC 53 The lab assignment type selected will determine which lab values will be changed. Select from LOV and click on [Apply] The assignment types are hierarchical and will only change ones equal to or at lower levels; if LOGIN were selected it would override lab assignments of type LOGIN, UNKNOWN and CRITERION, but not SYSTEM or USER
  • 54. Lab System NORMLAB2 Overview ā€¢ The standard Oracle Clinical lab system does not allow ranges to be applied to non-numeric responses ā€¢ This excludes a large set of lab responses such as >6, 7-9, etc. ā€¢ Such responses would create data type discrepancies and would be stored as null values for the actual response ā€¢ The NORMLAB2 approach handles this type of lab data by accepting all lab test responses as character text ā€¢ The character text is converted into numeric values using a variety of algorithms built into a standard derivation procedure ā€¢ The converted numeric values can have lab ranges values applied to them from the standard lab range system 54
  • 55. Lab System NORMLAB2 Overview ā€¢ The standard Oracle Clinical approach does not take into account all of the types of expected responses to lab test questions, as this chart illustrates Ā© 2008, Cognizant Technology Solutions. Confidential 55 Lab Question Response Result Hemoglobin 2.5 Lab ranges applied PSA <1 Data type discrepancy Urine_RBC 1 ā€“ 3 Data type discrepancy Urine_Color YELLOW Cannot be converted to numeric lab score
  • 56. Lab System NORMLAB2 Overview ā€¢ Using the NORMLAB2 approach, all lab DCMs (HEMA, URIN, etc.) have the same structure and contain five questions Ā© 2008, Cognizant Technology Solutions. Confidential 56 Question Intent Data Type Derived? LPARM Lab Test CHAR No LVALUE Lab Value CHAR No LVALUEN Numeric Value NUMBER Yes LVALSTD Standard Value NUMBER Yes RETESTSN Retest Seq No NUMBER No
  • 57. Lab System How NORMLAB2 Works ā€¢ Each response to LPARM is the name of the test (GLUCOSE) ā€¢ For each test, there must be a corresponding question in the Glib (GLUCOSE) of type LAB TEST, data type NUMBER ā€¢ The appropriate ranges are assigned to the question GLUCOSE ā€¢ A standard packaged procedure supplied with NORMLAB2 ā€¢ Matches the lab test name to the Global Library question ā€¢ Converts the character value of LVALUE into a numeric equivalent ā€¢ The NORMLAB2 data extract view includes the original data, the converted values, and comparisons to the range values 57
  • 58. Lab System How NORMLAB2 Works ā€¢ The NORMLAB2 derivation procedure converts lab questions based on their medical evaluation type ā€¢ Questions of type LAB NUMBER (1.4 mg/dl, >3.4) are stripped of the extra characters ā€¢ Questions of type LAB BANDED (.42 - 54) are split into two values ā€¢ Questions of type LAB CHAR (Bright Yellow) are associated with a DVG and then converted into either the number associated with the long value (6 Bright Yellow) of the DVG or the display seq no. of the short value 58
  • 59. Lab System NORMLAB2 Numeric Questions LPARM LVALUE LVALUEN LVALSTD Hemoglobin (g/dL) 2.5 2.5 2.5 (g/dL) Hemoglobin (mg/dL) 2.5 2.5 .025 (g/dL) Lymphocytes >.72 0.72 0.72 ā€¢ LVALUEN stores the numeric value with the ā€˜>ā€˜ stripped ā€¢ LVALSTD stores the numeric value converted to Standard Units based on the preferred copy group (to determine the standard units) and the lab unit conversion formula 59
  • 60. Lab System NORMLAB2 Banded Questions LPARM LVALUE LVALUEN LVALSTD Urine_RBC 3-5 3 5 ā€¢ LVALUEN is used to store the lower value of the band (3) ā€¢ LVALSTD is used to store the upper value of the band (5) ā€¢ There is no conversion to standard units for banded questions ā€¢ LVALUEN is assessed against the normal range for the lab test question (e.g., 1-2) to determine the range flag; the upper part of the band is not used in range comparisons 60
  • 61. Lab System NORMLAB2 Character Questions ā€¢ Create shadow questions with the same name as the lab test question concatenated with an ā€œ_Cā€, where medical evaluation type is LAB CHAR and data type is CHAR ā€¢ For example, HCG_C, URINE_COLOR_C ā€¢ Lab ranges are maintained for lab test questions HCG, URINE_COLOR which have data type NUMBER ā€¢ Assign a DVG to the shadow question ā€¢ Assign the standard lab DVG named LAB_CHAR_VALUES if all conversion values will be held in one DVG ā€¢ Alternatively, assign another DVG with the conversion values for that specific lab test question 61
  • 62. Lab System NORMLAB2 Character QuestionsLPARM LVALUE LVALUEN LVALSTD HCG NEGATIVE 0 Urine_Color YELLOW 1 Urine_Protein +++ 3 ā€¢ LVALUEN is used to store a numeric code for the character text based on the standard DVG LAB_CHAR_VALUES 62 Seq Short Value Long Value Value Used 6 NEGATIVE 0 0 7 YELLOW 1 1 8 +++ 3 3 ļ‚® +++ is converted to the value 3 and is checked against the normal range for the question Urine_Protein
  • 63. Lab System NORMLAB2 Set-up of Lab Differentials ā€¢ Add 2 new codes to the the installation codelist MEDICAL EVAL TYPE CODE ā€“ LAB WBC and LAB DIFF ā€¢ Change the medical evaluation type of appropriate lab questions to these types ā€¢ WBC would be type LAB WBC, and Monocytes, Eosinophils, Basophils, etc. would be type LAB DIFF ā€¢ Create a lab unit called ā€˜%ā€™, ā€˜PCTā€™, or ā€˜PERCENTā€™ ā€¢ Assign this percentage unit and the absolute units to each of the lab tests ā€¢ Identify the appropriate unit for the normal ranges for these questions for each lab 63
  • 64. Lab System Lab Differential Calculations ā€¢ If the WBC value is collected before the lab differential questions in the DCM, the NORMLAB2 procedure will automatically perform the conversion ā€¢ If the preferred units for the LAB DIFF questions are set up as (ā€˜%ā€™, ā€˜PCTā€™, or ā€˜PERCENT), then the converted value for the LAB DIFF question is automatically calculated as [100 * LAB DIFF question numeric value/WBC value] ā€¢ If the preferred units for the LAB DIFF questions are set up in absolute terms, then the converted value for the LAB DIFF question is automatically calculated as [LAB DIFF question numeric value * WBC value/100] 64
  • 65. Lab System NORMLAB2 Set-up ā€¢ All lab tests must have a question with that name in the Global Library (can be provisional) set up with the appropriate medical evaluation type ā€¢ Each of these questions must be assigned appropriate units in the LTQ Units menu ā€¢ Each lab question with any appropriate ranges must be assigned to the lab where the data is collected ā€¢ A standard lab DCM (e.g., HEMA) with the five questions must be created ā€¢ The data values for the lab test and lab values must be either manually entered or batch loaded into this DCM 65
  • 66. Lab System NORMLAB2 Set-up ā€¢ A super DVG with the name LAB_CHAR_VALUES must contain all the character responses that will be converted to numeric values ā€¢ Alternatively, create individual DVGs with the conversion values for each specific lab test question ā€¢ For each short value, the long value should contain a number which is used to determine if the value is Lo, Hi, or Normal ā€¢ The lab test question of data type CHAR must have the DVG LAB_CHAR_VALUES or the alternative DVG assigned to it 66
  • 67. Lab System NORMLAB2 Set-up ā€¢ A preferred copy group must be set up which contains all of the lab questions which may have multiple units; the unit defined in the preferred copy group is the standard unit ā€¢ The study must have a clinical objective of type LAB set up with the preferred copy group identified as the objective ā€¢ A lab unit conversion formula must be created for any lab question that has multiple units; this defines the conversion to the preferred unit, as defined by the preferred copy group not by the preferred conversion group ā€¢ A standard derivation procedure must be created for each DCM which calls the NORMLAB2 packaged procedure LAB2 67
  • 68. Lab System NORMLAB2 Set-upā€¢ Add a short value of LAB to the installation codelist OBJECTIVE TYPE CODE ā€¢ Add an objective to the study in the clinical studies screen of type LAB and with an objective equal to the name of the preferred copy group name; the name must be entered in caps and there is no list of values 68
  • 69. Lab System NORMLAB2 Set-upā€¢ The derivation procedure populates LVALUEN and LVALSTD ā€¢ The NORMLAB2 extract is created using the menu ā€¢ Admin ļƒŖ User Menu ļƒŖ Custom ļƒŖ Create NORMLAB2 ā€¢ The view can be generated using any of the four account types: CURRENT, TEST, STABLE, and SNAPSHOT; they must first be created using the normal view extract mechanism ā€¢ The NORMLAB2 extract contains the standard extract values, LPARM, LVALUE, LVALUEN, LVALSTD, unit, lo range and hi range (for question units and standard units), and out of range flag 69
  • 70. Lab System NORMLAB2 Extract Fields 70 STUDY CHAR(6) DOCNUM VARCHAR2(20) INVSITE VARCHAR2(10) LABID VARCHAR2(10) LABSUB NUMBER INV VARCHAR2(10) PT VARCHAR2(10) PFREZFLG VARCHAR2(1) DCMNAME VARCHAR2(16) DCMSUBNM VARCHAR2(8) SUBSETSN NUMBER DCMQGNAM VARCHAR2(4) EVALTYPE VARCHAR2(15) ACCESSTS DATE LOGINTS DATE LSTCHGTS DATE LOCKFLAG VARCHAR2(1) CPEVENT VARCHAR2(20) ACTEVENT NUMBER DCMDATE VARCHAR2(8) DCMTIME VARCHAR2(6) OBSSD NUMBER SEX VARCHAR2(1) BSAGE NUMBER SASNAME VARCHAR2(8) SASLABEL VARCHAR2(40) QUALVAL VARCHAR2(70) REPEATSN NUMBER RETEST NUMBER LPARM VARCHAR2(20) LVALUE VARCHAR2(30) LVALUEN NUMBER LVALSTD NUMBER STDUNIT VARCHAR2(10) STDLORNG NUMBER STDHIRNG NUMBER STDTYPE VARCHAR2(10) LOWRANG NUMBER HIRANG NUMBER LABUNIT VARCHAR2(10) RNGFLAG VARCHAR2(1)