2. Lab System
Overview
• Oracle Clinical provides a lab system to facilitate the
collection and reporting of laboratory data
• The lab system allows the user to establish and maintain
• Laboratories
• Lab units and assignment to lab test questions
• Conversions between lab units by lab test question
• Ranges for questions based on age and sex
• Assignment of labs to received DCMs
• Creation of lab extract views in oracle and SAS
2
3. Lab System Overview
• The standard lab system allows ranges to be assigned to any
question that is of type LAB TEST and data type NUMBER
• After a response is entered/loaded, the value can be compared
against lab normal ranges and identified as Hi, Lo, or Normal
• Lab data however is often non-numeric (>3, 5-8, +++, etc.)
• These values cannot be handled by the standard lab system
and require the use of the NORMLAB2 module
• 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 Questions 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
8. Lab System
Lab Test Question Units
• Any question from the Global Library of type LAB TEST and
data type NUMBER can be assigned lab units
• Lab units are assigned to questions via the menu
• Labs Lab Units LTQ Units
• All units which may ever apply to the question should be
assigned so that the ranges can be defined for those units
• All the lab units associated with the representative lab unit
become available in setting up ranges for that lab question
• 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
10. Lab System
Lab Unit Conversion
• Lab unit conversions provide a means to create a formula to
convert data for a lab test from one unit to another unit
• For each lab test question, multiple conversion formulas can be
created for the various lab unit combinations
• Conversion formulas are created in the menu
• Labs Lab Units LU Conversions
• The conversion formulas are available in reports and can be used
in derivation procedures to convert responses between units
• 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
• Labs define locations where data is collected or analyzed
• Each lab is identified by a code (Lab) and description (Name)
which must be unique across replicated locations
• Lab questions and normal ranges are associated with each lab
• Each lab can have subsets; this allows the assignment of the
same set of questions to the lab with different ranges
• A set of normal ranges for diabetic patients and one set for non-
diabetic patients
• Lab are created using the menu
• Labs Labs Labs 12
13. Lab System
Labs and Lab Subsets
• When a lab is created, a lab range subset named DEFAULT is
automatically created
• Other subsets are assigned to labs by selecting a subset name
from a LOV in the lab range subset window
• Lab range subset names must first be created in the installation codelist
LAB RANGE SUBSET CODE
• The naming convention used to reference lab range subsets is
• LABNAME$<SUBSET NAME> for non-default subsets
• LABNAME or LABNAME$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
• Other subsets can be assigned to the lab at any time
• Subsets can never be removed from a lab
• Ranges may be assigned directly, copied from the DEFAULT subset, or
electronically loaded
• 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
• Ranges represent the defined normal range of high and low
values for a particular unit for each lab test question
• Different ranges can be defined for each lab subset; note that
the primary lab is always the DEFAULT subset
• Every question that will have ranges in a lab subset must also
have ranges in the DEFAULT subset
• 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
• Gender, age, domain, and effective dates
17
18. Lab System
Lab Ranges
• The DEFAULT lab and subsets can have lab questions and
ranges
• Manually assigned
• Copied from another lab; subsets can only have ranges copied from
the DEFAULT lab
• Loaded electronically from an ASCII file
• Assigned via textbook ranges; these are only available for the
DEFAULT lab
• 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:
• Any question identified in the Global
Library of question type LAB TEST
and data type NUMBER
• The question does not have to be
active to have lab ranges assigned
22. Lab System
Lab Ranges
22
Question Domain:
• The question domain from the Global Library
• 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:
• The sex of the patient that this
normal range applies to
• List of values include M, F, or B;
defaults to B, for both
• The patient must be enrolled with a
sex assigned for the lab range to be
applied
24. Lab System
Lab Ranges
24
Age:
• The minimum and maximum age of the patient that this range applies to
• Optional
• The patient must be enrolled with a birth date assigned for the lab
range to be applied
• Ages may not overlap for the same lab test question for the same sex
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:
• The low and high range values
• 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:
• The lab units that this lab test is
collected in
• Ranges may be defined in different
units for different groups if
appropriate, e.g., mg/dL for M, IU/L
for F
• Units are not required for a range
30. Lab System
Lab Ranges
30
Range Type:
• Identifies whether the range was assigned directly (LAB)
or via textbook ranges (TEXTBOOK)
• This field is system set and cannot be manually changed
• TEXTBOOK range types have greater restrictions on
changes than LAB range type
32. Lab System
Electronic Load of Lab Ranges
• Range data for one or more labs can be electronically loaded
using a text file
• 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 (,,)
• 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)
• HLAB1, DEFAULT, CHOL, F, 18, 65, 135, 200, MMOL/L,,,,,LAB
(here the delimiter is ‘,’)
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33. Lab System
Electronic Load of Lab Ranges
33
This form is used to submit
the electronic file to load lab
ranges
Menu: Labs Lab Batch Data
Load 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
• Duplicate lab ranges cannot be loaded
• Ranges cannot be loaded if the subset referenced in the file
does not exist in the database
• If date ranges overlap they have to be ordered chronologically
• End date must be later than the start date and start date is
mandatory if end date is provided
• 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
• Default ranges must be loaded before subset ranges can be
loaded for a question; they can not be loaded in the same file
• Ranges that are loaded without a subset range name in the file
are loaded into the DEFAULT subset
• Effective dates are required if the Default Effective Dates
parameter of the batch job is set to N
• 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
• Oracle Clinical provides two methods for reviewing lab
electronic range loads
• The output file of the load job lists all of the errors along with the
erroneous records
• The LAB RANGES BATCH LOAD DATA FILE STATUS report
includes summary and status information for each lab range load
• If there are any errors in the load, the data file can be
corrected and the load can be re-executed
36
38. Lab System
Lab Range Load Status Report
38
Menu: Labs Lab Batch Data
Load 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
This report can be executed after several files have been
loaded to review which have failed
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
• 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
• Multiple textbook ranges can be defined for the same
question for different units
• 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
• Preferred copy groups identify for each lab test question the
preferred unit of measurement
• The preferred copy group is used to copy textbook ranges to
a lab
• 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
• Identifies Questions to copy
based on unit
• Allows for multiple questions
to be assigned to a lab
• 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
• Lab ranges must be assigned to entered or batch loaded data
for the ranges to be used in procedures or extracts
• Lab ranges are assigned to responses by assigning the lab to the
received DCM in one of the following ways
• By the data entry operator during data entry
• During batch data load (identified in the data file entry)
• Manually to the RDCM using the lab module
• Automatically by the system during data entry or batch Data load based
on pre-set lab assignment criteria (LAC)
• During or after data has been entered or batch loaded using the lab
assignment criteria module
47
48. Lab System
Lab Assignment Criteria
• Lab assignment criteria (LAC) allow the automatic
assignment of labs to a RDCM either during log-in or after it
has been received
• LAC can be created using any unique combination of the
following criteria
• Study
• Start date
• End date
• Site
• Investigator
48
DCI
DCM
Patient
Clinical planned event
Actual event
49. Lab System
Lab Assignment Criteria
49
Query for the study, then click
on [Lab Assignment Criteria]
Menu: Labs 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:
• Assigned by the system based on how lab was assigned to the received DCM
• The possible values are
UNKNOWN – No lab is assigned
CRITERION – Lab was assigned automatically during data entry or batch
data load based on lab assignment criteria
LOGIN – Lab was assigned during log-in by data entry operator
USER – Lab was assigned directly to received DCM in this form
• To assign a received DCM to another lab, select a different lab from the LOV
Menu: Labs Lab
Assignment Criteria
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
• The standard Oracle Clinical lab system does not allow ranges
to be applied to non-numeric responses
• This excludes a large set of lab responses such as >6, 7-9, etc.
• Such responses would create data type discrepancies and would
be stored as null values for the actual response
• The NORMLAB2 approach handles this type of lab data by
accepting all lab test responses as character text
• The character text is converted into numeric values using a
variety of algorithms built into a standard derivation procedure
• The converted numeric values can have lab ranges values
applied to them from the standard lab range system
54
57. Lab System
How NORMLAB2 Works
• Each response to LPARM is the name of the test (GLUCOSE)
• For each test, there must be a corresponding question in the Glib
(GLUCOSE) of type LAB TEST, data type NUMBER
• The appropriate ranges are assigned to the question GLUCOSE
• A standard packaged procedure supplied with NORMLAB2
• Matches the lab test name to the Global Library question
• Converts the character value of LVALUE into a numeric equivalent
• 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
• The NORMLAB2 derivation procedure converts lab questions
based on their medical evaluation type
• Questions of type LAB NUMBER (1.4 mg/dl, >3.4) are stripped of
the extra characters
• Questions of type LAB BANDED (.42 - 54) are split into two values
• 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
• LVALUEN stores the numeric value with the ‘>‘ stripped
• 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
• LVALUEN is used to store the lower value of the band (3)
• LVALSTD is used to store the upper value of the band (5)
• There is no conversion to standard units for banded questions
• 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
• Create shadow questions with the same name as the lab test
question concatenated with an “_C”, where medical evaluation
type is LAB CHAR and data type is CHAR
• For example, HCG_C, URINE_COLOR_C
• Lab ranges are maintained for lab test questions HCG, URINE_COLOR
which have data type NUMBER
• Assign a DVG to the shadow question
• Assign the standard lab DVG named LAB_CHAR_VALUES if all
conversion values will be held in one DVG
• 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
• 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
+++ 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
• Add 2 new codes to the the installation codelist MEDICAL
EVAL TYPE CODE – LAB WBC and LAB DIFF
• Change the medical evaluation type of appropriate lab questions
to these types
• WBC would be type LAB WBC, and Monocytes, Eosinophils, Basophils,
etc. would be type LAB DIFF
• Create a lab unit called ‘%’, ‘PCT’, or ‘PERCENT’
• Assign this percentage unit and the absolute units to each of the
lab tests
• Identify the appropriate unit for the normal ranges for these
questions for each lab 63
64. Lab System
Lab Differential Calculations
• If the WBC value is collected before the lab differential
questions in the DCM, the NORMLAB2 procedure will
automatically perform the conversion
• If the preferred units for the LAB DIFF questions are set up
as (‘%’, ‘PCT’, or ‘PERCENT), then the converted value for
the LAB DIFF question is automatically calculated as [100 *
LAB DIFF question numeric value/WBC value]
• 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
• 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
• Each of these questions must be assigned appropriate units
in the LTQ Units menu
• Each lab question with any appropriate ranges must be
assigned to the lab where the data is collected
• A standard lab DCM (e.g., HEMA) with the five questions
must be created
• 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
• A super DVG with the name LAB_CHAR_VALUES must
contain all the character responses that will be converted to
numeric values
• Alternatively, create individual DVGs with the conversion values for
each specific lab test question
• For each short value, the long value should contain a number
which is used to determine if the value is Lo, Hi, or Normal
• 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
• 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
• The study must have a clinical objective of type LAB set up with
the preferred copy group identified as the objective
• 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
• A standard derivation procedure must be created for each DCM
which calls the NORMLAB2 packaged procedure LAB2
67
68. Lab System
NORMLAB2 Set-up• Add a short value of LAB to the installation codelist
OBJECTIVE TYPE CODE
• 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-up• The derivation procedure populates LVALUEN and LVALSTD
• The NORMLAB2 extract is created using the menu
• Admin User Menu Custom Create NORMLAB2
• 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
• 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)