| Oracle® Clinical Creating a Study Release 4.6.2 E18820-01 |
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PDF · Mobi · ePub |
| Oracle® Clinical Creating a Study Release 4.6.2 E18820-01 |
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PDF · Mobi · ePub |
Lab ranges allow you to check the validity of lab data in a validation procedure. You can set standard ("textbook") ranges of acceptable values for lab test Questions according to company standards. If a particular study needs to use a different range of values for a particular Question, you can define an overriding lab range for that Question. In either case, you also enter information into the system about the labs that are processing the tests, and associate the appropriate lab ranges with the labs.
If a lab test result is out of range, Oracle Clinical creates a discrepancy in the Discrepancy Database that must be examined by clinical personnel.
You also enter information about each acceptable measuring unit for each Question, which unit is preferred, and how to convert to that unit so that all the data for the Question can be easily compared.
Before you begin working with the functionality available in the Lab Ranges subsystem, you must have all the required lab test Questions defined in the Global Library (see Chapter 7, "Questions and Question Groups").
You can batch load lab-related definitions, which is described in the final section of this chapter.
For replication across a distributed study, some lab information (Lab Units and panels) must be defined at the Global Library location, while other lab information (labs, lab ranges, and lab assignment criteria (LACs)) must be defined at the study-owning location.
This section covers the following topics:
For each lab test Question you must define each unit of measure acceptable for that Question, and how to convert Lab Units to a preferred unit. The following steps are required:
Defining Unit Conversions, if necessary
You must define all acceptable units of measure for all lab test Questions in the Maintain Lab Units window.
If you collect data using different units whose value is exactly the same (for example, percentages and decimal values), you can group those units into synonym groups by giving them the same Representative Unit Code. To do this, you must define a unit with the same name you want to use as the Representative Unit Code. This Code must not be longer than ten characters, and should be meaningful because it is what you will see in other Oracle Clinical lab definition windows. When you save this unit definition, its value becomes available to other units in the Representative Unit Code field list of values.
You have the option of adding free form text to help in pronunciation. Lab unit pronunciation appears only on this form and on the Lab Units Report.
You must define Lab Units at the Global Library location. You can add a new unit at any time. You can change a unit only if it has not yet been saved, and delete one only if it is not referenced by a lab test Question, but you can choose to make a unit inactive at any time.
To define Lab Units:
Navigate to Labs, Lab Units, and then Lab Units. The Maintain Lab Units window opens.
In the Lab Unit Code field, define the name of the Lab Unit. For example, g/ml.
In the Lab Unit Name field, enter a descriptive name for the Lab Unit.
Enter a Representative Lab Unit Code. These codes enable you to define Lab Units as equivalent in the system. For example, because the Lab Units mg/ml and mg/cc are equivalent, you can define mg/ml as their common Representative Lab Unit Code. You can enter a code of up to 40 characters.
(Optional) Describe how this Lab Unit is pronounced in the Lab Unit Pronunciation field.
Select the Active? box to enable this Lab Unit to be used, or clear it to hide it from the system.
Save. Oracle Clinical commits this Lab Unit to the database.
When you have defined all necessary Lab Test Units, associate each lab test Question you will be using with as many units of measure as apply, but at least one.
Lab units can be selected only by their representative Lab Unit code; however this code represents all the synonyms in the group—that is, all synonyms in the group are valid for the lab test Question.
In the Maintain lab test Question Units window you can insert representative Lab Units and delete those not referenced from Lab Unit conversions, ranges, Preferred Copy Groups, or preferred conversion groups. If the Lab Unit is referenced, you can choose to make it inactive. The Active? field controls whether the Lab Unit appears on lists throughout the Lab Ranges subsystem when Lab Units are called for. If a unit is marked inactive, it does not appear on lists.
To define lab test Question units:
Navigate to Labs, Lab Units, and LTQ Units. The Maintain lab test Question Units window opens.
Query for the lab test Question to which you want to associate units.
Define each representative Lab Unit name that you want to use as a unit measure for this Question, and either select the Active? box to enable this Lab Test Unit for the Question or clear it to render this unit inactive for this Question.
Save. Oracle Clinical enables you to use the representative Lab Test Unit or Units when you enter lab data for this Question.
You must define a unit conversion for each Question that has more than one acceptable unit of measure. You can write a Derivation Procedure that references this conversion formula (see Chapter 16, "Validation and Derivation Procedures").
If your study collects lab data for the same Question in multiple unit types (for example, kilos in Europe and pounds in the U.S.), you can specify conversion formulas to ensure that the data can be analyzed and reported using a single unit of measure. Use the Lab Unit Conversions window to set up standard conversion definitions.
The Lab Unit conversion must be unique in both source (the From: Lab Unit Name) and destination (the To: Lab Unit Name); the system checks for uniqueness when you leave the Lab Unit conversion record.
Always specify the conversion TO your preferred unit of measure, the one you will use to analyze the data. Later, in the Maintain Preferred Conversion Groups window, you specify which unit is preferred for each Question.
The conversion must be expressed in terms of multiplication and/or addition. To divide, multiply by a fraction; to subtract, add a negative number. However, you cannot enter a multiplier of zero or a negative number; doing this results in an error message. The system issues warning messages in the following circumstances:
The inverse of the reverse multiplier is not within 1/10000 of the new multiplier.
Another multiplier for the same lab test Question is within 1/10000 of the new one.
To define a Lab Unit conversion:
Navigate to Labs, Lab Units, and LU Conversions. The Maintain Lab Unit Conversions window opens.
Query for the lab test Question for which you want to define conversions.
Query for a Lab Test Unit you want to use as the From value. You can only choose Lab Test Units that have been defined for this Question in the Maintain lab test Question Units window.
Query for the Lab Test Unit you want to use as the To value. In addition to being defined as a Lab Test Unit for this Question, you must also choose a different unit than you selected as the From value.
Choose a Conversion Source.
Enter the Multiply Number and/or Add Number for this unit conversion.
(Optional) Enter a comment that describes this conversion further.
Save. Oracle Clinical saves this Lab Unit conversion for this Question.
A preferred conversion group is a set of lab test Questions and the preferred Lab Unit of measure for each Question. The preferred conversion group, together with the relevant Lab Unit conversion formulas, can be used by a Derivation Procedure to convert a response to the lab test Question collected in one unit of measure to a derived value in the preferred standard unit of measure (see Chapter 16, "Validation and Derivation Procedures").
Navigate to Labs, Lab Units, and Pref Conv Groups. The Maintain Preferred Conversion Groups window opens.
Define the unique group ID in the Group field. This ID can be up to 10 characters long, and you cannot change it once you save the group.
Define a Group Name.
(Optional) Enter a comment to describe supplementary information about this preferred conversion group.
Enter each Preferred Lab Unit for this group:
Query for a lab test Question. When you choose one, Oracle Clinical populates its domain as well.
Query for a Lab Unit Name associated with that Question.
Enter the number of decimal places that you want reports displaying this value to use. Once you save, you cannot change this value.
(Optional) Enter a comment with supplementary information about using this preferred Lab Unit for this group.
Save. Oracle Clinical commits this preferred conversion group to the database.
Once Oracle Clinical has the Lab Unit information to draw from, you can define a standard ("textbook") lab range for each lab test Question and put them into Preferred Copy Groups to copy them for use in multiple studies. If you need to override your company's standard range for a particular Question in a particular study, you can do so by navigating to Labs, then Labs, Labs, and Ranges.
This section includes the following steps:
Textbook lab range definitions serve as the company standard range for lab test Questions. They provide a default definition for each lab test Question where no lab-specific ranges have been defined. You can also use these definitions as a foundation from which to create more specific lab range definitions for particular labs.
Oracle Clinical enforces uniqueness for textbook ranges in a similar way to lab ranges, but considers one more column: the Lab Unit Name. Thus, each textbook range must be a unique combination of lab test Question, Domain, Sex, Maximum Age, Minimum Age, Effective Start and End Date, and Lab Unit Name.
The Maintain Textbook Ranges window only displays the representative unit names. Representative Lab Test Units are defined when you define lab test Question units; see "Defining lab test Question Units".
You can use the Maintain Textbook Ranges window to delete textbook ranges; however, you cannot delete a textbook range if a Preferred Copy Group uses it.
To define a textbook range:
Navigate to Labs, then Labs, and Textbook Ranges. The Maintain Textbook Ranges window opens.
Query for the Question for which you want to establish textbook ranges. The system displays only Questions that have a Question type of Lab Test.
Enter each textbook range for this Question:
Enter the gender to which this range applies. Valid choices are Male (M), Female (F), or Both (B).
Enter the minimum and maximum age ranges. You can leave either end of the age range blank, if no minimum or maximum age applies for this range.
Enter the low and high values for this textbook range, and the Lab Unit Code for the measurement you are specifying.
(Optional) Enter the dates during which the textbook range is in effect. You can leave one or both of these blank.
Save. Oracle Clinical commits these textbook ranges to the database for this lab test Question.
A Preferred Copy Group is a named set of lab test Questions and the units of measure that each question uses. Using Preferred Copy Groups enables you to create and copy groups of textbook ranges; each time you add a lab test Question to a Preferred Copy Group and choose a preferred unit of measure, Oracle Clinical associates the textbook ranges you have defined for that Question with the copy group. When you copy textbook ranges into a lab definition, the Use Textbook Ranges window only allows you to use textbook ranges that are grouped into Preferred Copy Groups.
You can create Preferred Copy Groups to group Questions that often need to be copied together when applying ranges to a lab; or for lab test Questions that are identical except for, perhaps, the unit of measure measured.
Differences in units of measure arise when you have locations in Europe and also in the United States. To handle these differences you might have a Preferred Copy Group called US and one called EURO. For example, the Hematocrit test would likely be collected as a fraction in Europe and as a decimal in the U.S., which you would translate as two identical textbook range definitions for Hematocrit:
Hematocrit Male 42-54 % Female 38-46 % Hematocrit Male .42-.54 fraction Female .38-.46 fraction
Preferred Copy Groups and Preferred Conversion Groups (from the Labs menu, select Lab Units, then Pref Conv Groups) take almost the same information about lab test Questions and their preferred units of measure, but are used for different things. Conversion groups are used by Derivation Procedures and copy groups are used to copy lab Questions and their preferred unit and textbook range for use in a new lab; see "Defining Preferred Copy Groups" and "Defining Preferred Conversion Groups".
To define a Preferred Copy Group:
Navigate to Labs, then Labs, and Pref Copy Group. The Maintain Preferred Copy Group window opens.
Enter a unique ID for this group. This ID can be up to 10 characters long.
Enter the name for this group. This name is required, but you can change it even after you save the Preferred Copy Group.
(Optional) Enter a comment with supplementary information about the Preferred Copy Group.
Enter each lab test Question and its preferred Lab Unit combination that you want to include in this Preferred Copy Group:
Query for the lab test Question. When you choose one, the Maintain Preferred Copy Group window also populates its domain.
Query for the Lab Test Unit you want to use for this Question.
(Optional) Enter a supplementary comment about including this Question and unit in the Preferred Copy Group.
Save. Oracle Clinical commits this Preferred Copy Group to the database, making it available for use in the Use Textbook Ranges window.
Navigate to Labs, then Labs, and Lab Panels. The Maintain Lab Panels window opens.
Define a unique identifier for the lab panel, not greater than 10 characters, in the Panel field.
Define a unique name for the lab panel, not greater than 60 characters, in the Panel Name field.
(Optional) Enter a comment to describe this lab panel. Descriptions in this field can be useful to other users browsing through lab panel records.
Enter the lab test Questions for this lab panel in the lower part of the window. For each lab test Question:
Click in an empty row. The Maintain Lab Panels window populates the sequence number (Seq #) field with the next unused number.
Enter a SAS Name for a Question defined and active in the Global Library with data type NUMBER and type LAB TEST.
When you choose a Question, Oracle Clinical automatically populates the lab test Question and lab test Question Domain fields with the corresponding information for that SAS Name.
Choose a lab test Question Type.
(Optional) Enter a comment about including this lab test Question in the Lab Panel.
Save.
You can modify existing lab panels in a similar way. Query for the lab panel you want to change using the fields in the upper part of the window, and add, remove or change lab test Questions.
This section describes how to define the basic lab settings using the Maintain Labs window. A Lab Definition consists of the necessary contact and related information, and the lab ranges to be applied to data from that lab. You have to define the information in this section before you establish the lab's ranges.
Use the Maintain Labs window to launch these tasks: define lab ranges and lab range subsets, use textbook ranges in the lab definition, and copy lab ranges. See the following sections for each one of these topics:
You can also delete labs using the Maintain Labs window; however, you can only delete a lab if it is not referenced by any received DCMs or lab assignment criteria.
To define a lab:
From the Labs menu, select Labs, then Labs. The Maintain Labs window opens.
Enter the Lab ID and its name. The ID must be no greater than 10 characters, all uppercase.
Select the Active? box to activate the lab, or clear it to render it inactive. Only active labs can supply lab ranges for the lab data entered or batch loaded for a study. You can change a lab's active status at any time.
Ranges Approved: If this field is checked, all ranges for this lab have a status of Approved. This is a display-only field.
Format Mask: Choose the default file format mask you want to use for batch loading data from this laboratory.
Owning Location: Name of the Oracle Clinical database that owns this lab data. This is a display-only field.
Replicate?: If checked, this lab must be replicated from an Oracle Clinical database other than your current database.You can change this flag from unchecked to checked at any time, but once checked, you cannot uncheck it.
Last Replication: Date and time this lab was last replicated from the Oracle Clinical owning location. This is a display-only field.
Enter the necessary information for the person who serves as the contact for this lab: the contact's first and last name, phone number and fax number.
Enter the lab's full mailing address.
Enter the start and end dates for this lab's accreditation.
Enter the certification agency and number for this lab, if applicable.
(Optional) Enter a supplementary comment to describe this lab.
Save. Oracle Clinical commits this lab definition to the database.
Use this window to specify ranges for this lab that are different from your company's textbook range for particular Questions.
As in textbook ranges, you can define a different range of valid values for each Question depending on the age or gender of the patient. Each range in the lab must have a unique combination of lab test Question, sex, maximum age, minimum age, and effective start and end date. If any range definition has a blank field for Lab Unit, low range, or high range, the range status is automatically set to MISSING, in which case the range is considered incomplete and not used for calculations.
The ranges you define here, and only the ranges you define here, will be available for Subsets definition (see "Defining Lab Subsets").
For a special use of the Ranges window, see "Using Textbook Ranges".
Note:
If you change any part of a lab range definition that has been used against production data, you must immediately execute the PSUB job; from the Labs menu, select Lab Procedures Re-Execution Pre-Process. If you do not run this job, your changes will not be applied to existing data.If you enter a value in the optional Age field, the value must be greater than zero. The minimum age is inclusive, and maximum age is exclusive. For example, an age span of 10 to 20 years would apply to patients from the day they turn 10 years old through the day before their twentieth birthday. When they turn 20 this lab range would no longer apply to their data for this Question. A set of age spans for ranges for a particular lab test might be 10-20, 20-30, 30-55. These spans do not overlap. Ages may be expressed in days, months, or years; the Age Unit field is to the right in the window.
Unless there is a specific date entered in either the Start or End field, the range is assumed to be continuous from the point it is defined. If you enter an end date, then you must define a range to start after that; otherwise the textbook range becomes the active range.
Two ranges can coexist if describing ranges for patients of different ages:
Table 15-1 Example of Coexisting Ranges
| lab test Question | Sex | Age | Age Unit | ||
|---|---|---|---|---|---|
| Min | Max | Min | Max | ||
|
CHOLESTEROL_SERU |
B |
10 |
20 |
YEARS |
YEARS |
|
CHOLESTEROL_SERU |
B |
20 |
30 |
YEARS |
YEARS |
|
CHOLESTEROL_SERU |
B |
30 |
55 |
YEARS |
YEARS |
The Effective Date and Sex fields are all components of the unique key for the range. In the example below the two ranges conflict because the unique key components overlap—that is, sex (because Both includes Men) and the date ranges overlap by one day. The ages do not overlap because the age units are different. Also, note that the units of the minimum and maximum can be different from each other, as well as different from the previous row.
If you enter a lab range record and leave either the Effective Start or Effective End Date field empty, the Lab Ranges window leaves that field blank when you save the record. However, Oracle Clinical does store a date value in the database for that record. The presentation of this date value in SQL*Plus can be counter-intuitive, so this section describes how Oracle Clinical stores this information.
If you leave the Effective Start Date field empty, Oracle Clinical stores the date January 1, -4712 in the effective start date column for that record. This date is 1 Julian, which is the beginning of time for an Oracle database. When you query for the record, SQL*Plus removes the negative sign from the year, displaying the values as 01-JAN-4712 or just 01-JAN-12. Despite the presentation, Oracle Clinical logically handles lab range records in this format as having no effective start date.
Similar logic applies to the Effective End Date. When you leave this field empty for a lab range record, Oracle Clinical stores the end date as August 15, 3501. This date is 3,000,000 Julian, and represents the end of time for an Oracle database. Depending on the date formats you use for SQL*Plus, the system might display lab ranges without effective end dates as having an end date of "15-AUG-3501."
To define a lab range:
Open the Maintain Labs window (from the Labs menu, select Labs, then Labs) and query for the lab you want to modify.
Click the Ranges button. The Maintain Lab Ranges window opens.
For each lab range you want to define:
Query for the lab test Question for this lab range. When you select a Question, the window displays its domain and the Range Type (which is the source of the range, and is either LAB or TEXTBOOK).
Choose the gender to which this range applies. Values are Male (M), Female (F), or Both (B).
Enter the minimum and maximum age ranges. You can leave either end of the age range blank, if no minimum or maximum age applies for this range.
Enter the low and high values for this textbook range, and the Lab Unit code for the measurement you are specifying.
(Optional) Enter the dates during which the textbook range is in effect. You can leave one or both of these blank.
Save. Oracle Clinical saves these lab ranges for this lab definition.
Oracle Clinical enables you to create (optional) subsets of existing lab ranges, which you can use for particular lab Questions where the normal range is affected by a predictable factor. For example, diabetes consistently influences the range of data considered normal for certain Questions.
To prepare for subset creation, when you define a lab Oracle Clinical creates it with a single default subset. When you define ranges for a lab, Oracle Clinical automatically associates them with the default subset as well. These are the only ranges that are available to other subsets for the lab.
Before creating subsets you must enter the values you plan to use for subset names in the LAB RANGE SUBSET CODE installation reference codelist. If you define no explicit subsets then the lab will have only one, lab_name$default. The name assigned to the default is also specified in the LAB RANGE SUBSET CODE reference codelist.
You also define these lab range subsets in the Lab Range Subsets window. When you create a subset, you are required to select the Questions from a list of the Questions included in the default subset. The default subset is created automatically when the lab is created. Subsets have the syntax lab_name$subset_name when a lab is referenced elsewhere in the system.
In this section, you establish the subset you want to use for this lab. To define a Lab Range Subset:
Open the Maintain Labs window (from the Labs menu, select Labs, then Labs) and query for the lab you want to modify.
Click the Subsets button. The Maintain Lab Range Subsets window opens.
Click in an empty row, and choose a Subset Code from the list of values. The window populates a default name for the subset, which you can modify at any time.
Select the Active? box to use this subset in the lab range, or clear it to prevent its use at this time. You can change this setting at any time.
Save. Oracle Clinical saves the subset name for this lab. Proceed to "Defining the Subset Range Values".
In this section, you specify the subset values for a particular lab range. There are two ways to do this:
You can enter the subset ranges manually. From the Lab Range Subsets window, click Ranges, then enter the ranges as you would for the default subset.
You can copy a set of ranges from the default subset, then edit them for the new subset.
To copy ranges from the default layout:
In the Lab Range Subsets window, confirm that the subset that you want to use is selected, then click Ranges.
In the Ranges window, click Copy Ranges from Default Subset. The Multiple Questions Selection from the Default Subset window opens.
Choose one or more Questions to include, and click OK. This window closes, and the ranges window adds all of the default lab ranges you selected to the subset.
Edit each subset range to include the values you want.
Save. Oracle Clinical saves this subset for the lab.
The List function in the pop-up window displays available copy groups. The New Dates Start/End field in the Use Textbook Ranges window substitutes for the original effective dates of each of the textbook ranges. If the textbook ranges have changed over time, the Text Range Date field lets you copy older textbook ranges.
You can copy a whole set of lab Questions, their preferred units of measure, and predefined company-standard textbook ranges (see "Defining Textbook Ranges") by clicking the Textbook Ranges button and entering the name of a Preferred Copy Group (see "Defining Preferred Copy Groups").
Note:
If you want to associate a textbook range for a unit with a particular Question rather than a whole set of Questions, from the Labs menu, select Labs, then Labs. Select the Ranges button. In the Ranges window that appears, enter the Question with which you want to associate a textbook range. Oracle Clinical populates the LOVs of the enterable fields, such as Min or Low under Age or Values, with textbook range values.To use textbook ranges in a lab:
From the Maintain Labs window (from the Labs menu, select Labs, then Labs), choose the lab for which you want to use textbook ranges.
Click the Use Textbook Ranges button. The Use Text Book Ranges window opens.
Select a Preferred Copy Group to use. Oracle Clinical will copy this group's test Questions, ranges and units into this lab.
If you want to use the current version of the textbook ranges, leave the remaining fields empty and click OK.
If you want to use earlier versions of the textbook ranges, enter a date when this textbook range was current in the Text Range Date field. You can only use previous versions of textbook ranges if these ranges are still active.
Enter the dates over which the copied ranges will be effective. Dates must be in the DD-MON-YY format.
Click OK to close the Use Text Book Ranges window, then save.
If you are creating a new lab definition for a lab that will perform a set of lab tests very similar to an existing lab, you can copy a whole set of lab ranges from another lab definition by pressing the Copy Lab Ranges button and choosing a valid lab to copy from. You can then edit the ranges, if necessary. You cannot edit them once the new lab has been used.
To copy lab ranges from another lab into the lab you have selected:
In the Maintain Labs window (from the Labs menu, select Labs, then Labs), choose the lab into which you want to copy lab ranges.
Click the Copy Lab Ranges button. The Copy Lab Ranges window opens.
Choose the lab from which you want to copy ranges, and click Copy.
The operation generates Alert messages, which list the number of ranges copied, number rejected, and which Questions were not copied because of a conflict. Lab ranges that copy successfully will appear in the selected lab with a Range Type of LAB and a Comment of COPIED.
Save.
Lab Assignment Criteria (LAC) link studies to labs. When you set up a study you define the labs that will process the physical patient samples collected during the trial. The lab test Question results are then associated with the lab in the database and compared to the lab ranges defined for that lab, and when the lab test results are entered during data entry, the name of the lab that did the testing is displayed.
If necessary, you can link different labs to different RDCIs, RDCMs, subsets, layouts, study sites, Investigators, or even visits or patients.
You can update or create new lab assignment criteria if circumstances change or if new sets of assignment criteria are required while the study is in progress.
Lab assignment criteria include:
Start Date/End Date
Study Site
Investigator
DCI Name
DCM Name, Subset and Layout
Patient
Clinical Planned Event Name, Visit Number
It is not necessary to complete all fields. If you leave a field blank, the lab is linked to all values for that field; for example, all sites or all Investigators. In matching lab assignment criteria to RDCMs, the system always uses the most specific set of criteria.
Each set of lab assignment criteria in the study must have a unique combination of criteria values.
A few logical restrictions apply in completing some LAC fields:
If you enter a DCM Subset Name, the DCM name is required.
If you enter the DCM Layout Sequence, the DCM name and subset are required.
If you enter a DCI Name in the LAC, the list of values for DCMs will contain only DCMs that belong to this DCI; otherwise, all DCMs are valid.
If you complete the Actual Event field, the clinical planned event is restricted to the correct event.
Clinical planned events must be valid for the selected study.
The following table illustrates how lab assignment criteria may evolve. Each line represents the creation of a new LAC in the same study. Each line is annotated below the table with the events that prompted the definition of a new LAC.
| Lab | Start/End Date | Site | Investigator | DCI | DCM | Patient | CPE | AE | |
|---|---|---|---|---|---|---|---|---|---|
| 1. | L1 | VI | |||||||
| 2. | L2 | S2 | |||||||
| 3. | L3 | 02-dec-97 15-jan-98 | VI | ||||||
| 4. | L1 | 02-dec-97 15-jan-98 | VI | LE | P1 |
The original LAC, created when the study began: Investigator V1 managed all patients and Lab L1 processed all lab tests.
A new site, S2, is added to the study. Lab L2 processes its lab tests.
The original Investigator, V1, is now working with a different lab, L3. Any RDCMs that come in between December 2, 1997 and January 15, 1998 are assigned to L3. If no new LAC is defined for the period following January 15, then assignments default back to the LAC on line 1, which has no date.
During the period when V1 is using a different lab, one of his patients, P1, continues to use the original lab, L1.
In addition to storing the lab to which each lab test RDCM is assigned, Oracle Clinical stores the method by which the lab was assigned. These methods are hierarchical and you can use this hierarchy to force Oracle Clinical to reassign certain RDCMs. The following table describes the five methods in order of descending precedence.
| Method | Description |
|---|---|
| USER | Explicitly assigned by user by choosing from the list of values for Lab in the Received DCMs window of the Maintain Lab Assignment Criteria window. |
| SYSTEM | Not currently used. |
| LOGIN | Lab name explicitly entered during data entry. |
| CRITERION | Assigned by running the Apply LAC job. |
| UNKNOWN | Lab is missing. Default setting. |
To apply Lab Assignment Criteria to a study:
Navigate to Labs, and Lab Assignment Criteria. The Maintain Lab Assignment Criteria window opens.
Query for, then select, the study to which you want to apply LACs.
Click Apply LAC. The Apply LAC to Study window opens.
Enter a Lab Assignment Type. This selection forces a batch process to examine each lab RDCM for the study. Any that have a lab assignment type equal to or lower in precedence that the method you entered is re-evaluated and reassigned according to the current lab assignment criteria.
Enter a Change Reason. A list of values is available.
(Optional) Enter an Audit Comment about applying this LAC to this study.
(Optional) Select the Process Locked RDCMs box to include locked RDCMs as well. This box may be grayed out if you only have update privileges, because processing locked RDCMs requires Privileged Update. See "Granting Privileged Update to a User" for instructions on being granted Privileged Update.
Click Apply. Oracle Clinical applies the LAC to this study.
Administrators can grant you Privileged Update status in the Data Entry Configuration settings if you need to perform activities such as processing locked RDCMs.
To grant a user Privileged Update status:
From the Admin menu, select Users, then choose Oracle Accounts. The Maintain Oracle Accounts window opens.
Choose the user's account name, and select Special, and DE Configs. The Maintain User Configuration window opens.
For Privileged Update, choose Enabled from the list of values.
Save. Upon your next visit to the Maintain Lab Assignment Criteria window, you will be able to select the Process Locked RDCMs box.
Lab data may not link to ranges because an RDCM is not linked to a lab or because necessary patient information, such as age or gender, is missing. These problems—Missing Lab References in the RDCMs and Missing Data in Patient Positions—can be identified in windows reached through the buttons in the Maintain Lab Assignment Criteria window.
To identify missing lab references in the RDCMs:
Navigate to Labs, and Lab Assignment Criteria. The Maintain Lab Assignment Criteria window opens.
Choose the study that you want to investigate.
Click the Received DCMs button.
The Received DCMs for Study window opens; this window enables you to identify received DCMs (documents) that have either not been assigned to a lab or have been assigned incorrectly. Only RDCMs that have lab test Questions may be queried.
The Lab Assignment Type field reflects how the lab was assigned to the RDCM. If you assign a lab using this form, the system updates the Lab Assignment Type to USER. USER is hierarchically the highest method Oracle Clinical recognizes, so this lab assignment can only be changed in the future by explicit user intervention. If you make the Lab field blank here, the Lab Assignment Type is set to UNKNOWN. Each document can be associated with one and only one lab.
To query all RDCMs where the lab is blank:
Enter Query mode.
Enter LAB in the Lab field.
Execute the query.
Enter LAB IS NULL in the window.
Save.
To examine patient positions where data is missing:
Navigate to Labs, and Lab Assignment Criteria. The Maintain Lab Assignment Criteria window opens.
Query for and select the study that you want to investigate.
Click the View Patient Positions button.
Oracle Clinical cannot compare lab test results to lab ranges if a patient's age and gender are not entered in the system. To identify patient positions with missing birth dates or gender, press the View Patient Positions button from the Maintain Lab Assignment Criteria form.
You can only query patient positions in this window; you cannot insert, modify, or delete patients.
Oracle Clinical accepts lab range data in batch mode. Batch loading data is more efficient and less prone to introducing new errors for large quantities of data than manually entering data. Loading of lab ranges is for new lab ranges only; you cannot perform updates of this data using the batch loader.
This section explains the three-step process—Loading Data, Validating Data, and Transferring Data—and includes a step-by-step procedure for Executing the Process.
The goal of the data load stage is to verify that a value is present for each mandatory key column. There are no checks for the validity of the data at this stage; only that it exists.
The system loads the data into a temporary table, TEMP_RANGES. If there are existing rows for the lab being loaded, then it aborts and displays a message, "Another Batch Data Load in Progress for this lab <Lab Name>." The input to the process is the lab name, the full pathname to the data file, the domain name, and the delimiters used for the data, which are entered using a form described in detail in "Executing the Process".
After all validations are complete, the entire data file is loaded into TEMP_RANGES. If there are errors, the status code in the LAB_DATA_FILES table is updated to BAD LOAD, but rows without errors are inserted in TEMP_RANGES.
The data file you load must be in a standard format, including the following columns in this order: Lab Name, Lab Range Subset Code, lab test Question, Sex, Minimum Age, Maximum Age, Minimum Value, Maximum Value, Lab Unit Name, Effective Start Date, Effective End Date, Minimum Age Unit, and Maximum Age Unit.
You can use whatever delimiter you want in the file and specify it in the execution window.
The delimiter here is a comma (,):
CENTRAL,,SODIUM,F,10,20,-5,10,u/ml,,,DAYS,DAYS
The two commas after the Lab Name and two commas after the Lab Unit Name mean that the Lab Range Subset, Effective Start Date and Effective End Date are not provided. Leading and trailing blanks must be stripped before insertion into the TEMP_RANGES table.
During preparation stage the system performs the following validations on the data loaded into the temporary table:
Checks input data against existing database definitions for duplicate rows for:
Lab Name
Question Name
Lab Unit
Performs lab range validations to check:
Relative values of the age fields—maximum_age should be greater than the minimum_age
Overlap in gender fields
Date range; with the last row having an open Effective End Date
minimum_value and maximum_value
These parameters can be zero, a positive value, or a negative value.
maximum_value should be greater than minimum_value, if both the values are not null.
After the error checking, the system produces a printable report of the results of the load and prepare stages, indicating the number of erroneous records and providing the PSUB job ID, which can be queried in the Batch Jobs window.
Following checks of the TEMP_RANGES table for validation errors and duplicate rows, the permanent lab ranges database tables are populated from the rows in the TEMP_RANGES table. If no duplicate rows exist then all the rows from the TEMP_RANGES are inserted into the RANGES table. Duplicate rows are handled as follows:
If you have the same lab range (combinations of key values, i.e. Lab, Question, Gender, minimum_age, maximum_age) and different minimum value or maximum value, update the record with the new minimum or maximum value, or both.
If the audit has to be recorded in the range_comment column, then the values of previous values and the updated values can be shown in the comment.
If the audit is not being recorded in the range_comment column, then the range_comment can also have a different value and can be updated.
If you have the same key combinations (Lab, Question, Gender, minimum_age, maximum_age) and different Effective Start and End Dates, rearrange data according to the rules to accommodate the new effective dates.
If your date ranges overlap in a record, rearrange all rows for that key set.
If the existing rows are as follows:
Question, Gender, Min.Age, Max.Age, Effective Start ,Effective End
adding the following new row, which comes in with the same combination of keys except for the minimum age and maximum age,
Question ,Gender, Min.Age, Max.Age, Effective Start, Effective End
QUESTION, B ,10 ,20, 10-FEB-1998 ,09-MAR-1998
results in the following final set of rows:
Question ,Gender ,Min.Age ,Max.Age ,Effective Start ,Effective End
You set parameters and execute batch data loads of lab range data from within Oracle Clinical. To execute a batch data load:
From the Labs menu, select Lab Batch Data Load, and Lab Ranges Batch Data Load.
Complete the fields as follows:
Run Error Check Only (Y/N)? specifies whether to run a preliminary error check on the file (Y) or execute the full batch load (N).
Lab Data File Name provides the full pathname to the data file.
Column Delimiter used in the Data File identifies the delimiter used in the file to separate data elements. There are no restrictions in choosing this delimiter.
Domain Name identifies the domain of the lab test Questions.
Default Effective Dates (Y/N)? specifies whether the program should set the effective dates (Y) or if you plan to specify them manually in Oracle Clinical (N).
Click Submit Job.
The program produces a detailed output file, providing a complete listing of the events that occurred during execution. If the process completes successfully, it places a new row in the RANGES table.
If you change any part of a lab range definition that has been used against production data, you must immediately execute the PSUB job by selecting Lab Procedures Re-Execution Pre-Process from the Lab menu. If you do not run this job, your changes will not be applied to existing data.
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