PWS Appendix 2.pdf

Information Technology Staff

Pathology Tracking System User Guide

ITS Doct #001-PTS-1.0

ITS

Pathology Tracking System

ITS Doct #001-PTS-1.0

This is the original version of the Pathology Tracking System User Guide, Doct #001-PTS-1.0.

Companion Publications: None

Prepared by R.O.W. Sciences Information Technology Staff National Center for Toxicological Research Jefferson, AR 72079

HFT-910

i

INFORMATION TECHNOLOGY STAFF

NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH

Pathology Tracking System User Guide

Table of Contents

SECTION PAGE NO.

1.0 INTRODUCTION .................................................... 1.1

1.1 SYSTEM DESCRIPTION ......................................... 1.1

1.2 PRINT CONVENTIONS .......................................... 1.1

1.3 FUNCTION KEYS .............................................. 1.2

2.0 SYSTEM OPERATION ................................................ 2.1

2.1 LOGGING ON THE SYSTEM ...................................... 2.1

2.2 SYSTEM MENU ................................................ 2.2

2.3 MAIN MENU .................................................. 2.3

2.3.1 Enter Counts ........................................ 2.4

2.3.2 Report and Inquiry Requests ......................... 2.7

2.3.3 Purge Experiments ................................... 2.10

2.3.4 Modify/Delete Count Data ............................ 2.11

2.3.5 Area Table Maintenance .............................. 2.13

2.4 REVIEW/PRINT REPORTS ....................................... 2.15

APPENDIX - Document Revision History ii

List of Figures

FIGURE PAGE NO.

Figure 2-1 System Menu .............................................. 2.2

Figure 2-2 Main Menu ................................................ 2.3

Figure 2-3 Enter Count Data Screen - Screen One ..................... 2.4

Figure 2-4 Enter Count Data Screen - Screen Two ..................... 2.5

Figure 2-5 Report/Inquiry Selection Menu ............................ 2.7

Figure 2-6 Purge Experiment Screen .................................. 2.10

Figure 2-7 Tracking File Correction Screen .......................... 2.11

Figure 2-8 Area Table Maintenance Screen ............................ 2.13

Figure 2-9 List of Report Filenames ................................. 2.15

Pathology Tracking System September 1990 User Guide #001-PTS-1.0

1.1

1.0 INTRODUCTION

This document provides both general and specific information related to the Pathology Tracking System. It is composed of two major sections. Section one describes the system and gives instructions for using this document. Section two explains how to enter data into the Pathology Tracking System.

1.1 SYSTEM DESCRIPTION

The Pathology Tracking System has three primary functions. The first function locates a case within the Pathology laboratory. The system displays the last area in which the case was located, allowing personnel to track a case's progress through the lab. The second function summarizes the status of all CIDs from a particular experiment. This allows personnel to estimate the amount of time it will take CIDs to go through all areas of the lab. The third function allows lab personnel to produce daily, monthly, and yearly workload reports, which summarize the number of slides, blocks, or CIDs processed in each area and gives totals by experiment and technician.

1.2 PRINT CONVENTIONS

This document uses different print styles to help you distinguish between

(1) data that you enter, (2) keys that you press, and (3) field names that appear on the screen. The following table summarizes the conventions used.

CONVENTION MEANING

ALL CAPS BOLDFACED, UNDERLINED Refers to an entry that you must type, or a field that you can change. For example:

Enter 1; The default response is N

<Boldfaced in angle brackets> Identifies a function key or function key sequence that you must press. For

Press <Enter>; Enter <GOLD><M>

Bold Faced Refers to a menu selection or field name on the screen. These may be in upper or lower case letters depending on how they appear on the screen. For

Select the 2 ENTER COUNTS option

Pathology Tracking System September 1990 User Guide #001-PTS-1.0

1.2

1.3 FUNCTION KEYS

The function keys you will use to enter data are described in the table below.

Note: Some function keys have different uses on different screens. These screen-specific functions are also listed in the table below.

FUNCTION KEY MEANING

<Enter> Brings up the selection you chose from the Main

Menu or allows you to continue to the next screen within a selection.

<GOLD><C> On the Enter Count Data Screen, <GOLD><C> allows you to complete a case. On the Tracking File Correction Screen and the Pathology Area Table <GOLD><C> modifies records.

<GOLD><D> Allows you to delete a record on the Pathology

Area Table.

<GOLD><M> Returns you to the Main Menu.

<GOLD><N> On the Tracking File Correction Screen, <GOLD><N> brings up the next record. On the Pathology Area Table, <GOLD><N> allows you to add records.

<GOLD><Q> Exits you from the screen you are working on and takes you back to the System Menu. Use this sequence at any time but be aware that your data will not be saved.

<GOLD><R> On the Enter Count Data Screen, <GOLD><R> allows you to restart a case. On the Pathology Area Table, <GOLD><R> allows you to retrieve a record.

<GOLD><X> Allows you to delete a record on the Tracking

File Correction Screen.

<Return> Use <Return> at the System Menu only. Once you have accessed the Main Menu, use <Enter>.

<Tab> Moves the cursor forward between fields.

Pathology Tracking System February 1994 User Guide 001-PTS-1.0

2.1

2.0 SYSTEM OPERATION

This section describes how to enter data into the system and run reports.

2.1 LOGGING ON THE SYSTEM

To log on to the Pathology Tracking System, type TPTH at the Project prompt and press <Return>. If you have done this correctly, the System Menu will appear.

2.2

2.2 SYSTEM MENU

When you type TPTH at the Project prompt and press <Return>, the System Menu appears. Figure 2-1 shows the System Menu.

Figure 2-1. System Menu

The table below describes each of the options on the System Menu.

FIELD DESCRIPTION

CHANGE PROJECT Allows you to exit the Pathology Tracking

System.

COLLECT DATA/CREATE REPORTS Allows you to choose one of the main functions of the system, such as data-entry functions, modify and delete functions, and report request functions.

REVIEW/PRINT REPORTS Lets you view or print reports that have been created. See Section 2.4 for a detailed description of Review/Print Reports.

PATHOLOGY TRACKING SYSTEM

CHANGE PROJECT ==> 1

COLLECT DATA/CREATE REPORTS ==> 2

REVIEW/PRINT REPORTS ==> 3

PLEASE ENTER SELECTION: _

2.3

2.3 MAIN MENU

When you choose option 2 COLLECT DATA/CREATE REPORTS from the System Menu and press <Return>, the Main Menu will appear. This menu lists the main functions of the Pathology Tracking System. Figure 2-2 shows the Main Menu.

Figure 2-2. Main Menu

The following table summarizes the options on the Main Menu.

FIELD DESCRIPTION

ENTER COUNTS Allows you to enter data for CIDs, including date received, area, technician, and count.

REPORT AND INQUIRY REQUESTS Allows you to generate reports.

PURGE EXPERIMENT DATA Allows you to delete all records associated with a selected experiment from the tracking file.

MODIFY/DELETE COUNT DATA Allows you to change or delete data.

AREA TABLE MAINTENANCE Allows you to add, delete, or modify

Pathology Area IDs and names.

A detailed description of each of these options is provided in the following sections.

P A T H O L O G Y T R A C K I N G S Y S T E M

PTM1M001

EXIT ==> 1

ENTER COUNTS ==> 2

REPORT AND INQUIRY REQUESTS ==> 3

PURGE EXPERIMENT DATA ==> 4

MODIFY/DELETE COUNT DATA ==> 5

AREA TABLE MAINTENANCE ==> 6

ENTER SELECTION ==> .

2.4

2.3.1 Enter Counts

To enter count data, select option 2 ENTER COUNTS from the Main Menu and press <Enter>; the first Enter Count Data Screen will appear. This screen (shown below in Figure 2-3) prompts you for the Carcass ID. Note: Only CIDs which have been received through the Pathology Receiving System are valid.

Figure 2-3. Enter Count Data Screen - Screen One

PTM2U001

ENTER COUNT DATA

09/05/90 08:36:52

ENTER CARCASS ID ==> ……………………

GOLD M MAIN MENU GOLD Q QUIT

2.5

When you have entered a valid CID, press <Enter> to display the second Enter Count Data Screen. Figure 2-4 shows this screen.

Figure 2-4. Enter Count Data Screen - Screen Two

The table below describes each of the fields on the second Enter Count Data Screen.

FIELD DESCRIPTION

DATE The date defaults to the current date; however, this date can be changed by the technician.

AREA Enter the code for the area in this field.

TECHNICIAN Enter the technician ID in this field.

COUNT Enter the count in this field.

PTM2U002

ENTER COUNT DATA

EXP/TEST 51901 CARCASS ID 5190100004

DATE ==> 900905

AREA ==> …..

TECHNICIAN ==> …..

COUNT ==> …..

GOLD M MAIN MENU GOLD Q QUIT GOLD R RESTART CASE GOLD C COMPLETE CASE

2.6

Enter the area, technician, and count data for the CID. Press <Enter> to view the corresponding text.

If you enter information that is not valid, the system will give you an error message. Press <Enter> to acknowledge and you will be allowed to re-enter data. Remember that the count units correspond to the area. If you change an area number, the count units will change accordingly.

Press <GOLD><C> to save your data when you are finished. If you have done this correctly, the system will display the message DATA ADDED TO DATA BASE - ENTER TO CONTINUE. Press <Enter> and the first Enter Count Data screen will appear. Continue entering data for more CIDs or press <GOLD><M> to return to the Main Menu. If you make a mistake entering data on the second Enter Count Data screen, press <GOLD><R> and you will return to the first screen without saving any data. From there, re-enter the CID or press <GOLD><M> to return to the Main Menu.

2.7

2.3.2 Report and Inquiry Requests

To generate reports and/or online queries, select option 3 REPORT AND INQUIRY REQUESTS from the Main Menu and press <Enter>, the Report/Inquiry Selection Menu will appear. Figure 2-5 shows your options on this menu.

Figure 2-5. Report/Inquiry Selection Menu

PTM2M001

REPORT/INQUIRY SELECTION MENU

CASE INQUIRY ==> 1 AREA WORKLOAD REPORT ==> 5

EXPERIMENT INQUIRY ==> 2 EXPERIMENT WORKLOAD REPORT ==> 6

AREA WORKLOAD INQUIRY ==> 3 AREA CID REPORT ==> 7

EXPERIMENT STATUS INQUIRY ==> 4

ENTER SELECTION ==>

GOLD Q QUIT GOLD M MAIN MENU

2.8

The table below describes each of the selections on the Report/Inquiry Selection Menu.

FIELD DESCRIPTION

CASE INQUIRY Displays the status of an individual case.

Enter the CID, and you will get a list of the areas the case has been through (sorted by date and area).

EXPERIMENT INQUIRY Displays the area, count, and units for an experiment. Enter the experiment and test number and you will get the number of items from that experiment which have been processed in each area of the lab.

AREA WORKLOAD INQUIRY Displays the total number of items processed in that area, broken down by experiment and technician. To select the areas, place an X by all the areas you want on the inquiry.

Note: Use <Tab> (not the arrow keys) to move between fields.

EXPERIMENT STATUS INQUIRY Displays the number of cases each area has processed. Enter the experiment and test number and you will get the number of CIDs from that experiment which have been processed in each area of the lab.

AREA WORKLOAD REPORT Generates most of the daily and monthly reports. Enter a date range and an area and you will get a list showing the total number of items processed in that area, broken down by experiment and technician. To select the areas, place an X by all the areas you want on the report. Note: Use <Tab> (not the arrow keys) to move between fields.

EXPERIMENT WORKLOAD REPORT Enter a date range to get a summary of the workload reports for all areas. Totals are given by experiment.

AREA CID REPORT Counts CIDs per area. Enter an experiment, test, and area for a date range, and you will get a list of CIDs processed by that area. To select the areas, place an X by all the areas you want on the report. Note:

Use <Tab> (not the arrow keys) to move between fields.

2.9

Choose the number of the inquiry or report you desire and press <Enter>. A second screen will appear which allows you to enter more detailed information.

(Each second screen is indigenous to a specific report.) If you selected one of the reports, you will have to enter either a date range, experiment/test, or a CID and press <Enter>.

Inquiries will be displayed on the screen; reports will go to the online report menu. To view reports, choose REVIEW/PRINT REPORTS from the System Menu (see Section 2.4).

When inquiries are displayed on the screen, the cursor is positioned at the MORE prompt. Press <Enter> once when the cursor is at the MORE prompt. Don't press <Enter> again until the system message changes. If you do, your inquiry will flash on the screen and the cursor will be back at the MORE prompt.

Press <Enter> when you are finished viewing the report and the system will prompt you with a yes or no question (also specific to the report you choose).

Type N and press <Enter> and you will return to the Report/Inquiry Selection Menu. From there, make another selection or press <GOLD><M> to return to the Main Menu.

2.10

2.3.3 Purge Experiments

To delete all records associated with a completed experiment from the tracking file, choose option 3 PURGE EXPERIMENT DATA from the Main Menu and press <Enter>. When you do this, the Purge Experiment Screen appears (shown in Figure 2-6).

Figure 2-6. Purge Experiment Screen

Enter the experiment and test number at the prompt and press <Enter>. The system will ask if you really want to delete this data. Press Y and the data for that experiment will be deleted. NOTE: If you want a yearly report containing this data, you must wait until after the end of the year to purge the experiment.

PURGE EXPERIMENT DATA

PLEASE ENTER THE EXPERIMENT/TEST NUMBER YOU WISH TO PURGE

2.11

2.3.4 Modify/Delete Count Data

To change or delete count data, choose option 4 MODIFY/DELETE COUNT DATA from the Main Menu and press <Enter>. The Tracking File Correction Screen shown in Figure 2-7 will appear.

Figure 2-7. Tracking File Correction Screen

The table below describes each of the fields on the Tracking File Correction

FIELD DESCRIPTION

CARCASS ID Enter the CID for the record you want to modify or delete.

DATE Enter the date of the record you want to modify or delete.

AREA Enter the area code for the record you want to modify or delete.

PTM2U006

TRACKING FILE CORRECTION

09/05/90 08:37:30

CARCASS ID ==> ………..

DATE ==> ……

AREA ==> …..

GOLD M MAIN MENU GOLD Q QUIT ENTER CONTINUE

2.12

Enter the key data for the record you want to modify or delete and press <Enter>. Data for the selected record will be displayed.

To modify data, type in your corrections and press <GOLD><C> to save them. If you have done this correctly, the system will display the message THIS RECORD

HAS BEEN MODIFIED ON THE FILE - ENTER TO CONTINUE.

To delete data, press <GOLD><X>. The system will ask if you really want to delete this data. Press Y, and the system will give the message THIS DATA HAS BEEN DELETED FROM THE FILE - ENTER TO CONTINUE. When you press <Enter> after the system message, you will return to the Tracking File Correction Screen.

From there, you can modify more data or press <GOLD><M> to return to the Main Menu.

2.13

2.3.5 Area Table Maintenance

To add, delete, or change a Pathology Area, choose option 6 AREA TABLE MAINTENANCE from the Main Menu and press <Enter>. Figure 2-8 shows the screen which appears.

Figure 2-8. Area Table Maintenance Screen

The table below describes each of the fields on the Area Table Maintenance

FIELD DESCRIPTION

PATHOLOGY AREA CODE A number that uniquely identifies the area.

PATHOLOGY AREA SHORT TEXT The abbreviated text that identifies the area.

PATHOLOGY AREA LONG TEXT The complete text that identifies the area.

EFFECTIVE START DATE The date the current status was set for the area.

PATHOLOGY AREA UNITS The unit of measure for the area.

ACTIVE INACTIVE FLAG Tells the current status of the area. Enter A or

I only.

PTNTABLE T A B L E M A I N T E N A N C E S Y S T E M 09/05/90

P A T H O L O G Y A R E A T A B L E

Path Area Code =========> Path Area Shor Text ====> Path Area Long Text ====> Effective Start Date ===> Path Area Units ========> Active Inactive Flag ===>

Gold M Main Menu Gold N Add Gold R Retrieve Record Gold Q Quit

2.14

To add a new Pathology Area, type in the data for the area and press <GOLD><N>. To modify an existing area, first retrieve the record by entering the Pathology Area Code and pressing <GOLD><R>. Then change or delete the record by using the appropriate function key. Press <GOLD><M> to return to the Main Menu.

2.15

2.4 REVIEW/PRINT REPORTS

When you select option 3 REVIEW/PRINT REPORTS from the System Menu, a list of report filenames will be displayed. Each filename is made up of several groups of characters which give information about the report. Figure 2-9 shows an example of a list of filenames and identifies each part of the filename.

Figure 2-9. List of Report Filenames

The table below describes the flags in Figure 2-9.

FLAG DESCRIPTION

1 The report number

2 Indicates that the report is a Pathology Tracking

Report.

3 The report type, where 001 = Experiment Workload Report 002 = Area Workload Report 003 = Area CID Report

4 The date (in YYMMDD format) when the report was created.

5 The time (in HHMMSS format) when you logged onto the

Pathology Tracking System.

6 The version number of the report.

2 5 3 6

1- TPTH_001_900906_143636.LIS;1

2- TPTH_002_900906_091221.LIS;1

3- TPTH_003_900906_143636.LIS;1

2.16

Select the number that corresponds to the report you want to view. When you are finished viewing the report, press <Control><Z> or <F10> to exit. The system will ask if you want a hardcopy of the report.

When you press Y, the system will prompt you for a printer destination. You may enter a printer or press <Return>. If you press <Return>, the report will print on the computer-room printer and reports will be placed in your distribution bin.

Information Technology Staff

Gross Pathology System

ITS Doct #001-GRPH-3.0

ITS

ITS Doct #001-GRPH-3.0

This is an updated edition of the Gross Pathology System User Guide.

Companion Publications: None

Prepared by ZTech, an ICF International Corporation

National Center for Toxicological Research Jefferson, AR 72079

MC-910

INFORMATION TECHNOLOGY STAFF

NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH

S ection Page No.

1.0 INTRODUCTION ............................................................................................................................... 1.1

1.1 SYSTEM OVERVIEW ............................................................................................................... 1.1

1.2 BEFORE GETTING STARTED ................................................................................................. 1.1

1.2.1 Document Print Conventions ......................................................................................... 1.1

1.2.2 System Buttons and Icons ............................................................................................. 1.2

1.3 ACCESSING THE SYSTEM ..................................................................................................... 1.2

1.4 EXITING THE SYSTEM............................................................................................................. 1.3

2.0 PROTOCOL DEFINITION ................................................................................................................. 2.1

2.1 PROTOCOL TISSUE LIST ....................................................................................................... 2.2

2.1.1 Modify/Delete Required Organs and Tissues ................................................................ 2.3

2.1.2 Copying Organs and Tissues ........................................................................................ 2.5

2.1.3 Add a New Organ and Tissue Set ................................................................................. 2.7

2.2 TISSUE LIST DRIVER .............................................................................................................. 2.9

2.2.1 Copying Drivers............................................................................................................ 2.10

2.2.2 Adding Drivers ............................................................................................................. 2.12

2.2.3 Modifying Drivers.......................................................................................................... 2.13

2.2.4 Deleting Drivers............................................................................................................ 2.14

2.3 COPY ALL PROTOCOL INFORMATION ............................................................................... 2.14

2.4 GPS MENU ACCESS ............................................................................................................. 2.14

2.4.1 Add A User to the Gross Pathology Menu ................................................................... 2.16

2.4.2 Delete A User from the Gross Pathology Menu........................................................... 2.17

2.4.3 Modify User Authorization Status on the Gross Pathology Menu................................ 2.17

2.5 TGL NOTES TABLE ................................................................................................................ 2.18 i Uncontrolled when printed

3.0 DATA COLLECTION ......................................................................................................................... 3.1

3.1 NECROPSY LAB ...................................................................................................................... 3.2

3.1.1 Receiving ....................................................................................................................... 3.3

3.1.2 Necropsy ....................................................................................................................... 3.6

3.1.3 Organ Weights ............................................................................................................ 3.13

3.1.4 Check MG Correct ....................................................................................................... 3.16

4.0 DATA CORRECTION ....................................................................................................................... 4.1

4.1 RECEIVING .............................................................................................................................. 4.2

4.2 OBS AND TGLS ........................................................................................................................ 4.4

4.2.1 Modifying Pathology Condition Observations ............................................................... 4.7

4.2.2 Modifying Organ Observations ...................................................................................... 4.8

4.2.2.1 Modify an Observation..................................................................................... 4.8

4.2.2.2 Remove an Organ .......................................................................................... 4.9

4.2.2.3 Add an Organ ............................................................................................... 4.10

4.2.3 Modifying Inlife Clinical Observations ......................................................................... 4.10

4.2.4 Modifying TGL Observations ....................................................................................... 4.11

4.2.4.1 Modify an Existing TGL ................................................................................. 4.11

4.2.4.2 Add a New TGL ............................................................................................ 4.13

4.2.4.3 Remove a TGL ............................................................................................. 4.14

4.3 ORGAN WEIGHTS .................................................................................................................. 4.15

4.3.1 Add Organ ................................................................................................................... 4.17

4.3.2 Deleting Organ Weights ............................................................................................... 4.18

4.3.3 Modifying Organ Weights ............................................................................................ 4.18

4.4 REC/NEC COMMENTS .......................................................................................................... 4.19

4.4.1 Add Comment .............................................................................................................. 4.20

4.4.2 Modify Comment .......................................................................................................... 4.21

4.4.3 Delete Comment ......................................................................................................... 4.21

5.0 PATHOLOGIST MENU ..................................................................................................................... 5.1

5.1 NECROPSY REVIEW ............................................................................................................... 5.2

5.1.1 Reviewing and Approving CIDs ..................................................................................... 5.2

5.1.2 Modify CID...................................................................................................................... 5.3 ii

5.2 ANIMAL REVIEW ...................................................................................................................... 5.4

5.3 MODIFY CID ......................................................................................................................... 5.4

6.0 REPORTS ........................................................................................................................................ 6.1

6.1 INDIVIDUAL ANIMAL NECROPSY REPORT (IANR) ............................................................... 6.2

6.2 PROTOCOL DEFINITION ........................................................................................................ 6.3

6.3 IANR LISTING ........................................................................................................................... 6.4

7.0 CORRECT/DELETE CID ................................................................................................................... 7.1

7.1 CORRECT CID .......................................................................................................................... 7.2

7.2 DELETE CID .............................................................................................................................. 7.3

Appendix - Document Revision History iii

Gross Pathology System November 2011 User Guide #001-GRPH-3.0

1.0 INTRODUCTION

This manual was written as a guide for using the Gross Pathology System. Section 1.0 provides an overview of this manual and of the system as a whole. The remaining sections describe the various types of transactions and database records maintained through use of the system.

1.1 SYSTEM OVERVIEW

The Gross Pathology Data Collection System is used to automate the processes of Pathology Receiving and Necropsy Lab. These data records are stored on the Oracle Database and will be available for adhoc query and reporting through the numerous tools available for that purpose.

1.2 BEFORE GETTING STARTED

Before using the Gross Pathology System, you should be familiar with the print conventions used in this document; as well as the available screen icons and buttons.

1.2.1 Document Print Conventions

Different print styles are used in this document to help you distinguish between instructional text and field names and messages that appear on the screens. The following table summarizes the conventions used.

CONVENTION MEANING

ALL CAPS, BOLDFACED, UNDERLINED Refers to an entry that you must type.

For example:

Enter C; Enter 3

<Boldfaced in angle brackets> Identifies a function key or function key sequence that you must press. For example:

Press <Enter>; Press <Ctrl><F2>

Bold Faced Distinguishes a prompt, system message, or field name from the surrounding text. These may be in upper or lower case letters depending on how they appear on the screen. For example:

. . . in the Function field of the Enter Function: and/or Cage: prompt.

1.1

1.2.2 System Buttons and Icons

The following buttons and icons appear on various system screens within the system. The following table describes these tools and their uses.

BUTTON/ICON USE

List Icon The List icon is present on a number of screens in this system. Depending on what information the icon is associated with, such as an animal ID, clicking the List icon displays an appropriate list of options from which to choose. Narrow your search and reduce the number of choices for selection by typing the first few letters or numbers of your entry into the Find field

1.3 ACCESSING THE SYSTEM

To access the Gross Pathology System, do the following:

1. Select the GPS icon available in the Network Applications Folder (NAF) to display the Gross Pathology Data System Main Menu (Figure 1-1).

Figure 1-1. Gross Pathology System Main Menu

1.2

1.3 Uncontrolled when printed

2. Select the desired Gross Pathology function to open that function's data maintenance options (these functions are discussed in Sections 2.0 - 7.0).

1.4 EXITING THE SYSTEM

When you have completed data collection for the current session and wish to exit the Gross Pathology System, select the Exit option on the Gross Pathology System Main Menu (Figure 1-1).

2.0 PROTOCOL DEFINITION

All data collection experiments must have a defined protocol. The Protocol Definition function drives the organ and tissue lists that appear in different areas of the Gross Pathology System. This function allows you to modify and/or add organs or tissues to a protocol, copy organs and tissues from one experiment set or experiment to another, and create new organ and tissue sets.

To access the Protocol Definition functions, do the following:

1. Select the Protocol Definition option on the Gross Pathology System Main Menu (Figure 1-1) to display the Protocol Definition Menu Screen (Figure 2-1)

Figure 2-1. Protocol Definition Menu Screen

The following table describes the fields and buttons on this screen.

FIELD/BUTTON DESCRIPTION

Protocol Tissue List Displays the Protocol Tissue List Screen (Figure 2-2)

Tissue Driver List Displays the Protocol Set List Screen (Figure 2-7)

Copy All Protocol Info Displays the Copy Organs and Tissues – Create Drivers

Screen (Figure 2-8)

GPS Menu Access Displays the window for granting access to the

Pathologist Menu, Protocol Definition and Delete Animal

2.1

TGL Notes Table Displays the TGL Notes Table, which contains “canned” or preset notes that are used during necropsy. (Figure 2-13)

Exit Displays the Gross Pathology System Main Menu

Screen (Figure 1-1)

2. Select the desired Protocol Definition function by clicking the appropriate button on the Protocol Definition Menu Screen. The options on this screen are discussed in Sections 2.1 – 2.5).

2.1 PROTOCOL TISSUE LIST

The Protocol Tissue List function displays a listing of protocol-defined sets of tissues to be collected at necropsy.

To access the Protocol Tissue List function, do the following:

1. Click the Protocol Tissue List button on the Protocol Definition Menu Screen (Figure 2-1) to display the Protocol Tissue List Screen (Figure 2-2).

Figure 2-2. Protocol Tissue List Screen

2.2

Experiment Nbr Number designation for the experiment

Set Nbr Number designation for the set

Set Description Long text description of the set number

Process All Tgls Field designating whether or not all Trace gross lesions must be accounted for at trimming: Y=Yes, N=No

Select Displays the Protocol Required Organs and Tissues

Screen (Figure 2-3) and allows you to modify, delete or add required organs to a protocol

Copy Displays the Copy Organs and Tissues Screen (Figure

2-4) and allows you to copy organs and tissues to another experiment set or experiment

Add Displays the Protocol Required Organs and Tissues

Screen (Figure 2-3) and allows you to create a new organ and tissue set

Close Displays the Protocol Definition Menu Screen (Figure

2-1)

2. Select the desired Protocol Tissue List option from the buttons on the right side of the screen.

These functions are discussed in sections 2.1.1 – 2.1.3.

2.1.1 Modify/Delete Required Organs and Tissues

To modify or delete required organs and tissues assigned to a protocol, do the following:

1. Select an experiment and set number on the Protocol Tissue List Screen (Figure 2-2), then click the Select button to display the Protocol Required Organs and Tissues Screen (Figure 2-3).

2.3

Figure 2-3. Protocol Required Organs and Tissues Screen

Protocol Nbr Number designation for the protocol

Protocol Set Nbr. Number designation for the protocol set

Protocol Set Description Text description of the protocol set

Process All TGLS for this set Flag field designating whether or not all Trace Gross Lesions must be accounted for at trimming

Default Tissue Set for This Protocol If checked, this set will be used when animal data doesn't meet the criteria for other sets. There is only one default set for a protocol.

Required Organs & Sites Listing of organs and sites required by the protocol for this set of tissues.

Weigh Organ

Observe Flag field used to designate whether or not an organ is to be observed at necropsy

Fresh Flag field used to indicate that the organ was not fixed in solution

2.4

Fixed Flag field used to designate whether or not an organ should be weighed after being fixed in solution

Fixed Time Amount of time an organ is to remain fixed in solution

Trim Flag field used to designate whether or not an organ is to be trimmed

Cassette Nbr Number designation for the cassette into which the organ trimming will be placed

Frozen Section Flag field used to designate whether or not an organ will be frozen prior to trimming

Lab Lab that will process the tissues: Histo or Immuno

Special Instructions Free-text box for applicable comments/instructions

Remove Record Deletes the selected record from the list

Save Saves changes to the database

Close Displays a warning message if you click this button without saving the session information. Displays the Protocol Tissue List Screen (Figure 2-2)

2. Click once on the organ/tissue in the Required Organs and Sites column you wish to modify.

The entire row will be highlighted in blue.

3. Do one of the following:

a. Delete the record by clicking the Remove Record button. The record is immediately removed from the list. Go to Step 4.

b. Modify the organ/tissue by changing the existing information in the Weigh Organ, Fixation

Time, Cassette Nbr, Lab or Special Instructions columns as needed. Go to Step 4.

4. Click the Save button to save the modifications.

5. Repeat Steps 3 – 4 as needed, then click the Close button to display the Protocol Tissue List Screen (Figure 2-2).

2.1.2 Copying Organs and Tissues

To copy protocol organs and tissues from one experiment set to another set or to another experiment, do the following:

1. Highlight an experiment number on the Protocol Tissue List Screen (Figure 2-2), then click the Copy button to display the Copy Organs and Tissues Screen (Figure 2-4). The Protocol/Set Number to Copy fields will autofill with the information from the experiment number selected on the Protocol Tissue List Screen.

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Figure 2-4. Copy Organs and Tissues Screen

Protocol/Set Number to Copy Number designation for the protocol and set number that will be copied

Enter Protocol/Set Number to Create

Protocol Nbr Number designation for the protocol that will be created

Set Nbr Number designation for the set that will be created

Set Description Long text description of the set

Copy Data Creates a new required organs and tissues list by coping data from one protocol to another

Close Displays the Protocol Tissue List Screen (Figure 2-2)

2. Enter the new protocol number in the Protocol Nbr field.

3. Enter the new set number in the Set Nbr field.

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4. Enter the new long text set description in the Set Description field.

5. Click the Copy Data button. A system message displays and verifies that the required organs were copied to the new experiment/set.

6. Select Close to display the Protocol Tissue List Screen (Figure 2-2)

2.1.3 Add a New Organ and Tissue Set

To add a new organ and tissue set to a protocol, do the following:

1. Display the Protocol Tissue List Screen (Figure 2-2), then click the Add button to display the Protocol Required Organs and Tissues Screen (Figure 2-3).

2. Enter the number for the new protocol in the Protocol Nbr field.

3. Enter the number of the new protocol’s set number in the Protocol Set Nbr field.

4. Enter the long text description for the new protocol set in the Protocol Set Description field.

5. Check the Process All TGLs for this set and Default Tissue Set for This Protocol checkboxes if necessary.

6. Click the List Icon in the first blank line of the Required Organs & Sites column to display the PCT Organ List (Figure 2-5).

Figure 2-5. PCT Organ List

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7. Do one of the following to choose the organ/tissue you wish to add:

a. Scroll down the list and click once on the desired organ/tissue, then click the OK button. The PCT Organ List closes and the organ/tissue you chose is displayed in the first Required Organs & Sites column on the Protocol Required Organs and Tissues Screen.

b. Enter all or part of the name of the organ/tissue in the Enter Search field, then click the Find button. The PCT Organ List closes and the organ/tissue you chose is displayed in the first Required Organs & Sites column on the Protocol Required Organs and Tissues Screen.

8. Click the List Icon in the second Required Organs & Sites column. The Site List (Figure 2-6) displays a listing of sites pertinent to each organ/tissue.

Figure 2-6. Site List

9. Select a site by either double-clicking on the desired site name, or by clicking on the site name once, then clicking the OK button. The Site List closes and the site name is displayed in the second Required Organs & Sites column.

10. Click either Observe, Fresh or Fixed in the Weigh Organ column to reflect whether the organ/tissue is to be observed at necropsy, if it is to be weighed fresh or if it is to be weighed after being fixed in solution, respectively.

11. Enter a time in the Fixation Time field to reflect the time an organ/tissue is to remain fixed in solution.

12. Check the Trim checkbox if the organ/tissue is to be trimmed.

13. Enter a number in the Cassette Nbr field to designate which cassette the trimmed organ/tissue is to be placed after trimming.

14. Check the Frozen Section checkbox if the organ will be frozen prior to trimming.

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15. Choose either Histo or Immuno from the Lab dropdown list to indicate which lab will process the organ/tissue.

16. Type any pertinent instructions into the Special Instructions text box.

17. Click the Save button to save the new organ/tissue set information to the new protocol.

18. Click the Close button to display the Protocol Tissue List Screen (Figure 2-2).

2.2 TISSUE LIST DRIVER

The Tissue List Driver option displays the criteria that determines which tissue list is used to necropsy a given animal. This function allows you to copy drivers from one experiment to another, add a new tissue driver to the protocol set and modify or delete a tissue driver.

To access the Tissue List Driver function, select the Tissue List Driver option on the Protocol Definition Menu (Figure 2-1) to display the Protocol Required Organs & Tissues Screen (Figure 2-7).

Figure 2-7. Protocol Required Organs & Tissues Screen

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Copy Drivers Displays the Copy Organs and Tissues – Create Drivers

Screen (Figure 2-8)

Select Displays the Protocol Driver Screen (Figure 2-10)

Close Displays the Protocol Definition Menu Screen (Figure

2-1)

The instructions for copying protocol drivers from one experiment to another and adding, modifying and deleting protocol drivers are discussed in Sections 2.2.1 – 2.2.4, respectively.

2.2.1 Copying Drivers

To copy protocol drivers from one experiment to another, do the following:

1. Select the Copy Drivers option on the Protocol Set List Screen (Figure 2-7) option to display the Copy Organs and Tissues - Create Drivers Screen (Figure 2-8).

Figure 2-8. Copy Organs and Tissues – Create Drivers Screen

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The following table describes the fields and buttons on this screen.

FIELD/BUTTON DESCRIPTION

Protocol Number to Copy Number designation for the protocol that will be copied

Enter Protocol Number to Create Drivers

Protocol Nbr Number designation for the protocol to which the drivers will be copied

Copy Data Copies experiment drivers from one experiment to another

Close Displays the Protocol Set List Screen (Figure 2-7)

2. Enter a protocol number into the Protocol Number to Copy field, or do the following if the number is not known:

a. Click the List Icon to display the Experiments with Required Organs List (Figure 2-9).

Figure 2-9. Experiments with Required Organs List

b. Scroll if necessary to locate the desired experiment, then select it by either double-clicking the experiment number in the list, or by clicking the experiment number once, then clicking the OK button. You may also use the Find function by entering a whole or partial number in the Find field, then clicking the Find button.

Go to Step 3.

3. Enter a protocol number into the Enter Protocol Number to Create field, or do the following if the number is not known:

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a. Click the List Icon to display the Experiments with Required Organs List (Figure 2-9).

b. Scroll if necessary to locate the desired experiment, then select it by either double-clicking the experiment number in the list, or by clicking the experiment number once, then clicking the OK button. You may also use the Find function by entering a whole or partial number in the Find field, then clicking the Find button.

Go to Step 4.

4. Click the Copy Data button. A Forms dialog box displays a message stating that the data has been copied.

5. Click the OK button on the Forms dialog box. The Copy Organs and Tissues Screen displays.

6. Select Close to display the Protocol Set List Screen (Figure 2-7).

2.2.2 Adding Drivers

To add drivers to an experiment’s protocol set list, do the following:

1. Highlight the experiment in the Protocol Set List (Figure 2-7) to which you wish to add drivers, then click the Select button to display the Protocol Drivers Screen (Figure 2-10).

Figure 2-10. Protocol Drivers Screen

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Priority Number designation for the order in which organ and tissue lists will be used

Organ/Tissue List List of protocol required organs and tissues

Driver Text designation for when the specified list of protocol organs and tissues is to be used

Driver Value List of more specific circumstances for the use of the selected driver

Remove Record Removes the selected record from the system

Save Saves changes to the database

Close Displays the Protocol Set List Screen (Figure 2-7)

2. Enter a priority number in the first blank field in the Priority column for the driver you wish to add.

3. Click the down-arrow in the first blank field after the last list entry in the Organ/Tissue List column and select an organ/tissue list.

4. Click the down-arrow in the first blank field after the last list entry in the Driver column and select a driver.

5. Click the List Icon in the Driver Value column to select a driver value.

6. Select Save to save your changes to the database.

7. Select Close to display the Protocol Set List Screen (Figure 2-7).

2.2.3 Modifying Drivers

To modify the drivers on an experiment set list, do the following:

1. Highlight the experiment on the Protocol Set List Screen (Figure 2-7) for which you wish to modify the drivers, then click the Select button to display the Protocol Drivers Screen (Figure 2-10).

2. Make any necessary changes to the Priority, Organ/Tissue List, Driver and Driver Value fields.

3. Click the Save button to save the modifications.

4. Click the Close button to display the Protocol Set List Screen (Figure 2-7).

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2.2.4 Deleting Drivers

To delete a driver from an experiment list, do the following:

1. Highlight the experiment on the Protocol Set List Screen (Figure 2-7) for which you wish to modify the drivers, then click the Select button to display the Protocol Drivers Screen (Figure 2-10).

2. Click in any field in the row containing the driver you wish to delete, then click the Remove

Record button. The entry will be removed immediately from the list.

3. Repeat Step 2 as needed.

4. Click the Save button to save the deletion.

5. Click the Close button display the Protocol Set List Screen (Figure 2-7).

2.3 COPY ALL PROTOCOL INFORMATION

The Copy All Protocol Info function on the Protocol Definition Menu (Figure 2-1) allows you to copy both the protocol list and the protocol drivers from one experiment to another one.

To copy an existing protocol list and the included protocol drivers to another experiment, select the Copy All Protocol Info option to display the Copy Organs and Tissues – Create Driver Screen (Figure 2-8).

Follow the instructions in Steps 2 - 6 of Section 2.2.1.

2.4 GPS MENU ACCESS

The GPS Menu allows Gross Pathology System administrators to authorize personnel to perform restricted functions. System administrators may also modify a person’s authorized actions or remove personnel from the menu.

To access the GPS Menu Screen, do the following:

1. Select the GPS Menu Access function on the Protocol Definition Menu Screen (Figure 2-1) to display the GPS Menu Screen (Figure 2-11). This screen lists all authorized personnel and the functions they may perform. The checkboxes and buttons on this screen are described in the following table.

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Figure 2-11. GPS Menu Screen

CHECKBOX/BUTTON DESCRIPTION

Pathologist Authorizes selected personnel to review and approve necropsy data, as well as enter cause of death information.

Protocol Definition Authorizes selected personnel to determine which organ tissues and organ weights will be collected.

Delete Animal Authorizes selected personnel to delete all data pertaining to a selected animal in the Gross Pathology System.

Misidentified Animal Authorizes selected personnel to copy captured data from an incorrect CID to the correct CID.

2. Do one of the following:

a. To authorize a new user to perform restricted functions within the Gross Pathology System, go to Section 2.4.1.

b. To delete a user from the Gross Pathology Menu, go to Section 2.4.2.

c. To modify a user’s authorization status, go to Section 2.4.3.

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2.4.1. Add a User to the Gross Pathology Menu

Gross Pathology System administrators may authorize new users to perform the various functions within the system by adding the users to the Gross Pathology Menu.

To add a user to the Gross Pathology Menu, do the following:

1. Click inside the first blank line after the last list entry, then click the List Icon to display the Pathology Staff List (Figure 2-12).

Figure 2-12. Pathology Staff List

2. Choose the person you wish to assign the new functions to from this list by doing one of the following:

a. Double-click the name you wish to add to the list

b. Click the name you wish to add, then click the OK button

c. Enter all or part of the name in the Find field, then click the OK button

The Pathology Staff List will close and the Gross Pathology Menu will redisplay with the person’s name in the field next to the List Icon you clicked.

3. Select one or more of the following options to assign those options to the selected personnel:

Pathologist, Protocol Definition, Delete Animal or Misidentified Animal.

4. Click the Save button to save the changes to the database.

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5. Repeat Steps 1 - 4 as needed.

6. Click the Close button to display the Protocol Definition Menu Screen (Figure 2-1).

2.4.2 Delete a User from the Gross Pathology Menu

Gross Pathology System administrators may delete users from the Gross Pathology Menu (Figure 2-11) as needed.

To delete a user from the Gross Pathology Menu, do the following:

1. Follow the instructions in Section 2.4 to display the Gross Pathology Menu.

2. Click the name of the user you wish to delete from the menu. The name and row will be highlighted in blue.

3. Click the Remove Record button. The name and all information related to that user is removed from the list and from the system.

4. Click the Save button.

5. Repeat steps 2 – 4 as needed.

6. Click the Close button to display the Protocol Definition Menu Screen (Figure 2-1).

2.4.3 Modify User Authorization Status on the Gross Pathology Menu

Gross Pathology System administrators may modify a user’s authorization status on the Gross Pathology Menu (Figure 2-11).

To modify a user’s authorization status, do the following:

1. Follow the instructions in Section 2.4 to display the Gross Pathology Menu.

2. Check or uncheck the authorization levels as needed.

3. Click the Save button.

4. Repeat steps 2 – 3 as needed for additional users.

5. Click the Close button to display the Protocol Definition Menu Screen (Figure 2-1).

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2.18 Uncontrolled when printed

2.5 TGL NOTES TABLE

The TGL Notes Table function on the Protocol Definition Screen (Figure 2-1) is used to build a table of “canned” or preset notes that are used during necropsy. The Necropsy Screen in Figure 3-6 has a Select A Note button that, when clicked, displays a dialog box listing the notes contained in the TGL Notes Table.

To add notes to the TGL Notes Table, do the following:

1. Click the TGL Notes Table button on the Protocol Definition Menu Screen (Figure 2-1) to display the TGL Notes Table (Figure 2-13).

Figure 2-13. TGL Notes Table

2. Type a new note into the first blank field on the list.

3. Click the Save button.

4. Click the Close button. The Protocol Definition Screen displays (Figure 2-1).

3.0 DATA COLLECTION

Data Collection functions collect and capture data for necropsy based on experiment workflow setups determined by selections made within the Protocol Definition element of the Gross Pathology System.

To access the Data Collection functions, do the following:

1. Select the Data Collection option on the Gross Pathology System Main Menu (Figure 1-1) to display the Data Collection Screen (Figure 3-1).

Figure 3-1. Data Collection Screen

FIELD/BUTTON…