-----------------------------------------------------------------------
  Pathology protocol analysis system procedures

  -----------------------------------------------------------------------

National Toxicology Program Support

Pathology PAS Procedures

National Toxicology Program Support

Pathology PAS Procedures

Prepared for: National Institute of Environmental Health Sciences

> Research Triangle Park, NC 27709

Contract no.: 273-95-I-0012

Prepared by: Technology Planning & Management Corporation

Imperial Center

Canterbury Hall, Suite 310

4815 Emperor Boulevard

Durham, NC 27703

Revision Summary

  ------------- -------------- -------------- -----------------------------
  **Date        **Document     **Revision     **Reason for Revision**
  Released**    Number**       Level**        

  4/99          LP-1012        3.1            Place manual in new template.
                                              Update for Hazel and TPMC
                                              references.

  10/95         LP-1012        2.1            Added hamsters to protocol
                                              required tissues and updated
                                              print destination field.

  12/94         LP-1012        2.0            Menu updates and procedure
                                              changes.

  2/94          LP-1012        1.0            New
  ------------- -------------- -------------- -----------------------------

Table of Contents

Revision Summary

Table of Contents

Chapter 1

Introduction

Overview

Chapter 2

Pathology PEX Procedures

Copy Universal Download

Figure 1, TDMS Main Menu

Figure 2, PAS Main Menu

Figure 3, PEX PEIS Operation Selection Menu

Figure 4, PEX PEIS Copy Selection List

Enter Protocol Required Tissues

Add Segments

Figure 5, PEX PEIS Segment Selection Menu

Figure 6, Segment OPERATION Selection Menu

Figure 7, Protocol Required Tissue Definition

Figure 8, Protocol Required Tissue Definition ADD

Modify Protocol Required Tissues

Chapter 3

PAS Validation Report Procedures

Generate the PAS Validation Report

Figure 9, PAS Validation Report Request- PEIS

Verify the PAS Validation Report

Chapter 4

Pathology Download Procedures

Create Pathology Download Files

Figure 10, Select Transaction Type

Perform a Partial Download of Modified Transactions

Figure 11, Select PEIS Transactions to Download

Appendix a a

PEX Checklist a

Appendix b b

Protocol Required Tissues b

Introduction

The purpose of this document is to provide Toxicology Data Management
System (TDMS) liaison personnel with instructions for using PEX, the
interactive maintenance system, to conduct the pathology phase of the
TDMS studies.

# Overview

PAS consists of two distinct subsystems. The Experiment Information
System (EIS) is used to define the protocols for in-life data
collection. The Post-Experiment Information System (PEIS) is used to
define the protocols for pathology data collection. This document covers
the pathology procedures.

First, the liaison copies a Universal Download for the appropriate
species into the database and modifies this download for the specific
experiment. Protocol required tissues are included in the file if it is
for a chronic study.

The liaison then generates and prints the pathology Validation Report to
verify that all tables are complete.

Finally, the liaison downloads the test protocol files to the on-site
laboratory Communications Workstation. The downloaded files control the
screen displays that are used to record data on the Pathology
Workstation. The chart below gives an overview of the Pathology PAS
Procedures.

![](media/image1.emf)

Pathology PEX Procedures

This chapter outlines how to complete Pathology protocol.

PEX is the interactive maintenance system for PAS. Liaisons use PEX to
indicate and define new Toxicology Data Management System (TDMS) studies
and to modify existing study definitions.

# Copy Universal Download

Follow these steps to copy the appropriate Universal Download to the
database:

1.  At the prompt, type \@TDMS. The TDMS Main Menu is displayed:

2.  ![](media/image2.emf){width="5.495138888888889in"
    height="3.0881944444444445in"}

Figure 1, TDMS Main Menu

3.  At the Please enter the NUMBER of your choice prompt, press 1 for
    Protocol Analysis System. Press ENTER on the numeric keypad to
    advance. The PAS Main Menu is displayed:

4.  ![](media/image3.emf){width="5.498611111111111in"
    height="3.1680555555555556in"}

Figure 2, PAS Main Menu

5.  At the Enter Selection Code prompt, type PP (PEX-PEIS). Press
    \<ENTER\>. THE PEX-PEIS Operation Selection Menu is displayed:

6.  ![](media/image4.emf){width="5.4944444444444445in"
    height="3.532638888888889in"}

Figure 3, PEX PEIS Operation Selection Menu

7.  At the Please enter the NUMBER of your choice prompt, type 2 (Copy
    PEIS Segments from Existing Experiments).

8.  Type the nine-digit study number. Press \<ENTER\>. The PEX PEIS Copy
    Selection List is displayed:

9.  ![](media/image5.emf){width="5.49375in"
    height="3.1305555555555555in"}

Figure 4, PEX PEIS Copy Selection List

10. Enter the nine-digit experiment number of the Universal Download for
    each segment you wish to copy.

11. The experiment numbers for the Universal Download are:

-   050505005 - Inhalation Rats

-   050505006 - Inhalation Mice, Hamsters

-   050505007 - Other Rats

-   050505008 - Other Mice, Hamsters

12. There are four segments that will be entered for all studies:

13. Organ Identification

14. Organ Morphology

15. Sites

16. Micropath Tables

> Segment 5, *Protocol Required Tissue*, can also be copied for chronic
> studies. Segments 4, *Micropath Procedure Text*, and 7, *Site
> Accountability*, became obsolete with the advent of a new data
> collection system.
>
> Enter the Universal Study number in the Copy From Study Number field.
> If no copy is to be made to a particular segment, leave the field
> blank.

17. Verify that the study numbers you entered are accurate.

18. Press \<ENTER\>. The following message is displayed at the bottom of
    the PEX PEIS Copy Selection List screen:

19. Are you sure you want to copy ALL replicates for selected segments?
    (Y/N)

20. Type Y and press \<ENTER\>. The following message is displayed on
    the next screen:

21. Copying of selected segments has been completed. Hit 'ENTER'.

NOTE

> The number of replicates copied to the target study for each segment
> are also displayed on this screen.

The correct numbers for replicates for Organ Morphology and Sites are

+------------------+---------------------------+----------------------+
| -   050505005 -  | Inhalation Rats           | 67 REPS COPIED       |
+------------------+---------------------------+----------------------+
| -   050505006 -  | Inhalation Mice, Hamsters | 68 REPS COPIED       |
+------------------+---------------------------+----------------------+
| -   050505007 -  | Other Rats                | 65 REPS COPIED       |
+------------------+---------------------------+----------------------+
| -   050505008 -  | Other Mice, Hamsters      | 66 REPS COPIED       |
+------------------+---------------------------+----------------------+

Press \<ENTER\>. The PEX PEIS Operation Selection Menu is displayed.

22. At the Please enter the NUMBER of your choice: prompt, type 6
    (Terminate TDMS).

# Enter Protocol Required Tissues

If the experiment is a chronic study, the liaison adds the Protocol
Required Tissues in the database and they are downloaded to the
laboratory.

NOTE

> When the liaison enters the in-life PEX data, the flag is set for 'L'
> if the Protocol Required Tissues are to added by the laboratory
> pathologist and 'M' if the Protocol Required Tissues are to be entered
> by the liaison.

Follow these steps to enter Protocol Required Tissues for the download
file of a chronic study:

23. Repeat Steps 1 through 5 of *Copy Universal Download*, in the
    beginning of this chapter.

24. At the PEX PEIS Copy Selection List screen (see Figure 4, page 4),
    enter the nine-digit study number of the experiment you wish to copy
    in field 5 (Protocol Required Tissue).

25. Select a study for this field that has the same dose route and the
    same number of Treatment Groups as the current study.

26. When the pathology Validation Report is generated, the correct Text
    ID for the current study will be written in the Treatment Group
    field.

# Add Segments

Follow these steps to add segments for more treatment groups.

27. Repeat Steps 1 through 3 of *Copy Universal Download*, in the
    beginning of this chapter.

28. At the Please enter the NUMBER of your choice: prompt on the PEX
    PEIS Operation Selection Menu (see Figure 3, page 3), type 1 (Modify
    Experiment). Type the nine-digit study number at the Please enter
    the nine-digit study number: prompt. Press \<ENTER\>. The PEX PEIS
    Segment Selection Menu is displayed:

29. ![](media/image6.emf){width="5.496527777777778in"
    height="2.939583333333333in"}

Figure 5, PEX PEIS Segment Selection Menu

30. Type 5 (Protocol Required Tissues). Press \<ENTER\>. The Segment
    OPERATION Selection Menu is displayed:

31. ![](media/image7.emf){width="5.495138888888889in"
    height="3.051388888888889in"}

Figure 6, Segment OPERATION Selection Menu

32. At the Segment OPERATION Selection Menu, type 1 (ADD Segment). Press
    \<ENTER\>. The first substructure of the Add Segment is displayed:

33. ![](media/image8.emf){width="5.49375in" height="2.80625in"}

Figure 7, Protocol Required Tissue Definition

34. Enter the Treatment Group Number. The Date Range and Removal Reasons
    can be modified on this screen. The Default Date Ranges on LDAS II
    are 01/01/70 to 09/17/29/ Press G-6. The next substructure is
    displayed:

35. ![](media/image9.emf){width="5.49375in"
    height="2.8493055555555555in"}

Figure 8, Protocol Required Tissue Definition ADD

36. The number of Protocol Required Tissues on this screen will vary.
    Delete the excess tissue codes and add the missing male or female
    protocol required tissues. Refer to *Appendix B, Protocol Required
    Tissues* to modify this screen.

NOTE

> The Date Range cannot be modified on this screen. The Removal Reasons
> can be modified.

37. Press G-3 to save the segment. The first Protocol Required
    Definition screen is displayed. See Figure 7 on the previous page.

38. Repeat Steps 3 through 5 to add all treatment groups.

39. Press G-2 to save the segment. The Segment OPERATION Selection Menu
    is displayed. See Figure 6 on the previous page.

40. Type 6 (Terminate TDMS).

# Modify Protocol Required Tissues

After the segments are copied to the study, they may have to be modified
or more segments may need to be added. Follow these steps to modify the
Protocol Required Tissues segment:

41. Repeat Steps 1 through 3 of *Copy Universal Download*, in the
    beginning of this chapter.

42. At the Please enter the NUMBER of your choice: prompt on the PEX
    PEIS Segment Operation Selection Menu (see Figure 6, page 8), type 1
    (Modify Experiment). Type the nine-digit study number at the Please
    enter the nine-digit study number: prompt. Press \<ENTER\>. The PEX
    PEIS Segment Selection Menu is displayed. See Figure 5, on page 7.

43. Type 5 (Protocol Required Tissues). Press \<ENTER\>. The Segment
    OPERATION Selection Menu is displayed. See Figure , on page .

44. If you wish to modify Protocol Required Tissue segments, type 2
    (MODIFY SEGMENT). Press \<ENTER\>. Modifications are made on the
    Protocol Required Tissue Definition screen. See Figure 7, on page 8
    of the *Add Segments* section of this chapter.

PAS Validation Report Procedures

This chapter describes the procedures user to generate and review the
Pathology PAS Validation Report.

Liaisons generate and print a Pathology PAS Validation Report to verify
that all of the tables are correct. Print the Error Report on Starprint
Directory. If errors are found, the liaison corrects them (using PEX)
and then reruns the Validation Report.

# Generate the PAS Validation Report

Follow these steps to generate the PAS Validation Report:

45. At the prompt, type \@TDMS. Press \<ENTER\>. The TDMS Main Menu is
    displayed. See Figure 1, on page 2.

46. At the Please enter the NUMBER of your choice prompt, type 1
    (Protocol Analysis System). Press \<ENTER\>. The PAS Main Menu is
    displayed. See Figure 2, on page 3.

47. At the Enter Selection Code prompt, type PV for PEIS Validation
    Report Request. Press \<ENTER\>. The PAS Validation Report
    Request-PEIS screen is displayed:

48. 

![](media/image10.emf){width="5.496527777777778in"
height="3.147222222222222in"}

Figure 9, PAS Validation Report Request- PEIS

Follow these steps to generate validation reports:

49. At the Please enter the NUMBER of your choice: prompt, type 6 (Total
    Validation Set (All Reports)) or an alternate report.

50. In the Agency/Experiment/Test field, type the study number.

51. To print the report, type a Y in the Print (Y/N)? field.

If you wish to store the validation report, type NOPRINT in the
Destination field. It will be stored on the STARPRINT directory.

52. In the Store (Y/N)? field, type N. This field refers to ESS storage.

53. Press \<ENTER\>. The following message is displayed:

54. Submit successful. Hit ENTER to continue.

55. Press \<ENTER\>.

56. Press G-2. The PAS Main Menu is displayed. See Figure 2 on page 3.

57. Press G-5 to exit TDMS.

58. At the prompt, type the following character string:

show queue starbatchq

This will indicate whether the file is waiting in the queue or
executing. When the job completes, a message is displayed indicating the
validation report has been generated. A sample message follows:

Job SPAPEITOTAL1_050999902 (queue STARBATCHBQ, entry 24) completed

59. IF you entered NOPRINT in the Destination filed, follow these steps
    to print the report:

60. At the prompt, type the following character string:

DIR/SIN STARPRINT: SPAEISTOTAL1\*)

Press \<ENTER\>.

61. Print the report using landscaped format.

# Verify the PAS Validation Report

Follow these steps to verify the Pathology Validation Report:

62. Even if no errors were found during the generation of the report,
    the Error Report displays one of the following messages:

  ---------- --------------- ---------- ------------------------ ---- --------------
  \*\*\*\*   WARNING ERROR   \*\*\*\*   ORGAN SEGMENT CONTAINS   65   ORGANS

  \*\*\*\*   WARNING ERROR   \*\*\*\*   ORGAN SEGMENT CONTAINS   66   ORGANS

  \*\*\*\*   WARNING ERROR   \*\*\*\*   ORGAN SEGMENT CONTAINS   67   ORGANS

  \*\*\*\*   WARNING ERROR   \*\*\*\*   ORGAN SEGMENT CONTAINS   68   ORGANS
  ---------- --------------- ---------- ------------------------ ---- --------------

The number of organs listed in the warning message depends on which
Universal Download was copied to the experiment. It refers to the number
of organs in the Organ Morphology and Sites tables. Disregard this error
message.

63. Verify that all reports you requested are included in the total
    Validation Report. Also verify that they are all complete.

64. 

Pathology Download Procedures

This chapter addresses the pathology download system.

Liaisons use the PAS Download system to transfer TDMS protocol data from
the mainframe at NIEHS to microcomputers at designated laboratories.

# Create Pathology Download Files

To create the pathology download files, follow these steps:

65. At the prompt, type \@TMDS and press \<ENTER\>. The TDMS Main Menu
    is displayed. See Figure 1, page 2.

66. At the Please enter the NUMBER of your choice prompt, press 1
    Protocol Analysis System. The PAS Main Menu is displayed. See Figure
    2, page 3.

67. Select Create Download File by typing CD at the Enter Selection Code
    prompt. Press \<ENTER\>. The Select Transaction Type screen is
    displayed:

68. ![](media/image11.emf){width="5.498611111111111in"
    height="3.1034722222222224in"}

Figure 10, Select Transaction Type

69. Complete the fields of the Select Transaction Type screen by
    following these steps.

70. In the Experiment/Test field, type the number of the study you wish
    to download. The cursor will move to the next field.

71. Type in the three-letter lab facility code in the Destination Site
    field. The cursor will move to the next field.

72. Use the down arrow to move to the Download All PEIS Transactions
    field. Type an X in the space provided. Press \<ENTER\>. The
    following message is displayed.

73. Download job submitted for all PEIS transaction types. Press ENTER
    to continue.

74. Press \<ENTER\>. The PAS Main Menu is displayed. See Figure 2, page
    3.

75. Press G-5 to exit TDMS.

76. At the prompt, type the following character string:

show queue starbatchbq

The download job will be pending in this queue.

Job SPDDOWNLOAD_050999902 (queue STARBATCHBQ, entry 130) completed

77. Verification of a successful download is sent via e-mail.

78. If the download was successful, type DIR YYYDOWNLOAD to verify that
    the file is on the lab download directory. (YYY-three-letter lab
    facility code).

For example, PXXXXXXX.DNL;1

79. To delete a download file that contains errors from the Lab Download
    directory, do the following:

80. At the prompt, type in the file to be deleted using the following
    format:

DEL YYYDOWNLOAD:PXXXXXXX.DNL;1

81. Complete Steps 1 through 4 to create a new download.

# Perform a Partial Download of Modified Transactions

To perform a partial download of pathology files, follow these steps:

82. Repeat Steps 1 through 3 of *Create Pathology Download Files*.

83. At the Select Transaction Type screen, use the down arrow to move to
    the Select PEIS Transactions field. Type an X in the space provided.

84. Press \<ENTER\>. The Select PEIS Transactions To Download screen is
    displayed.

85. ![](media/image12.emf){width="5.134722222222222in"
    height="2.5506944444444444in"}

Figure 11, Select PEIS Transactions to Download

86. Use the tab or arrow keys to move to the transaction file to be
    downloaded. Type an X in the space provided.

NOTE

> Refer to Chapter 3 in the *LDAS Technical Reference Manual* to
> determine which Test Protocol Tables to download.

87. Press \<ENTER\>. The following message is displayed at the top of
    the screen:

88. Download job submitted for selected PEIS transaction types.

89. Press \<ENTER\>. The PAS Main Menu is displayed.

90. Press G-5 to exit TDMS.

91. Repeat Steps 8 and 9 of *Create Pathology Download Files* to verify
    that the partial download was successful and to perform a new
    download if necessary.

PEX Checklist

The PEX Checklist, which is displayed on the following page, is used to
track the completion of liaison procedures relative to the study.

Update the pathology section of the original PEX Checklist that was
filed with the experiment at the beginning of the study.

**PEX Checklist**

Chemical Name:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Study Number:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Facility:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Species:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Route:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Study Type:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Start Date:
\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

**PAS DATA ENTRY**

  ------------- -- ------ -------------------------------------------------
  Date                    Segment

                          

                   1\.    Weighed Items Range Validation

                   2\.    Loading Requirements and Weight Validation

                   3\.    Selected Clinical Observations

                   4\.    Animal Removal Actions

                   5\.    Balance Calibration Weights

                   6\.    Rack-Cage Configuration

                   7\.    Census Definition

                   8\.    Preparation Definition

                   9\.    Procedure Definition

                   10\.   Treatment Definition

                   11\.   Facility/Chemical Linkage Information

                   12\.   Responsible Parties
  ------------- -- ------ -------------------------------------------------

**VALIDATION REPORT**

  ------------- -- ------------------------------------------------------
                   Validation Report Printed

                   Validation Report Sent to Laboratory

                   Schedules sent to Laboratory

                   Certification Report received from Laboratory
  ------------- -- ------------------------------------------------------

**IN-LIFE DOWNLOAD**

  ------------- -- ------------------------------------------------------
                   EIS Download to Laboratory

  ------------- -- ------------------------------------------------------

**PATHOLOGY PEX**

  ------------- -- ------------------------------------------------------
                   Pathology Tables copied to the study

                   Pathology Required Tissues copied to chronic study

                   Pathology Validation Report Printed
  ------------- -- ------------------------------------------------------

**PATHOLOGY DOWNLOAD**

  ------------- -- ------------------------------------------------------
                   Pathology Download to Laboratory

  ------------- -- ------------------------------------------------------

Protocol Required Tissues

Use the tables contained in this appendix to manually enter protocol
required tissues or to verify tissue copied from another experiment.

  ----------------- ------------- -------------------- --------------------
  **Tissues**                     **Notes**            **Totals**

  Adren Cortex      25463                              

  Adren Medulla     25464                              

  Brain             25018                              

  Clitoral Glands   25030                              

  Esophagus         25052                              

  Bone              25013                              

  Bone Marrow       25012                              

  Gallbladder       25058         Mice, Hamsters       

  Heart             25068                              

  Int Sm Duoden     25457                              

  Int Sm Jejunum    25458                              

  Int Sm Ileum      25459                              

  Int Lg Colon      25460                              

  Int Lg Rectum     25461                              

  Int Lg Cecum      25462                              

  Kidneys           25083                              

  Larynx            25415         Inhalation studies   
                                  only                 

  Liver             25094                              

  Lungs             25097                              

  Lym Node Mesen    25452         All Studies          
  ----------------- ------------- -------------------- --------------------

+-----------------+------------+-------------------+-------------------+
| Lym Node Mand   | 25453      | All Studies       |                   |
+-----------------+------------+-------------------+-------------------+
| Lym Node Bron   | 25454      | Inhalation        |                   |
|                 |            | Studies only      |                   |
+-----------------+------------+-------------------+-------------------+
| Lym Node Media  | 25467      | Inhalation        |                   |
|                 |            | Studies only      |                   |
+-----------------+------------+-------------------+-------------------+
| Mammary Gland   | 25100      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Nose            | 25233      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Ovaries         | 25114      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Pancreas        | 25115      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Parathyroid     | 25116      |                   |                   |
| Glands          |            |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Pituitary Gland | 25121      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Preputitial     | 25125      |                   |                   |
| Glands          |            |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Prostate        | 25126      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Salivary Glands | 25148      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Skin            | 25153      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Spleen          | 25156      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Stomach Forst   | 25465      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Stomach Gland   | 25466      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Testes          | 25169      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Epididymus      | 25051      |                   | 44 - Inhalation,  |
|                 |            |                   | Rats              |
+-----------------+------------+-------------------+-------------------+
| Seminal Vesicle | 25149      |                   | 45 - Inhalation,  |
|                 |            |                   | Mice,             |
|                 |            |                   |                   |
|                 |            |                   | Hamsters          |
+-----------------+------------+-------------------+-------------------+
| Thymus          | 25172      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Thyroid Gland   | 25173      |                   | 41 - Other, Rats  |
+-----------------+------------+-------------------+-------------------+
| Trachea         | 25176      |                   | 42 - Other, Mice, |
|                 |            |                   | Hamsters          |
+-----------------+------------+-------------------+-------------------+
| Urinary Bladder | 25189      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Uterus          | 25148      |                   |                   |
+-----------------+------------+-------------------+-------------------+
| Islets,         | 25153      |                   |                   |
| pancreas        |            |                   |                   |
+-----------------+------------+-------------------+-------------------+

**End of Document**