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  pathology code table reference

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Toxicology Data Management System

  ----------------------------------- -----------------------------------
  **Document Number:**                TS-1006-6.1

  **Version:**                        6.1

  **Issued:**                         January 29, 1999

  **Reviewed & Approved by:**         John Minnich, Program Director

  **Signature:**                      

  **Date:**                           

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

PEIS Pathology Code Table Reference Manual

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National Toxicology Program Support

Post Experiment Information System Pathology Code Table Reference Manual

> 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

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Revision History

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

  January 1999      TS-1006-6.1       6.1               Release latest
                                                        data. Minor
                                                        document template
                                                        revisions.

  July 1998         TS-1006-6.0       6.0               Release latest
                                                        data. Changed
                                                        document
                                                        appearance and
                                                        made revisions

  September 1995    TS-1006-5.1       5.1               Release latest
                                                        data

  November 1994     TS-1006-5.0       5.0               Delete Gross
                                                        References
  ----------------- ----------------- ----------------- -----------------

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Table of Contents

Revision History i

Section 1 1a

Introduction 1a

Topographies 1b

Morphologies 1b

Qualifiers 1b

Table/Reference List Description 1b

Using This Manual 1c

Section 2 2a

Micropathology 2a

Micro Systems and Organs Table 2a

(pages 1-3)

Micro Qualifier Table 2b

(pages 1-4)

Micro Topography Hierarchy Level Table 2c

(pages 1-73)

Microscopic Terms by Organ Table 2d

(pages 1-178)

Section 3 3a

Reference Lists 3a

Morphologies Sorted Alphabetically by Short Text 3a

(7 pages)

Morphologies Sorted Numerically by TDMS Code 3b

(7 pages)

Topographies Sorted Alphabetically by Short Text 3c

(8 pages)

Topographies Sorted Numerically by TDMS Code 3d

(8 pages)

Appendix 1

User Documentation Request Form 1

Glossary 2

**All Pathology Code tables are available on the NTP Web server at:**

**http://ntp-server.niehs.nih.gov/main_pages/ntp_path_tbl_pg.html**

Introduction

This document contains the standard nomenclature used by the Post
Experiment Information System (PEIS). The tables and lists contained
herein are built from data maintained in the Pathology Code Table (PCT).

The Pathology Code Table was designed for use by the National Toxicology
Program (NTP) and its affiliates as a tool for cross-chemical analysis.

The NTP's goals are to better define the origination and development of
toxic disease and, when possible, to correlate specific host responses
to toxic injury with tumorigenecity in that same target organ over time.
In order to accomplish these goals, it is necessary that the pathologist
describe the essential components of a specific target organ response.
The PCT contains the terms necessary for this description.

A PCT entry consists of a unique code for the Toxicology Data Management
System (TDMS), a unique short text description and a unique long text
description. Unlike other standard nomenclatures, the TDMS code has no
significance other than providing a means for uniquely identifying each
entry. The TDMS code is used in data base transactions and data base
records. The short text of terms is used for the PEIS automated data
collection system and the PEIS manual data collection forms. The long
text of terms is used for the PEIS reports. Other information contained
in each entry's record allows for the elimination of certain logical
errors at the time of data entry. In addition, the information contained
in a PCT entry provides more flexible data retrieval and reporting
capabilities. It is the basis of the table in this document.

The terms contained in this table for microscopic observations consists
of the following:

-   Topographies

-   Morphologies

-   Qualifiers

#   {#section .unnumbered}

# Topographies

The topography terms are comprised of a hierarchy of the three term
types: systems, organs, and sites. The topographies in this document are
indicated as appropriate for microscopic observations. The PCT record
for each system contains specific organs that are considered part of
that system. An organ may not be found in more than one system. The PCT
record for each organ identifies the appropriate sites for that organ.
If the organ can be found in a certain sex or species, it is indicated
in the record also. These relationships are reflected in the tables
containing topography terms.

# Morphologies

The morphology terms may be used during the microscopic evaluation of
tissues. A morphology may be sex dependent, species dependent or organ
dependent. Morphologies are indicated in this document as
neoplastic/non-neoplastic, malignant/benign/uncertain and
metastatic/-non-metastatic/uncertain. A morphology is indicated as
appropriate for microscopic observations. The PCT morphology record
includes the qualifier group identification numbers that are appropriate
for that term. This information is reflected in the table containing
morphology terms. Each morphology record also may contain generic
morphology type (i.e., the generic type for abscess would be
inflammation).

# Qualifiers

The qualifier's terms may be used in conjunction with morphology,
allowing further description of the abnormality present in the organ.
The qualifiers are grouped into categories associated with the
appropriate morphologies. This relationship is used by the PEIS and is
reflected in the tables containing qualifiers. At the time of data
collection, only the applicable qualifier groups are available. The
pathologist may then select the appropriate terms for further
description.

# Table/Reference List Description

The table illustrates hierarchical increments of information. For
example, the initial table in **Section 2,** ***Micropathology***
includes systems and organs. The second table extends the hierarchy by
adding site terms to the appropriate organs. The third table outlines
the qualifier groups and their related qualifiers. Finally, the fourth
table compiles the previous table information, adding morphologies and
illustrating their relationship between the various terms. This table
may also be used as a functional tool for the PEIS protocol definition
process.

The Reference Lists are organized both alphabetically and numerically
for convenience. Alphabetic or numeric listings can be identified by the
table title. The listings (TDMS code, short text, long text) are
organized similarly in all four *Reference Lists*.

All table headings within this document are formatted to reflect the
following information: table, module, table date, table time, and page.
The table field reflects the short text of the table name. The module
field is an internal identification of the table program. The table date
and time fields reflect the date and time the table was generated. The
page field indicates the number of the page within the table.

# Using This Manual

The micropathology data collection system relies on the PCT for the
current list of available text and code. The tables and listings in this
document organize this information to assist the pathologist in entry
procedures.

The Pathology Code Table Reference Manual includes section and
subsection tabs that reflect the Table of Contents organization and
provide easy access to specific tables and listings. For example, the
pathologist would reference Tab 2.0 (Micro Systems and Organs Table),
located in **Section 2, *Micropathology***, to determine all associated
organs for a particular system. To locate the sites available for a
specific organ, the pathologist could select Tab 2.0 (Micro Topography
Hierarchy Level Table) or Tab 2.2 (Microscopic Terms by Organ Table),
also located in the **Section 2, *Micropathology****.*

When Referencing the availability of certain topographies or
morphologies, the pathologist could locate the term by referencing Tab
3.0 (Morphologies Sorted Alphabetically by Short Text), located in
**Section 3.0, *Reference Lists***. The topographies and morphologies
are also listed numerically by TDMS code in this section.

Through consistent use of this manual, pathologists should develop
reference methods suitable to their individual needs.

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Micropathology

This section reflects terms available to the pathologist during the
microscopic evaluation of tissues.

The Micropathology section includes the following tables:

-   Micro Systems and Organs Table

-   Micro Topography Hierarchy Level Table

-   Micro Qualifier Table

-   Microscopic Terms by Organ Table

These tables contain only those terms currently active in the Pathology
Code Table.

# Micro Systems and Organs Table

This table lists micropathology systems and their related organs. The
ENTRY DESCRIPTION FIELD identifies terms as either a system or an organ
within the specified system. The TDMS code, short text description and
long text description also are listed for each system.

The table organization is alphabetical by short text, using the
following conventions:

-   Alphabetized systems

-   Alphabetized organs within each system

The table fields are:

-   ENTRY DESCRIPTION (SUYSTEM, ORGAN)

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Micro Systems and Organs Table:
http://hazel.niehs.nih.gov/starprint/rowley/pctsor.txt

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# Micro Qualifier Table

This table lists micropathology qualifier groups, each group consisting
of a set of related qualifiers.

This table may be helpful in referencing the qualifier group
identification numbers that are listed in the Microscopic Terms by Organ
Table.

Each qualifier is identified by qualifier group identification number,
TDMS code, short text description and long text description. The
qualifier group identification number is unique to a particular group of
qualifiers and allows the group to be linked with the appropriate
morphologies. The qualifiers may be used to further define the
morphologies to which they are linked.

The table organization is both numerical and alphabetical, using the
following conventions:

-   Qualifier groups are listed numerically by qualifier group
    identification number

-   Qualifiers within each group are listed alphabetically by short text
    description

The table fields are:

-   GROUP ID

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Micro Qualifier Table:
http://hazel.niehs.nih.gov/starprint/rowley/pctqual.txt

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#   {#section-1 .unnumbered}

# Micro Topography Hierarchy Level Table

This table illustrates the hierarchical relationship between the three
types of topographies for micropathology: systems, organs, and sites.

The pathologist will find this table useful in locating available organs
for each system and available sites for each organ.

The system is identified by TDMS code, short text description and long
text description in the table heading. The ENTRY DESCRIPTION field
designates the terms that follow as either an organ within the specified
system or a site within the specified organ. If a particular system
spans more than one page of the table, the heading reflects the
continuation: \*\*\*\*CONTINUED\*\*\*\*

The organization is alphabetical by short text, using the following
conventions:

-   Alphabetized systems

-   Alphabetized organs within each system

The table fields are:

-   SYSTEM

-   ENTRY DESCRIPTION (ORGAN, SITE)

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Micro Topography Hierarchy Level
Table: http://hazel.niehs.nih.gov/starprint/rowley/pctlvl.txt

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#   {#section-2 .unnumbered}

# Microscopic Terms by Organ Table

This table illustrates the relationship between organs, sites and
qualifier groups within related morphologies.

The organ/system is identified by short text and TDMS code in the table
heading. The appropriate sites for the specified organ are listed by
short text beneath the table heading. Following sites, the table lists
non-neoplastic morphologies and neoplastic morphologies by short text.
An asterisk (\*) to the left of the morphology short text indicates that
the morphology is appropriate for the organ appearing on the table
heading. The corresponding TDMS code and qualifier group identification
numbers are listed for each morphology.

The table organization is alphabetical by short text, using the
following conventions:

-   Alphabetized organs

-   Appropriate sites for each organ are alphabetized

-   Alphabetized morphologies

The table fields:

-   ORGAN

-   SHORT TEXT

-   TDMS CODE

-   QUALIFIER GROUPS

Click on the following link to view the Microscopic Terms by Organ
Table: http://hazel.niehs.nih.gov/starprint/rowley/pctpas.txt

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Reference Lists

This section reflects all active terms in the current version of the
Pathology Code Table.

Reference Lists include the following:

-   Morphologies Sorted Alphabetically by Short Text

-   Morphologies Sorted Numerically by TDMS Code

-   Topographies Sorted Alphabetically by Short Text

-   Topographies Sorted Numerically by TDMS Code

These lists contain only those terms currently active in the Pathology
Code Table.

# Morphologies Sorted Alphabetically by Short Text

This list provides the pathologist with an alphabetical reference for
all active morphologies in the PCT.

It includes morphologies appropriate to micropathology and may assist in
pathology data collection.

The morphologies are identified by TDMS code, short text description and
long text description.

The table organization is alphabetical by short text.

The table fields are:

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Morphologies Sorted
Alphabetically by Short Text:
http://hazel.niehs.nih.gov/starprint/rowley/pctmorat.txt

#  {#section-3 .unnumbered}

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\-

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#   {#section-4 .unnumbered}

# Morphologies Sorted Numerically by TDMS Code

This list provides a numeric reference for all active morphologies in
the Pathology Code Table.

It includes morphologies appropriate for micropathology. The
morphologies are identified by TDMS code, short text description, and
long text description. The table organization is alphabetically TDMS
code.

The table fields are:

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Morphologies Sorted Numerically
by TDMS Code: http://hazel.niehs.nih.gov/starprint/rowley/pctmornt.txt

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#   {#section-5 .unnumbered}

# Topographies Sorted Alphabetically by Short Text

This list provides a numeric reference for all active topographies in
the Pathology Code Table.

It includes topographies for micropathology and may be used to assist in
pathology data collection.

The topographies are identified by TDMS code, short text description and
long text description. The table organization is alphabetical by short
text.

The table fields are:

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Topographies Sorted
Alphabetically by Short Text:
http://hazel.niehs.nih.gov/starprint/rowley/pcttopat.txt

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#   {#section-6 .unnumbered}

# Topographies Sorted Numerically by TDMS Code

This list provides a numeric reference for all active topographies in
the Pathology Code Table.

It includes topographies appropriate for micropathology.

The topographies are identified by TDMS code, short text description,
and long text description.

The table organization is alphabetically TDMS code.

The table fields are:

-   TDMS CODE

-   SHORT TEXT

-   LONG TEXT

Click on the following link to view the Topographies Sorted Numerically
by TDMS Code: http://hazel.niehs.nih.gov/starprint/rowley/pcttopnt.txt

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User Documentation Request Form

<table>
<colgroup>
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</colgroup>
<tbody>
<tr class="odd">
<td colspan="10">TODAY’S DATE: ____/____/____</td>
</tr>
<tr class="even">
<td colspan="8">REQUESTOR:
____________________________________________________</td>
<td colspan="2">PHONE NO: ______________</td>
</tr>
<tr class="odd">
<td colspan="8">DOCUMENT NAME:
______________________________________________</td>
<td colspan="2">DOCUMENT NO: ______________</td>
</tr>
<tr class="even">
<td colspan="4">PROJECT NO: _________________</td>
<td colspan="5">MILESTONE: ______________________________</td>
<td>TASK: _____________</td>
</tr>
<tr class="odd">
<td colspan="7">NUMBER OF VOLUMES:
__________________________________________</td>
<td colspan="3">DATE REQUIRED: ____/____/____</td>
</tr>
<tr class="even">
<td colspan="10">SITE OF INSTALLATION:
____________________________________________________________________________</td>
</tr>
<tr class="odd">
<td colspan="10">RECIPIENT (CIRCLE ONE):</td>
</tr>
<tr class="even">
<td>SELF</td>
<td>SITE SUPPORT</td>
<td colspan="3">NCTR</td>
<td>GOVERNMENT</td>
<td colspan="4">NTP</td>
</tr>
<tr class="odd">
<td colspan="10">OTHER (SPECIFY):
__________________________________________________________________________________</td>
</tr>
<tr class="even">
<td colspan="10">*************************</td>
</tr>
<tr class="odd">
<td colspan="3">DATE SHIPPER: ____/____/____</td>
<td colspan="7">BY:
________________________________________________________________</td>
</tr>
<tr class="even">
<td colspan="10">RESPONDING CORRESPONDENCE COMPLETED:
____/____/____</td>
</tr>
<tr class="odd">
<td colspan="10">*************************</td>
</tr>
<tr class="even">
<td colspan="10">RECIPIENT’S MAILING ADDRESS:</td>
</tr>
<tr class="odd">
<td
colspan="10"><p>___________________________________________________________________________________________________</p>
<p>___________________________________________________________________________________________________</p>
<p>___________________________________________________________________________________________________</p>
<p>___________________________________________________________________________________________________</p></td>
</tr>
</tbody>
</table>

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  ------------------------------- ---------------------------------------------
  **Entry Description**           This table field indicates a category of
                                  either sites or organs.

  **Long Text**                   The formal text description of a term.

  **Malignant/Benign**            Terms used to describe neoplastic
                                  morphologies.

  **Metastatic/Non-metastatic**   Terms used to indicate whether or not a
                                  malignant neoplastic morphology may
                                  metastasize.

  **Micropathology**              The microscopic study of the anatomic and
                                  physiologic deviations form the normal that
                                  constitute disease or characterize a
                                  particular disease.

  **Morphology**                  A pathological change or process occurring in
                                  cells, tissues, or organs.

  **Neoplastic Morphology**       Indicates observations of normal cell growth
                                  within a particular site.

  **Non-Neoplastic Morphology**   Indicates morphologic observations of
                                  partially structured or unstructured units of
                                  rapid, abnormal cell growth.

  **NTP**                         National Toxicology Program.

  **Organ**                       Divisions comprising systems; organs are the
                                  basis for all pathological observations.

  **Organ Dependent**             Indicates a morphology that may be found in a
                                  particular organ(s).

  **Paired Organ**                Two corresponding organs designed for use
                                  together.

  **PCT**                         Pathology Code Table

  **PEIS**                        Post Experiment Information System

  **Qualifier**                   A term used to further define a morphology.

  **Qualifier Group**             A set of related qualifiers.
  ------------------------------- ---------------------------------------------

  ------------------------- ---------------------------------------------
  **Qualifier Group         A number unique to a particular qualifier
  Identification Number**   group used to identify that group.

  **Sex Dependent**         Indicates existence in only male or only
                            female animals.

  **Short Text**            A 14-character abbreviated from of a long
                            text description.

  **Site**                  Sites represent a specific location within an
                            organ.

  **Species Dependent**     Indicates existence only in particular
                            species.

  **Stains**                The Pathology Code Table define stains as
                            those which are not normally used in routine
                            processing in the laboratory.

  **System**                Related organs are grouped logically into
                            systems.

  **TDMS**                  Toxicology Data Management Systems.

  **TDMS Code**             This number represents a unique entry.

  **Topography**            A topography is a detailed and accurate
                            description of a definite anatomical region.
  ------------------------- ---------------------------------------------

**END OF DOCUMENT**