{Deliverable Type (End User Manual)}

Document Change History

  ----------------- ------------ ------------------ ----------------------
  **Version         **Date**     **Contributor**    **Description**
  Number**                                          

  V1.0                                              What changes
                                                    (additions and
                                                    deletions) were made
                                                    for this version?

                                                    

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

![](media/image1.jpeg){width="3.9298611111111112in"
height="1.1631944444444444in"}

This is a U.S. Government work. May 2, 2008

Copyright and License Information

This page can include Creative Commons or GNU Free Documentation,
software and documentation; may include a summary with a link if
licenses are available online. Note: You should have the page you use
here approved by your legal advisors.

*Example:* Copyright 2004 {**Fill in organization name**}. This software
was developed in conjunction with the National Cancer Institute, and so
to the extent government employees are co-authors, any rights in such
works shall be subject to Title 17 of the United States Code, section
105.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

1\. Redistributions of source code must retain the above copyright
notice, this list of conditions and the disclaimer of Article 3, below.
Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.

2\. Affymetrix Pure Java run time library needs to be downloaded from
([http://www.affymetrix.com/support/developer/runtime_libraries/index.affx](http://www.affymetrix.com/support/developer/filesdk/GDACFiles/Pages/GDAC_Download.affx))
after agreeing to the licensing terms from the Affymetrix.

3\. The end-user documentation included with the redistribution, if any,
must include the following acknowledgment:

\"This product includes software developed by the {**Fill in
organization name**}and the National Cancer Institute (NCI)."

If no such end-user documentation is to be included, this acknowledgment
shall appear in the software itself, wherever such third-party
acknowledgments normally appear.

4\. The names \"The National Cancer Institute\", \"NCI\" and "{**Fill in
organization name**}" must not be used to endorse or promote products
derived from this software.

5\. This license does not authorize the incorporation of this software
into any proprietary programs. This license does not authorize the
recipient to use any trademarks owned by either NCI or {**Fill in
organization name**}.

6\. THIS SOFTWARE IS PROVIDED \"AS IS,\" AND ANY EXPRESSED OR IMPLIED
WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. IN
NO EVENT SHALL THE NATIONAL CANCER INSTITUTE, SAIC, OR THEIR AFFILIATES
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.

  ----------------------- ---------------- --------- -----------------------
  ***Insert Names of                                 
  Development Team(s)                                
  here***                                            

  ***Development***       ***User's                  ***Program
                          Guide***                   Management***

  Names of developers     Names of                   Names of program
                          technical                  managers
                          writers and                
                          reviewers                  

  This is table format.   To display                 
  Move from cell to cell  grids, select              
  by clicking the Tab     the table (click           
  key.                    4-headed arrow             
                          at upper left of           
                          table). Click on           
                          table areas                
                          where you want             
                          grids to show.             

                                                     

                                                     

                                                     

                                                     

                                                     

                                                     

                                                     

                                                     

                                                     

                                                     

                                                     

  ^1^ Footnote                             ^3^       
  contributing companies/                  company   
  contractors/ divisions                             

  ^2^ department or                                  
  division                                           
  ----------------------- ---------------- --------- -----------------------

+----------------------------------+-----------------------------------+
| ***Contacts and Support***       |                                   |
+----------------------------------+-----------------------------------+
| Enter training contact           | name                              |
|                                  | ([em                              |
|                                  | ail](mailto:covitzp@mail.nih.gov) |
|                                  | address)                          |
+----------------------------------+-----------------------------------+
| Enter customer support contact   | [Web                              |
|                                  | hyperlink](../web%20hyperlink)    |
|                                  |                                   |
|                                  | Telephone: 111-222-3456           |
|                                  |                                   |
|                                  | Toll free: 888-234-1234           |
+----------------------------------+-----------------------------------+

  ------------------ ------------------------------------------------------- ---------------------
  ***LISTSERV                                                                
  Facilities                                                                 
  Pertinent to                                                               
  software teams***                                                          

  ***LISTSERV***     ***URL***                                               ***Name***

  caBIO_Users        <https://list.nih.gov/archives/cabio_users.html>        caBIO Users
                                                                             Discussion Forum

  caBIO_Developers   <https://list.nih.gov/archives/cabio_developers.html>   caBIO Developers
                                                                             Discussion Forum

  caDSR_Users        <https://list.nih.gov/archives/cadsr_users.html>        Cancer Data Standards
                                                                             Repository

  NCIEVS-L Listserv  <https://list.nih.gov/archives/ncievs-l.html>           NCI Vocabulary
                                                                             Services Information

  caArray_Users                                                              

  Add appropriate                                                            
  listservs and or                                                           
  websites here                                                              

                                                                             

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

Contents

[Illustrations iii](#__RefHeading___Toc187030340)

[About This Guide 1](#__RefHeading___Toc187030341)

[Purpose 1](#purpose)

[Audience 1](#typical-user)

[Typical User 1](#typical-user)

[Prerequisites **Error! Bookmark not
defined.**](#__RefHeading___Toc187030345)

[Topics Covered 1](#topics-covered)

[Additional References 1](#additional-references)

[Text Conventions Used 2](#text-conventions-used)

[Credits and Resources **Error! Bookmark not
defined.**](#__RefHeading___Toc187030349)

[Chapter 1 {Chapter Name} 4](#chapter-name)

[About (Heading 2) 4](#about-heading-2)

[Using the (Heading 3) 4](#using-the-heading-3)

[Appendix A {Appendix Name} 15](#appendix-name)

[Index 23](#__RefHeading___Toc187030354)

[]{#__RefHeading___Toc187030340 .anchor}Illustrations (optional)

[Figure 1.1 **Error! Bookmark not
defined.**](#__RefHeading___Toc187038669)

[Figure A.1. \<Caption\> 15](#__RefHeading___Toc187038670)

[Figure A.2. \<Caption Indent\> 15](#__RefHeading___Toc187038671)

If your manual images are mostly screen shots, a list may not be
necessary. They don't mean much outside of the text context.

[]{#__RefHeading___Toc187030341 .anchor}About This Guide

This section introduces you to the {Title Property (File \>
Properties)}. Topics in this section include

-   Purpose on this page

-   Write a brief paragraph introducing the software for which this
    manual is written. Then tie that into the purpose of this chapter
    which is to describe the purpose, objectives, and brief directions
    for using this manual. on page [1](#typical-user)

-   Typical User on page [1](#typical-user)

-   Error: Reference source not found on page [Error: Reference source
    not found](#_Ref185394661)

-   Topics Covered on page [1](#topics-covered)

-   Getting Started with {Software} on page [1](#additional-references)

-   Text Conventions Used on page [2](#text-conventions-used)

-   Error: Reference source not found on page [Error: Reference source
    not found](#_Ref185394707)

## Purpose {#purpose .unnumbered}

Write a brief paragraph introducing the software for which this manual
is written. Then tie that into the purpose of this chapter which is to
describe the purpose, objectives, and brief directions for using this
manual.

## Typical User {#typical-user .unnumbered}

This guide is designed for ... who want to...

## Topics Covered {#topics-covered .unnumbered}

If you have worked with previous versions of {Application Name}, see
Getting Started with {Software} on page [1](#additional-references).

If you are new to {Application Name}, read this brief overview, which
explains what you will find in each chapter and appendix.

-   {Chapter

-   {Chapter

-   {Chapter

-   {Appendix

-   {Appendix

-   {Appendix

## Getting Started with {Software} {#getting-started-with-software .unnumbered}

Bulleted list of sections in this guide to help user get started. You
could include:

-   List Bullet Circle Style

-   Review Chapter 1 to learn about the manual structure

-   Review Chapter 2 for a brief overview of the software

-   Review Chapter X to learn system requirements

-   Refer to .... To learn about activating your license

To start the software, refer to *.....*

## Additional References {#additional-references .unnumbered}

NOTE: If you have a long list of references, use an appendix instead of
this section.

For more information about {Application Name}, see the following
references:

-   {Reference}

-   {Reference}

-   {Reference}

## Text Conventions Used {#text-conventions-used .unnumbered}

This section explains conventions used in this guide. The various
typefaces represent interface components, keyboard shortcuts, toolbar
buttons, dialog box options, and text that you type.

  -------------------------------------------------------------------------------
  Convention            Description                       Example
  --------------------- --------------------------------- -----------------------
  **Bold**              Highlights names of option        Click **Search**.
                        buttons, check boxes, drop-down   
                        menus, menu commands, command     
                        buttons, or icons.                

  URL                   Indicates a Web address.          http://domain.com

  text in [Small        Indicates a keyboard shortcut.    Press
  Caps]{.smallcaps}                                       [Enter]{.smallcaps}.

  text in [Small        Indicates keys that are pressed   Press
  Caps]{.smallcaps} +   simultaneously.                   [Shift]{.smallcaps} +
  text in [Small                                          [Ctrl]{.smallcaps}.
  Caps]{.smallcaps}                                       

  *Italics*             Highlights references to other    See *Figure 4.5*.
                        documents, sections, figures, and 
                        tables.                           

  ***Italic boldface    Represents text that you type.    In the **New Subset**
  monospace*** type                                       text box, enter
                                                          ***Proprietary
                                                          Proteins***.

  **Note:**             Highlights information of         **Note:** This concept
                        particular importance.            is used throughout this
                                                          document.

  { }                   Surrounds replaceable items.      Replace {last name,
                                                          first name} with the
                                                          Principal
                                                          Investigator's name.
  -------------------------------------------------------------------------------

#  {#section .unnumbered}

Leave the last page of a chapter blank if it is even-numbered
(left-facing).

# {Chapter Name}

Introductory paragraph

Topics in this chapter include...

-   {Topic}

-   {Topic}

-   {Topic}

## About (Heading 2) {#about-heading-2 .unnumbered}

### Using the (Heading 3) {#using-the-heading-3 .unnumbered}

#### How to... (Heading 4) {#how-to-heading-4 .unnumbered}

##### By using the... (Heading 5) {#by-using-the-heading-5 .unnumbered}

To ..., follow these steps:

1.  Click the **Open** button.

The window opens.

2.  Select ... from the drop-down list.

3.  Follow these steps:

```{=html}
<!-- -->
```
a.  Do this.

Another window opens!

b.  Do that.

c.  Close the window.

```{=html}
<!-- -->
```
4.  Click **OK**.

```{=html}
<!-- -->
```
a.  Then do that.

```{=html}
<!-- -->
```
d.  Then do that.

    **Note:** To change the name of the manual in the left-facing page
    headers, select **File \> Properties**. On the **Summary** tab,
    change the name of the book title. The header name will change
    correspondingly.

    Text in a note is a 0.5 inch hanging indent. Select **Format \>
    Paragraph**. On the **Indents and Spacing** tab, select **Hanging**
    in the **Special** drop-down list, and enter ***0.5"*** in the
    **By** section.

# Overview of {software}

This chapter provides an overview of the software.

Topics in this chapter include: (bullet list *and cross reference to
sections in chapter)*.

-   *Software Overview on this page*

-   *Component of software and functions on page sss*

-   *Etc.*

## Software Overview {#software-overview .unnumbered}

Background of the software, if appropriate. Include pertinent website
links, if appropriate. General description and scope of the system.

caBIG compatibility level

Images can be inserted where appropriate. Figure 1 is an example of an
image copied and pasted in metafile format.

![](media/image2.wmf){width="4.807638888888889in"
height="1.8319444444444444in"}

Figure 1 If captions are inserted automatically, when you update the
book, captions also update automatically..

Sections of this chapter could also include:

## Components of the Software {#components-of-the-software .unnumbered}

## Features and Functions of the Software  {#features-and-functions-of-the-software .unnumbered}

# User Interface

Description of user interface, viewer windows if appropriate,
descriptions of graphical tools. This chapter can also include
descriptions of global operations used consistently throughout the
software. Examples of topics might be:

-   Launching the interface

-   Online help description

-   The Application Workspace\--This could include description of the
    viewer panes, expanding and collapsing folders, zoom functions,
    scrolling, layout options.

-   Miscellaneous Interface Features\--This could include selection
    techniques, edit functions, print functions, import and export
    features, etc.

# Overview of User Types and Workflows

This chapter could include the following topics:

## User and/or Workflow {#user-andor-workflow .unnumbered}

Task name

-   Purpose of task

-   Rerequisite information or other requirements

-   Step by step instructions

-   Related topics (include cross references, where appropriate)

Repeat for all tasks

## Repeat for all user types {#repeat-for-all-user-types .unnumbered}

See Chapter 5 for an alternative to this outline.

# Error Messages/Indicators and Problem Resolutions

This chapter could include:

-   Description and interpretation of error messages.

-   How to resolve problems

-   Troubleshooting section

-   FAQs

A good format for FAQs:

  ------------------ ---------------------------------------------------------
  **What is the      The semantic layer
  Semantic           ([gov.nih.nci.semantic.\*](../gov.nih.nci.semantic.*)),
  Directory?**       is a self-contained package for semantic connector
                     classes. The semantic connector is described in *Insert
                     Cross-reference*.

  **What is the      The Delegate layer, (gov.nih.nci.system.delegator)uses
  Delegate/Service   the resource locator
  Locator?**         (gov.nih.nci.system.servicelocator)to identify the data
                     source where a query would be performed. For instance, if
                     a query is for a Gene object for a criterion Taxon, this
                     layer identifies the data source information as an
                     internal RDBMS data base and uses the Object Relational
                     Mapping (ORM) data access layer instance.
  ------------------ ---------------------------------------------------------

Arranging the space to put questions in a narrow column alongside their
answers allows users to quickly find the questions that interest them.
(These table borders do not print, but allow easy organization of
material.)

# Glossary/Acronyms/ Abbreviations

You could divide this into separate chapters, depending on the number of
entries here. You could also make this an appendix.

For an examples, see Appendix B

######### Glossary/Acronyms/ Abbreviations 

######### {Appendix Name}

Use the following appendix figure number format. Just copy and paste.

To include these in the Illustrations list, select each one, then press
Alt + Shift + O (letter O). Select F as the table identifier.

Figure B.1. \<Caption\>[]{#__RefHeading___Toc187038670 .anchor}

Figure B.2. \<Caption Indent\>[]{#__RefHeading___Toc187038671 .anchor}

######### References

This appendix could include lists and hypertext links, where
appropriate, to technical manuals, articles, scientific publications,
etc. Examples are shown:

## Technical Manuals/Articles {#technical-manualsarticles .unnumbered}

1.  National Cancer Institute. \"caCORE 2.0 Technical Guide\",
    <ftp://ftp1.nci.nih.gov/pub/cacore/caCORE2.0_Tech_Guide.pdf>

2.  Java Bean Specification:
    <http://java.sun.com/products/javabeans/docs/spec.html>

3.  Foundations of Object-Relational Mapping:
    <http://www.chimu.com/publications/objectRelational/>

4.  Object-Relational Mapping articles and products:
    <http://www.service-architecture.com/object-relational-mapping/>

5.  Hibernate Reference Documentation:
    <http://www.hibernate.org/hib_docs/reference/en/html/>

6.  Basic O/R Mapping:
    <http://www.hibernate.org/hib_docs/reference/en/html/mapping.html>

7.  Java Programming: <http://java.sun.com/learning/new2java/index.html>

8.  Javadoc tool: <http://java.sun.com/j2se/javadoc/>

9.  JUnit: <http://junit.sourceforge.net/>

10. Extensible Markup Language: <http://www.w3.org/TR/REC-xml/>

11. XML Metadata Interchange:
    <http://www.omg.org/technology/documents/formal/xmi.htm>

## Scientific Publications {#scientific-publications .unnumbered}

## caBIG Material {#cabig-material .unnumbered}

5.  caBIG: <http://cabig.nci.nih.gov/>

6.  caBIG Compatibility Guidelines:
    <http://cabig.nci.nih.gov/guidelines_documentation>

## caCORE Material {#cacore-material .unnumbered}

7.  caCORE: <http://ncicb.nci.nih.gov/core>

8.  caBIO: <http://ncicb.nci.nih.gov/core/caBIO>

9.  caDSR: <http://ncicb.nci.nih.gov/core/caDSR>

10. EVS: <http://ncicb.nci.nih.gov/core/EVS>

11. CSM: <http://ncicb.nci.nih.gov/core/CSM>

######### Glossary

Following is an *example* list of terms and their definitions. You may
use any of these you consider appropriate for your glossary.

  -------------------------------------------------------------------------------
  ***Term***       ***Definition***
  ---------------- --------------------------------------------------------------
  API              Application Programming Interface

  caArray          cancer Array Informatics

  caBIG            cancer Biomedical Informatics Grid

  caBIO            Cancer Bioinformatics Infrastructure Objects

  caCORE           cancer Common Ontologic Representation Environment

  caDSR            Cancer Data Standards Repository

  caMOD            Cancer Models Database

  cardinality      Cardinality describes the minimum and maximum number of
                   associated objects within a set

  CDE              Common Data Element

  CGAP             Cancer Genome Anatomy Project

  CMAP             Cancer Molecular Analysis Project

  CN               Common Name

  CS               Classification Scheme

  CSI              Classification Scheme Item

  CSM              Common Security Module

  CTEP             Cancer Therapy Evaluation Program

  CUI              Concept Unique Identifier

  CVS              Concurrent Versions System

  DAML             DARPA Agent Markup Language

  DAO              Data Access Objects

  DARPA            Defense Advanced Research Projects Agency

  DAS              Distributed Annotation System

  DL               Description Logic

  EA               Enterprise Architect

  EBI              European Bioinformatics Institute

  EVS              Enterprise Vocabulary Services

  GAI              CGAP Genetic Annotation Initiative

  GEDP             Gene Expression Data Portal

  HIPPA            Health Insurance Portability and Accountability Act

  HLGT             High Level Group Term

  HLT              High Level Term

  HTTP             Hypertext Transfer Protocol

  ISO              International Organization for Standardization

  JAAS             Java Authentication and Authorization Service

  JAR              Java Archive

  Javadoc          Tool for generating API documentation in HTML format from doc
                   comments in source code (<http://java.sun.com/j2se/javadoc/>)

  JDBC             Java Database Connectivity

  JET              Java Emitter Templates

  JMI              Java Metadata Interface

  JSP              JavaServer Pages

  JUnit            A simple framework to write repeatable tests
                   (<http://junit.sourceforge.net/>)

  LDAP             Lightweight Directory Access Protocol

  LLT              Lowest Level Term

  LOINC            Logical Observation Identifier Names and Codes

  MAGE             MicroArray and Gene Expression

  MAGE-OM          MicroArray Gene Expression - Object Model

  MedDRA           Medical Dictionary for Regulatory Activities

  metadata         Definitional data that provides information about or
                   documentation of other data.

  MGED             Microarray Gene Expression Data

  MMHCC            Mouse Models of Human Cancers Consortium

  MO               MGED Ontology

  multiplicity     Multiplicity of an association end indicates the number of
                   objects of the class on that end may be associated with a
                   single object of the class on the other end

  NCI              National Cancer Institute

  NCICB            National Cancer Institute Center for Bioinformatics

  OIL              Ontology Inference Layer

  OilEd            Ontology editor allowing you to build ontologies using
                   DAML+OIL

  OLLT             Obsolete Lower Level Terms

  OMG              Object Management Group

  ORM              Object Relational Mapping

  PT               Preferred Term

  RDBMS            Relational Database Management System

  SDK              Software Development Kit

  Semantic         A development kit to link model elements to NCICB EVS
  connector        concepts.

  SOC              System Organ Class

  SPORE            Specialized Programs of Research

  SQL              Structured Query Language

  SSC              Special Search Categories

  UI               User Interface

  UID              User Identification

  UML              Unified Modeling Language

  UMLS             Unified Medical Language System

  UPT              User Provisioning Tool

  URL              Uniform Resource Locators

  VD               Value Domain

  WAR              Web Application Archive

  WSDL             Web Services Description Language

  XMI              XML Metadata Interchange
                   (<http://www.omg.org/technology/documents/formal/xmi.htm>) -
                   The main purpose of XMI is to enable easy interchange of
                   metadata between modeling tools (based on the OMG-UML) and
                   metadata repositories (OMG-MOF) in distributed heterogeneous
                   environments
  -------------------------------------------------------------------------------

[]{#__RefHeading___Toc187030354 .anchor}Index

It is very easy to generate an index and extremely helpful to the manual
user. See the Style Guide
(<https://cabig.nci.nih.gov/working_groups/Training_SLWG/Documents/Technical_Pubs_Style_Guide_021405_jbh.pdf>)
for suggestions for inserting index markers and generating an index.

Glossary, 17

References

caBIG materials, 15

caCORE material, 15

scientific publications, 15

technical manuals, guides, 15

Text conventions, Supplement, 3