Document Change History

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

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

                                                    

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

**\*\* Note to Document Author --** Red and blue text (with the
exception of the title and document name above) in this document is
directed at the template user to describe processes, build standards and
help build the document from the template. As a general rule, the blue
text is directive/informative and the red text is used to illustrate
examples. All such red and blue text should be removed before submitting
any formal documentation, including both draft and/or final,
deliverables.**\*\*\*\***

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

Copyright and License page

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 SAIC. 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 Science Applications
International Corporation (SAIC) 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\", "Science
Applications International Corporation", and \"SAIC\" 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 SAIC.

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***       ***Programmer's             ***Program
                          guide***                    Management***

  \<\<Names of            \<\<Names of                \<\<Names of program
  developers\>\>          technical writers           managers\>\>
                          and reviewers\>\>           

  This is table format.   To display grids,           
  Move from cell to cell  select the table            
  by clicking the Tab     (click 4-headed             
  key.                    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       | [Web                              |
| contact\>\>                      | 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                                                              

                                                                             

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

Table of Contents

[Chapter 1 Introduction to the {*document name*} Guide
1](#introduction-to-the-document-name-guide)

[Chapter Organization and Content 2](#chapter-organization-and-content)

[Overview of the Guide 2](#overview-of-the-guide)

[Organization of the Technical Guide
2](#organization-of-the-technical-guide)

[Getting Started with this programmer's guide
2](#getting-started-with-this-programmers-guide)

[Using This Template 3](#using-this-template)

[Viewing Style Headings 3](#viewing-style-headings)

[Examples of Style Headings 3](#examples-of-style-headings)

[(Style Heading 2\--Second level heading)
3](#style-heading-2--second-level-heading)

[Style Heading 3\--Third level heading (Palatino Linotype 14-point)
3](#style-heading-3--third-level-heading-palatino-linotype-14-point)

[Installing the Software 4](#installing-the-software)

[Headers and Footers 4](#headers-and-footers)

[Document Text Conventions 4](#document-text-conventions)

[Chapter 2 Overview of the Software 6](#overview-of-the-software)

[Software Overview 6](#software-overview)

[System Requirements 6](#system-requirements)

[Design and Architecture 7](#design-and-architecture)

[Chapter 3 {product name} Installation 9](#product-name-installation)

[Chapter 4 {Product} Requirements 10](#product-requirements)

[Chapter 5 {Product} Design and Architecture
13](#product-design-and-architecture)

[Architecture 13](#architecture)

[Chapter 6 Security and Security Management
15](#security-and-security-management)

[Software Authorization 15](#software-authorization)

[Configuring Software Authorizations
15](#configuring-software-authorizations)

[Chapter 7 {Product} APIs 17](#product-apis)

[Major Function, Features or API Subset
17](#major-function-features-or-api-subset)

[Repeat as appropriate 17](#repeat-as-appropriate)

[Chapter 8 Information Models 19](#information-models)

[Chapter 9 Grid and Web Services 21](#grid-and-web-services)

[Chapter 10 Customized Tools and Features
23](#__RefHeading___Toc142277030)

[Technical Manuals/Articles 25](#technical-manualsarticles)

[Scientific Publications 25](#scientific-publications)

[caBIG Material 25](#cabig-material)

[caCORE Material 25](#cacore-material)

[Index 31](#index)

List of Illustrations (optional)

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

#  Introduction to the {*document name*} Guide  {#introduction-to-the-document-name-guide .Section-Heading}

**Before you Begin:**

It's important that you decide early in this process the focus of this
programmer's manual and its target audience and that you write
accordingly. This guide can be written to describe software
requirements, architecture, and information for programmers writing new
APIs and tools that will integrate with your software. Your developers
and those of adopter centers will have important input regarding the
contents of this technical guide.

Some of the chapters in the technical guide are essential and others are
optional. It is up to your writing team and subject matter experts to
make the final decision about content and to adapt this template to your
specific situation.

-   Chapters 1, 2 and 4 through 8 are essential. Chapter 3 material is
    preferably included in a separate installation guide. Chapters 9 and
    10 are optional and should be included if your application warrants
    it.

In other cases, chapters can be combined or separated, depending on the
nature and length of the material.

-   Chapters 4 and 5 on Requirements and Design could be combined into
    one chapter.

-   Chapter 7 could be divided into two chapters about APIs

**Notes about an Administration Guide:**

Information for your system that falls under the category of
"administration" can be included in specified chapters in this technical
guide, or if the amount of the information warrants it, you can create a
separate administration guide, using this template for that document, as
well.

Examples of "Administration" topics that can be included (but are
optional) are:

-   Managing users and processes

-   Importing and deleting {datatype} data

-   Maintaining databases

-   Updating data files

-   Installing plug-ins

It is important to remember that the chapters and suggested sections in
the technical guide are to be adapted to your particular context. If you
have questions, contact the caBIG™ Training Workspace lead or NCICB
Application Support: <http://ncicb.nci.nih.gov/NCICB/support>

## Chapter Organization and Content {#chapter-organization-and-content .unnumbered}

**Chapter content:** For this first chapter, write a very 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.

Chapters always begin with an introductory statement and list of topics
as shown in this example. List topics in the chapter and cross reference
them. If you add automatic cross-references, then the user can use the
cross-ref as a hyperlink. (For example, use CTRL + SHIFT on the page
number of the last bulleted item in this list.)

For instance, "Topics in this chapter include": (You could include the
following:)

-   *Overview of the Guide on this page*

-   *Organization of the Guide on page 2*

-   *The {Software} User (background and experience expected to use
    software)*

-   *Getting Started with the Software on page
    [2](#document-text-conventions)*

## Overview of the Guide {#overview-of-the-guide .unnumbered}

Brief overview of this developer's guide.

## Organization of the Technical Guide {#organization-of-the-technical-guide .unnumbered}

Summarize each chapter in the table.

+----------------------------+-----------------------------------------+
| ***Chapter in {name}       | ***Chapter Contents***                  |
| Technical Guide***         |                                         |
|                            |                                         |
| ***Table Title Style***    |                                         |
+============================+=========================================+
+----------------------------+-----------------------------------------+

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

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

Table 1. 1Include captions for each table and figure in the guide

## Getting Started with this programmer's guide {#getting-started-with-this-programmers-guide .unnumbered}

Bulleted list of sections in this guide to help user get started. You
could include statements similar to the following to help programmer's
get started:

-   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 *.....*

*If the installation guide is a separate document, be sure and name the
document. If it is posted to a website, include a URL.*

## Using This Template {#using-this-template .unnumbered}

This template is written using formats defined with Microsoft Word 2003
styles. For more information about using Word while creating your
software user's guides, see Chapter 4 in the Technical Publications
Style Guide downloaded from the caBIG website:

<https://cabig.nci.nih.gov/working_groups/Training_SLWG/Documents/Technical_Pubs_Style_Guide_021405_jbh.pdf>

### Viewing Style Headings {#viewing-style-headings .unnumbered}

There are three ways to view the various Style names of the template
sample text:

1.  Style List number style

2.  Select **Format \> Styles and Formatting.** The style for the
    selected text shows in the **Styles and Formatting** task pane,
    **Formatting of selected text**, at the top right of the viewer
    window.

3.  Click in any paragraph and view the style name on the Formatting
    toolbar.

4.  With the document open in **Normal** view or **Outline** view (under
    the **View** menu), select **Tools \> Options**. Click the **View**
    tab. In the **Style Area Width** box, specify the width and click
    **OK**. Each paragraph's style name displays in the Style area while
    you work .

To apply styles, select text, then click on the style in the Styles and
Formatting task pane, or select the style on the Formatting toolbar,
**Styles** drop-down list. A simple way to apply heading styles is to
select the heading text, then press CTRL + ALT + 1 (Heading 1), ...+ 2
(Heading 2) , or ... + 3 (Heading 3).

**Note:** If you get frustrated using styles, apply formatting manually.
It will override any applied styles.

### Examples of Style Headings {#examples-of-style-headings .unnumbered}

##  (Style Heading 2\--Second level heading) {#style-heading-2--second-level-heading .unnumbered}

### Style Heading 3\--Third level heading (Palatino Linotype 14-point) {#style-heading-3--third-level-heading-palatino-linotype-14-point .unnumbered}

Style Heading 4---Fourth-level heading (Palatino linotype 12-point bold)

Style Heading 5---Fifth-level heading(Palatino linotype 12-point italic)

**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.

### Installing the Software {#installing-the-software .unnumbered}

Example of Heading 3.

Downloading Software Files

Example of Heading 4

### Headers and Footers {#headers-and-footers .unnumbered}

The headers and footers in this template were preconfigured. The header
for even-numbered pages is the book title. To change the header, select
**File \> Properties**. On the **Summary** tab, change the name of the
title. The header should change automatically. If it does not,
double-click on the header and make the change manually. It will change
concurrently throughout the guide. The header for odd-numbered pages is
the chapter title. As you type in new chapter titles, the associated
headers should change automatically. Although they were preconfigured,
they sometimes seem buggy, so you can make changes in the header
manually, as a last resort.

## Document Text Conventions {#document-text-conventions .unnumbered}

The following table shows various typefaces to differentiate between
regular text and menu commands, keyboard keys, and text that you type.
This illustrates how conventions are represented in this guide.

+----------------------+------------------------+----------------------+
| ***Convention***     | ***Description***      | ***Example***        |
+======================+========================+======================+
| **Bold & Capitalized | Indicates a Menu       | **Admin \> Refresh** |
| Command**            | command                |                      |
|                      |                        |                      |
| **Capitalized        | Indicates Sequential   |                      |
| command \>           | Menu commands          |                      |
| Capitalized          |                        |                      |
| command**            |                        |                      |
+----------------------+------------------------+----------------------+
| [text in small       | Keyboard key that you  | Press                |
| caps]{.smallcaps}    | press                  | [enter]{.smallcaps}  |
+----------------------+------------------------+----------------------+
| [text in small       | Keyboard keys that you | Press [shift +       |
| caps + text in small | press simultaneously   | ctrl]{.smallcaps}    |
| caps]{.smallcaps}    |                        | and then release     |
|                      |                        | both.                |
+----------------------+------------------------+----------------------+
| Special typestyle    | Used for filenames,    | URL_definition ::=   |
|                      | directory names,       | url_string           |
|                      | commands, file         |                      |
|                      | listings, source code  |                      |
|                      | examples and anything  |                      |
|                      | that would appear in a |                      |
|                      | Java program, such as  |                      |
|                      | methods, variables,    |                      |
|                      | and classes.           |                      |
+----------------------+------------------------+----------------------+
| **Boldface type**    | Options that you       | In the Open dialog   |
|                      | select in dialog boxes | box, select the file |
|                      | or drop-down menus.    | and click the        |
|                      | Buttons or icons that  | **Open** button.     |
|                      | you click.             |                      |
+----------------------+------------------------+----------------------+
| *Italics*            | Used to reference      | *caCORE Software     |
|                      | other documents,       | Development Kit 1.0  |
|                      | sections, figures, and | Programmer's Guide*  |
|                      | tables.                |                      |
+----------------------+------------------------+----------------------+
| ***Italic boldface   | Text that you type     | In the New Subset    |
| type***              |                        | text box, enter      |
|                      |                        | ***Proprietary       |
|                      |                        | Proteins.***         |
+----------------------+------------------------+----------------------+
| Note:                | Highlights a concept   | **Note:** This       |
|                      | of particular interest | concept is used      |
|                      |                        | throughout the       |
|                      |                        | installation manual. |
+----------------------+------------------------+----------------------+
| **Warning!**         | Highlights information | **Warning!**         |
|                      | of which you should be | Deleting an object   |
|                      | particularly aware.    | will permanently     |
|                      |                        | delete it from the   |
|                      |                        | database.            |
+----------------------+------------------------+----------------------+
| {}                   | Curly brackets are     | Replace {root        |
|                      | used for replaceable   | directory} with its  |
|                      | items.                 | proper value such as |
|                      |                        | c:\\cabio            |
+----------------------+------------------------+----------------------+

Table 1. 2 Document Conventions

#  Overview of the Software

A good rule of thumb is to always start new chapters on odd-numbered
(right-facing) pages.

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

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. **Note:** Each figure in
your guide should be referenced in the text.

![](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:

## System Requirements  {#system-requirements .unnumbered}

Define any system requirements that apply to your software. These
requirement should fit easily within table format.

(Include a link to system requirements document(s) in GForge
<http://gforge.nci.nih.gov/>)

You might also include in this section brief information about
third-party software that the application relies upon, but which has its
own documentation. The description should describe whether or not the
user must download and install such software or whether it is downloaded
and installed by default when you download the caBIG software
application.

Do not include information that would appear in the third party
application's own documentation. Do include relevant information about
how the third party software integrates with your software, specific
configurations for your environment, etc.

The setting of parameters that apply to your software installation and
deployment should be included in your {product} Installation Guide.

## Design and Architecture {#design-and-architecture .unnumbered}

Include only brief descriptions, because more detailed material would be
included in the Requirements and Design chapter, or a separate Design
chapter, if you so choose.

Include links to relevant architecture documents in GForge
<http://gforge.nci.nih.gov/>).

# {product name} Installation 

> **Note:** We strongly recommend that you create a separate
> installation guide for your application rather than including it in
> this technical guide. If you do choose to include installation
> instructions in this guide, place them in this chapter. The following
> paragraph describes the material that should be included in
> installation directions. For more information about content, see the
> caBIG Installation Guide template that you can download from:
> <https://cabig.nci.nih.gov/working_groups/Training_SLWG/Documents/index_html>.
>
> This installation guide outlines the supported configurations and
> installing, setting up and configuring the application and/or
> databases. It can also include information about importing and
> exporting data for or from databases. If testing instructions are also
> included, you might include a sentence similar to this: Directions for
> testing the {product} are also included here.

# {Product} Requirements

This chapter can include descriptions of the requirements for your
software, or the descriptions of what the user requires in the software.

-   It can include information about the nature of the data which is
    housed and/or managed in the application and how it relates to the
    requirements

-   This chapter can also include information about application security
    requirements

The requirements chapter can include software design or you may want to
include a design chapter (see Chapter 4).

# {Product} Design and Architecture

This chapter could include the following topics:

-   Design is how the requirements of the software are implemented in
    the product

-   Include links to developer design documents such as use case
    documents and to the latest UML models for the software

## Architecture {#architecture .unnumbered}

You might want to include architecture diagram and have legend that
walks users through the components of the high-level architecture.

Include links to architecture documents in GForge
<http://gforge.nci.nih.gov/>).

# Security and Security Management

This chapter could include sections describing:

## Software Authorization {#software-authorization .unnumbered}

Describe permissions and structure

## Configuring Software Authorizations {#configuring-software-authorizations .unnumbered}

Descriptions of how to add administrators/supervisors/groups/users.

.

# {Product} APIs

The purpose of this chapter is to describe the APIs and how to use them.
This chapter should not repeat material in the Javadocs, if they are
complete, but should reference important sources such as Javadocs for
API information not included in the chapter.

It is important to remember that the chapters and suggested section in
the guide are to be adapted to your particular context. If you have
questions, contact the Training Workspace lead or NCICB Application
Support: <http://ncicb.nci.nih.gov/NCICB/support>

## Major Function, Features or API Subset {#major-function-features-or-api-subset .unnumbered}

-   Purpose

-   Input: commands/functions, data/parameters, format/ option selection

-   Step-by-step instruction for use (if appropriate)

-   Expected Results and exception handling

-   Related function (cross-references, if appropriate)

## Repeat as appropriate {#repeat-as-appropriate .unnumbered}

This chapter could include comprehensive examples of how to use the APIs
and how to extend them. Where appropriate, include example of the code.
An API example, for instance, might describe chaining three or four APIs
for a useful extension of the software's functions.

You could create a separate chapter for the API examples, if the length
of the material warrants it.

You might include a link to downloadable code.

# Information Models

This chapter contains necessary information about the different types of
object models and other artifacts of the object-oriented programming
language (such as Unified Modeling Language or UML) used to generate
your software.

-   This presents objects in a data model type view, as opposed to text
    descriptions that might be included in previous chapters.

-   You could include links to the latest UML models: use case diagrams,
    class diagrams, sequence diagrams, etc.

For example, you might include a paragraph about how your application
models biospecimens and their tracking attributes: "...with a total of
60 classes and 150 attributes. A detailed model can be found at {url for
the model}."

# Grid and Web Services

This chapter, essential only if your application includes grid (or web)
services, could include the necessary information about how to use the
services unique to your application. It could include the following
topics:

-   Usage of web or grid service

-   Web service description language

-   Links to appropriate documents

-   Examples of usage

It may make sense with your application to roll this information in with
the API chapter. This is another example of the wisdom of adapting this
technical guide to the context of your own application.

Of course, if your application is caBIG™ Gold Compliant, this chapter
covering your integration with caGrid is essential.

# Customized Tools and Features

This optional chapter would be written only if your application includes
customized tools. The chapter could include material describing:

-   Descriptions of customized tools and features.

-   How to extend the software tools

-   How to integrate the software with other applications

-   How to add data sources

# References {#references .Appendix1}

This appendix could include lists and hypertext links, where
appropriate, to technical manuals, articles, scientific publications,
etc. Examples are shown. You can use any of these examples you consider
appropriate.

## 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}

1.  **caBIG:** <http://cabig.nci.nih.gov/>

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

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

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

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

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

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

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

# Glossary {#glossary .Appendix1}

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

  -------------------------------------------------------------------------------
  ***Term***       ***Definition***
  ---------------- --------------------------------------------------------------
  {jboss-home}     The base directory where JBoss is installed on the server

  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

  XML              Extensible Markup Language (<http://www.w3.org/TR/REC-xml/>) -
                   XML is a subset of Standard Generalized Markup Language
                   (SGML). Its goal is to enable generic SGML to be served,
                   received, and processed on the Web in the way that is now
                   possible with HTML. XML has been designed for ease of
                   implementation and for interoperability with both SGML and
                   HTML
  -------------------------------------------------------------------------------

#  {#section .unnumbered}

#  {#section-1 .unnumbered}

# Index {#index .unnumbered}

It is very easy to generate an index and extremely helpful to the manual
user. See the *Technical Style Guide* located at:
[https://cabig.nci.nih.gov/working_groups/Training_SLWG/Documents/Technical_Pubs_Style_Guide_021405_jbh.pdf](https://cabig.nci.nih.gov/working_groups/Training_SLWG/Documents/Technical_Pubs_Style_Guide_021405_jbh.pdf )
for directions for inserting index markers and generating an index in MS
Word (PC).

Document conventions, Supplement, 8

Glossary, 31

References

caBIG materials, 29

caCORE material, 29

scientific publications, 29

technical manuals, guides, 29

terms, 31

Text conventions, Supplement, 8