Content
SapMaker Content 2.0
User Guide
ClinTrialStat Inc
What is SapMaker Content?
SapMaker Content 2.0 is a tool to efficiently make
Statistical Analysis Plans (SAP) documents for clinical trials. It can be used as a guide to write each
section of SAP in Word document by providing the title, instructions for the
content of the section, and sample paragraphs through pre-set templates. The
author can also use the ¡°search-engine¡± utility of the software to retrieve
paragraphs from other Word document such as the Study Protocol to get study
specified contents for the section of SAP.
Who should use
SapMaker Content 2.0?
Biostatisticians and Medical Writers who are working on clinical trials.
Features
¡€
Provides
instructions for each section of a SAP;
¡€
Write
the title of a selected section of the SAP into a Microsoft Word document;
¡€
Provide
¡°search-engine¡± utility for the author to retrieve relative paragraphs
associated to the topic of the section from other study specified Word
documents such as Study Protocol.
¡€
Provide editor to let user to change pre-set titles,
instructions, and sample paragraphs in templates.
Requirements
¡€ Supported Operating Systems: Microsoft Windows 9X/NT/2000/XP (Windows 9X/NT/2000 need to be updated with NET. Framework)
¡€ Software Requirements: Microsoft Word.
Table of Contents
Features
and Icons of SapMaker Content
Quick Start of SapMaker Content 2.0
Overview of Panels of SapMaker Content Window 2.0
Creating Content Document of the Statistical Analysis
Plan
Overview Creating Content Document of the Statistical
Analysis Plan
Select Sections from TOC Panel
Write Section of SAP in Word Document
Search Contents Related to SAP Sections from Other Word
Document
Tell Software to Search for Which Word Document
Insert Found Content into SAP Word Document
Modify SAP Section Templates Using XML Editor
Edit Instruction and Sample Paragraphs of Section
Convert Statistical Analysis Plan Template in Word
document to SapMaker XML Templates Document
Word Document for SAP Template
Convert Word Document Template to XML Template
Features and Icons of SapMaker Content
SapMaker Content Window 2.0 provides its users with fourteen
features to efficiently write Statistical Analysis Plan documents for a
clinical study. Five common features are associated with an icon,
which when clicked executes the desired feature. These icons are presented
in the menu bar of the SapMaker Content Window as shown in Figure 1. When an
icon is double clicked, the action associated with the icon or the feature will
be executed. The icons and its associated features are summarized in Figure
2.
¡¡
Figure 1.
Icons in menu bar
Figure 2. Icons of SapMaker and
Associated Features
|
Icon |
Action |
Feature |
|
|
Opens a dialog window to setup information of a
study (e.g., protocol number, study name, etc.) for a SapMaker project. |
|
|
|
Open Project |
Open an existing project information ((e.g.,
protocol number, study name, etc.) |
|
|
Save Project |
Save current project to the project profile file. |
|
|
List Title of SAP Content |
List titles of each sections of SAP in a Tree-View
format. |
|
|
Write SAP Document in Word |
Write title and paragraphs of selected Section of
SAP to a Word document. |
|
|
Search Related Paragraphs |
Retrieve relative paragraphs associated to the topic of the section
from other study specified Word documents such as Study Protocol. |
|
|
Exit Project |
Exit SapMaker project, quit SapMaker,
and close related windows |
Quick
Start of SapMaker Content 2.0
Step 1: Start Application
First click the SapMaker Content 2.0 icon to start
it:
Step 2: List Title of Content
Then select the option Content
Template from the
top menu bar, or double click the 
icon, to list
titles of the sections of the Statistical Analysis Plan
You can see that the titles of the sections in this SAP were listed in a ¡°Tree-View¡± style šC meaning that you can get sub-titles by clicking the ¡°+¡± symbol and each node of the list
Once you highlight a title from the list, you will see instructions for this section will be listed in the bottom panel of the window.
Step 3: Write Selected Section of SAP in Word Document
In this step you will create the SAP document that contains pre-set
templates in a Word document by either selecting the menu button Write
SAP Word Document (as following figure),
or by double clicking the 
icon
:
The SAP document created in Word document is as follows:
You can further continue work on this SAP documents by retrieving the study specified information from other Word document such as the Study Protocol.
Overview of Panels of SapMaker Content Window 2.0
SapMaker
Content Window 2.0 provides its users with five panels for helping them
efficiently create a Statistical Analysis Plan. These panels are presented in
the following figure, their functions are described in the following paragraphs.
Project Explorer TOC Panel Comment Panel
- Project Explorer panel:
Project Explorer panel lets users manage metadata documents.
- TOC panel: the Title of
Content panel lists titles of individual sections of Statistical Analysis
Plan. The list is represented
in a ¡°Tree-View¡± style that means the users can retrieve sub-titles of a
title by clicking the ¡°+¡± symbol on the left side of the title.
- Comment panel: the Comment
panel lets users to read information related to a selected section. Once the users have highlighted
the title of a section, the instruction for what should be included in the
section, or sample paragraphs will be displayed in this panel. .
Overview of SapMaker Project
To organize documents created by SapMaker such as
Word or Excel documents, SapMaker will store these documents into a SapMaker
Project folder. This project folder is named SapMaker
Project. It has three sub-folders, doc, log, and prog. The doc subfolder
will store Word and/or Excel documents, and the log sub-folder will store the
location of the project folders. SapMaker Metadata will automatically create
these folders when the user clicks the menu button Project
New or double clicks the 
icon ¡¡
SapMaker Content Project Folders
¡¡
Project Explorer¡¡
The Project explorer window will
help users to manage the process of creating documents for a Statistical
Analysis Plan.
Users can browse
these folders within the Project Explorer window. They can restart
work on a SAP document previously saved by clicking the name of the document in
the Project Explorer window. SapMaker Metadata will open the
document and automatically add new materials to the document.
Project Explorer
Start New Project¡¡
To start a new project you must first setup a SapMaker
Project folder to save the documents into. The newly created documents will
then be saved into the three subfolders doc, log, and prog. The doc sub-folder
will store Word and/or Excel Sap documents, and the log sub-folder will store
information about the project folder. When you start a new project, SapMaker
will automatically create the SapMaker Project folder and the three subfolders
doc, log, and prog. To start a new project, select the menu button ProjectNew or double click the 
icon.
This action will trigger SapMaker to pop up a dialogue window allowing the user
to browse the directories to create the SapMaker Project folder and its
subfolders.
Popup select folder dialogue window for browsing directories
Once user
has selected a working folder, a dialog window will pop out to let the user to
input information of study such as protocol number, study name, and treatment
groups.
Popup project information dialogue window for project global
information
Open Project
You can call back a previously saved SapMaker project by
opening the folder for the project. The documents created before will be
presented in the Project Explorer window. You can then double click a
document listed in the Project Explorer window to continue to add additional
content into it. To do so, you can either select the menu button Project
Open or double click the 
icon, which will lead to a pop up of an open-file dialogue window
so that you can browse the directories to locate the folder in which
the documents were stored.
Open project
Open-file dialogue window for
browsing the project folder
This will
trigger a dialog window that will retrieve information of study (e.g., protocol
number, study name, treatment groups, etc.) saved in the project log file.
Saving Project
Before exiting SapMaker, you can
save treatment groups, project folders, or the directory of customized
templates of your organization into a file stored in the log
subfolder. The next time you come back to SapMaker, the saved the
project folders can then be recalled into SapMaker Metadata. To do so the you
can either select the menu button Project
Save, or Project
Save As or click the 
icon, which will lead to a popup save file dialogue window so
that you can choose a file name in the log subfolder of the project to store
the project folder information.
The data of your project were stored into a XML document.
Save project
Save file dialogue window for browsing the project folder
Modify Project
After starting the project, you can modify the set up of the
study by selecting the menu button Project
Modify, which will pop up the dialog
window for you to modify the study information.
.
Exit Project
After saving the project, you can exit SapMaker Metadata by
selecting the menu button Project
Exit or click the 
icon, which will close any Word or Excel documents opened by
SapMaker Metadata and quit SapMaker Metadata.
Creating Content
Document of the Statistical Analysis Plan¡¡
Overview Creating Content Document of the Statistical Analysis
Plan¡¡
SapMaker Content 2.0 will help users to
document each section of Statistical Analysis Plan based on the Study Protocol
of a clinical trial in Word document.
This tool can help users to create SAP documents, using
instructions summarized from ICH guidance and other regulatory agencies, or
instructions specified by individual organizations. The users can also use the tool to retrieve information from
other Word document such as Study Protocol.
When writing their own statistical analysis plan (SAP),
users can select a subset of section titles provided by SapMaker and then
working on these selected sections. By selecting an option from the
command bar, SapMaker will write SAP section in a Word document with the
following options:
¡€
Write
section titles, instructions for writer, and sample paragraphs
¡€
Write
section titles and instructions for writer
¡€
Write
section titles and sample paragraphs
¡€
Write
section titles only
The user can select any one of the
above options (see following figure). The default option is "write section titles, instructions
for writer, and sample paragraphs".
Set
Option for Writing Style
List Titles of SAP Sections
To start working on SAP content document, a user has to
first open titles of sections of SAP and then select these sections applying to
his or her analysis. To load SAP sections stored in XML template file into
SapMaker Content 2.0, the user needs to select option Content
Template from the top menu bar or by double clicking the 
icon.
Once the sections have been loaded, the titles
of these sections will be represented in a ¡°Tree-View¡± style that means the
users can retrieve sub-titles of each title by clicking the ¡°+¡± symbol on the
left side of the title.
Lists of Titles of
SAP Sections
Select Sections from TOC Panel
When you have opened sections of SAP and listed titles of
sections onto the TOC panel, you can also select sections that are applicable
to your study from the TOC panel, write these sections into a Word document as
template, and then modify these sections to complete your SAP. To do so, first select and click
each title and read instructions shown in the Comment panel, and choose whether
or not the section is needed in your SAP.
Write Section of SAP in Word
Document
When you have selected a section from TOC panel and want to
add it to your SAP document, you can write this section by either selecting the
menu button Write
SAP Word Document (as following figure),
or by double clicking the 
icon:
The SAP document created in Word document is as follows:
Note:
You should not close any Word Document opened by SapMaker until you
exist from SapMaker.
Search Contents Related to SAP
Sections from Other Word Document
When writing a Statistical Analysis
Plan, authors need to retrieve certain information such as study objectives
etc. from study protocol or other documents. SapMaker Content 2.0 provides a ¡°search-engine¡± utility
to let users to search and retrieve these study specified information. This ¡°search-engine¡± utility will search a Word document for
sentences, paragraphs, or sections that contain query clauses used in the
searching.
Tell Software to Search for Which Word Document
To start retrieving content from other document, a user has
to first tell the software which Word document needs to be looked at. There are two ways to do this: First one is to use Project Information
Dialogue Window to set ¡°Search File¡± as shown in the following figure before open
the Search Window:
The other method is to use option Content
Search from the top menu bar to
open the Search Window. Then tell
the Search Window which Word document needs to be looked at.
Search Window
The ¡°search-engine¡± is including in Search Window of the software. To retrieve content from other
document, a user has to use the Search Window to query Word document. Following figure shows using the
Search Window to conduct a query for paragraphs contain ¡°sample size or
power¡±. The top long-box is used
for users to type query clause.
The left panel lists identifies of paragraphs found, and right panels
lists found paragraphs. User
can use option View from the top menu bar to list all found
paragraphs, or click the ¡°Tree-View¡± list on the left panel to list individual
paragraph. You can use the option Search
Paragraph, or Search
Sentence from the top menu bar to
search for paragraphs or sentences that contain the query clause, respectively.
Search Window
Syntax of Query Clause
The query clause can be simple
English clause, or complex one that is a combination of a few English clauses
with logic relationship of ¡°AND¡±,
¡°OR¡±, and ¡°NOT¡±.
A simple query clause can be a sequence of English words and/or English
clauses. A complex is a logic
combination of simple query clauses by logic relationships of ¡°AND¡±, ¡°OR¡±, or
¡°NOT¡±. The logic
relationship ¡°AND¡±, ¡°OR¡±, and
¡°NOT¡± is represented by symbol ¡°&&¡±, ¡°||¡±, and ¡°!¡±, respectively. The priority of simple query
clauses within logic relationships will be identified by symbol of ¡°( )¡± brackets (i.e., simple query clause
within ¡°( )¡± brackets has higher
priority than simple query clause outside the brackets).
For example, SapMaker Content 2.0
will conduct a query for searching contents of ¡°study objectives or primary and
secondary parameters¡± by using a query clause of ¡°study objectives || (primary parameter && secondary
parameter )¡±. The
symbol ¡°&&¡± and ¡°||¡± represents logic relationship of ¡°AND¡± and ¡°OR¡±,
respectively. The clauses
inside ¡°( )¡± brackets have higher priority to be
processed than clauses outsides the brackets. In the next a few sections we will discuss how to use
this search capacity to quickly retrieve contents.
Search within Founds
When a query returns too many
paragraphs or sentences, users can
re-type a new query clause, and then use option Search
Within Founds from the top menu
bar to search for paragraphs or sentences from these have been found that
contain the new query clause.
Inside the ¡°search-engine¡± of this software, search of paragraphs or sentences by simple query clause will check all paragraphs or sentences of the searching Word document to find and return those ones containing query clause. The speed for conduct a simple query without relationship ¡°AND¡± or ¡°OR¡± will be much faster that a complex query having relationship ¡°AND¡± or ¡°OR¡±. Query from ¡°Within Founds¡± will be much faster from original document. Therefore, when users need to search for a complex query such as ¡°Adverse Event && ( Serious || Clinically Significant )¡±, we suggest to first search for a simple query clause of ¡°Adverse Event¡±, and then use this query-within-founds to search for another query clause of ¡°Serious || Clinically Significant¡± within those have been found.
When re-query returned
paragraphs or sentences are not these wanted, the users can re-type a new query clause, and then use option Search
Undo Within Founds from the top
menu bar to re-do the search.
Search Query Clause
SapMaker Content 2.0 provides
pre-set query clauses for each sections of SAP. When you select option View 
Query Clause from the top menu bar, and then click the section title, you
will see pre-set query clauses for the section will be listed in the bottom
panel. When you
click one of the listed query clause, the search window will be appear.
Insert Found Content into SAP Word Document
When user click identify of a found paragraph and highlight
the paragraph from the left panel, and then use option Insert from
the top menu bar, the selected paragraph will be inserted into the SAP word
document the author is working on. (Note: to use the function the SAP Word document
needs to be opened.)
When user click option
Clean
from the top menu bar, the listed
paragraphs will be removed from the right panel.
Modify SAP Section Templates Using
XML Editor
SapMaker Content 2.0 uses its
defined XML document to store texts needed for producing sections of
Statistical Analysis Plan. The
title, instructions, and sample paragraphs of each section of SAP are strode as
XML elements in a XML file as a template of SAP. You can give the elements of this XML document different
values to change the SAP template.
You can use any XML editor or text editor to modify this XML document if
you understand XML language.
However, if you use the SAP template editor provided by SapMaker Content
2.0, you can easily modify this XML document without knowing XML. In this chapter we will explain to you
how to use this editor to modify data to change the template of SAP. The definitions of the elements and
attributes of this XML document are explained in Appendix I.
Edit Title of Section¡¡
You can change the level and title
of a section by changing texts in the boxes under the label TitleProfile
and besides labels level and Title,
respectively.
(Please see following Figure.) The level 1, 2, etc. means this title is in Word
format of Heading1, Heading 2, etc. If you want to add more sub-titles to you
section, you can first click ¡®+¡¯ under the label TitleProfile and type
the sub-title into the box besides the label Title. (In XML syntax,
TitleProfile is an element of the XML document, while level and Title are
children elements of TitleProfile.)
Edit Instruction and Sample
Paragraphs of Section¡¡
You can change the instructions of
a section by changing texts in the boxes under the label Instruction and
besides labels Instruction. (Please see above Figure.) If you want to add more
instructions to you section, you can first click ¡®+¡¯ under the label Instruction
and type an additional paragraph of instructions into the box besides the label
Instruction. If you want to change content of other
instructions, you can click ¡®>¡¯ or ¡®<¡¯ under the label Instruction to
move to the previous or latter paragraphs of instructions.
Similarly, you can change the
sample paragraphs of a section by changing texts in the boxes under the label Paragraph
and besides labels paragraph. (Please see above
Figure.) If you want
to add more sample paragraphs to you section, you can first click ¡®+¡¯ under the
label Paragraph and type an additional sample paragraph into the box
besides the label paragraph. If you want to change content of other
sample paragraph, you can click ¡®>¡¯ or ¡®<¡¯ under the label Paragraph to
move to the previous or latter sample paragraphs.
The Query Clause can be added or
changed by the same method.
You can change the query clauses of a section by changing texts in the
boxes under the label Query and besides labels Query. (Please
see above Figure.) If
you want to add more query clauses to you section, you can first click ¡®+¡¯
under the label Query and type an additional query clause of into the
box besides the label Query. If you want to change content of other query clauses, you
can click ¡®>¡¯ or ¡®<¡¯ under the label Query to move to the previous
or latter query clauses of the section.
If you want to move to other
section, you can click ¡®>¡¯ or ¡®<¡¯ under the label Section to move
to the previous or latter sections.
You can also click the section title on the left panel to move to the
section.
Convert Statistical Analysis Plan
Template in Word document to SapMaker XML Templates Document ¡¡
You will prepare your own statistical analysis plan template or other templates in a Word document. SapMaker provides a feature for you to convert this word document template to XML template that can be used by the software. In this chapter we explain to you how to use this feature to create you own XML template document by reading from Word documents.
Word Document for SAP Template¡¡
You will prepare
a Word document for statistical analysis plan template or other templates. The Word document will have any number
of sections. A section will have
three parts of (1) title, (2) instructions, and (3) sample paragraphs. A section should have one and
only one Title, but it can have many or none instructions or sample paragraphs.
The font format
of a Title should be in ¡°Heading¡± format. A section is identified by Title in such a way:
if the title of one section has ¡°Heading 1¡± font format, while another section
after this section has it¡¯s Title in ¡°Heading 2¡± font format, the second
section with ¡°Heading 2¡± font format is a sub-section of the one with ¡°Heading
1¡± font format. Following figures
show a template section in word document and in converted XML document.
Convert Word Document Template to
XML Template¡¡
To start using SapMaker to read
and convert Word template to XML template, you will select Edit Convert Word Template to XML Template.
You will a popup open window for reading and converting Word document to a XML
template (as following figure).
When the converting is completed, you will see another popup open window
for saving the converted XML template to a file. Following figures show these steps.
