SIR Case Study
MNYR Database
Presented at
SIR International
Users’ Conference
Columbia University
New York, N.Y.
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
May 2005
©Tom Shriver, DataVisor
& Columbia U, 2005
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Topics for the Case Study
I.
II.
III.
IV.
Photo: Greg Neils,
Columbia U
SIR Case Study: MNYR
Overview of the MNYR Database
What makes SIR/MNYR “Sophisticated”?
Factors Contributing to Sophisticated Applications
Features Implemented in MNYR, explained with:
a. The original need
b. The thought process and logic of design
c. The tools used to implement the feature
d. How it is used by the MNYR Staff
©2005 Tom Shriver, Columbia U, DataVisor
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Metropolitan New York Registry
of Breast and Ovarian Cancer Families
 Funded
by the National Cancer Institute at the
Mailman School of Public Health, Columbia U.
 Largest
family breast cancer database in the world.
 Participates
in the
Cooperative Family Registry of Breast & Colon Cancer
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SIR Case Study: MNYR
12 Sites (6 Breast, 6 Colon)
International (USA, Canada, Australia)
Data from all sites merged in the central CFR registry
Data made available to Cancer Researchers world-wide
©2005 Tom Shriver, Columbia U, DataVisor
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MNYR Data Collection:
Participant Recruitment

Participants recruited at 7 New York Sites

“Clinic Based” recruitment begins with a known cancer
subject and the family is invited to participate

Family History given by “family rep” for cancer, age &
sex info about each member (3-4 generations)

Some Family Members are asked to Participate Fully
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SIR Case Study: MNYR
Answer 3-5 questionnaires
Provide Blood Samples
Grant Access to Medical Records
©2005 Tom Shriver, Columbia U, DataVisor
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MNYR Data Collection:
Detailed Data

Full Participants Provide
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Consent for use of data and access to medical info
Epidemiological Questionnaire
Diet Questionnaire
Blood Sample for DNA & Genetic Testing; Cryopreserved
Kept in Campus Lab, Data kept separately but Interfaced to MNYR
Breast & Ovarian Cancer Affected Participants


Cancer Surgery History & Treatment Questionnaire
We request materials from Hospital
o Hospital’s Pathology Report on the case
o Sample of Tumor Tissue for confirmation & future research
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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MNYR (brief) History
 Six
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Original New York Sites
Joined forces, created single registry at Columbia
Currently new recruitment at only two sites
 Original
MNYR Registry was SQLServer with
MS-Access front-end
 Complexity
 DCC
created problems, DCC was consulted
Recommended SIR and DataVisor in 2003
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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MNYR Data in a Nutshell
 Family
History Info about many People & Families
 Questionnaire
 Biospecimen
 Genetic
Data
Samples and Associated Data
Test Results
 Detailed
Pathology Info on Tumor Specimens
 Tracking
Data to Assure Collection
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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Metropolitan New York Registry of
Breast & Ovarian Cancer Families
Database Structure
Ind Summary
Genetic Test
Family
Indiv Fam Hx
Consent
Epi / Followup
Family Summary
Epi Ov Surg
Treatment
Pregnancies
Vital Status
Diet
BioSp Dispatch
Biospecimens
Blood
Buccal
LCL
DNA
48 hr Qnr
Tracking
Detailed Results
Epi Breast Surg
Biospecimen Data maintained in
separate database (in Lab)
Nutrient Summ
Specimen
Registry Slides
Memos
Tumors
Slide Box
Reported Tumors
Path Report
Path Review
Breast Surgery
Reference Data Tables
Hospitals
SIR Case Study: MNYR
MNYR Staff
Ovarian Path
Invasive Details
Mutation Names
©2005 Tom Shriver, Columbia U, DataVisor
CFR Data Dict
CFR Errors
Non Invasive
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Why Consider MNYR
“Sophisticated”?
 An

“Sensitive” Application
Database & Application mirror the MNYR world
 Takes Advantage
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of the “State of the Art”
Database Tools
Application Development Tools
Combines Various Tools into Powerful Machine
 MNYR
Database Manages nearly all related
computerized functions from a single central
location (the MNYR database)
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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How to Create a Sophisticated Application:
Application Developer Imperatives
 Study
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& Play
Review Current Tools
Stay abreast of developing technology
Take the time to Play with the tools
 Integrate
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Build tools you can use in other contexts
Time invested today pays off tomorrow
 Use
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SIR Case Study: MNYR
the Future into Everyday Operations
the New Tools
They were designed as an improvement – take a chance
©2005 Tom Shriver, Columbia U, DataVisor
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How to Create a Sophisticated Application
Client Factors
 Listen
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Understand what they do & how they do it
The Database & Application should model their world
It has to make sense to the user
 Never
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SIR Case Study: MNYR
to the Client
Say “No”
“It’s a computer, it can do anything.”
©2005 Tom Shriver, Columbia U, DataVisor
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Details of Some Features
that Make MNYR Sophisticated
 For
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SIR Case Study: MNYR
various features I’ll try to provide:
The original need
The thought process in developing the feature
How the guidelines I’ve just provided impacted it
The tools used to implement the feature
©2005 Tom Shriver, Columbia U, DataVisor
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A Walk Through to Give the
Overall Sense of MNYR
 A Quick
walk through showing how the database
is used on a daily basis.
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SIR Case Study: MNYR
As we go, I’ll point out the features we
will discuss in detail
©2005 Tom Shriver, Columbia U, DataVisor
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Controlling Color & Fonts on the
Main SIR Window
 Impetus

The first comment in my first demo of MNYR was:
“My son does databases and his are always colorful”.
 Thought
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Process:
Tony had said that the main window did HTML
I had used it to center things on the screen
I figured it probably knew about colors & fonts
 A few
SIR Case Study: MNYR
for Coloring Screen:
minutes of Study ended with a colored screen
©2005 Tom Shriver, Columbia U, DataVisor
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Coloring the Main Window &
Writing to it with Various Fonts
 Main

SIR Window knows some HTML
A few PQL GUI controls like TEXT object do also
 Set
up HTML tags with:
call sysproc.tools.htmlcode
 Use
WINDOW OUTPUT command in PQL, e.g.
window output '<body bgcolor="#FFF000">' html
{Example Available}
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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The Letter Writing Facility
The Rationale
 Impetus
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SIR Case Study: MNYR
for developing a Letter Writing facility
The staff each writing their own letters to participants;
- Need for “templates”
Letters stored locally, i.e. Invisible to others on Staff;
- Need for central accessibility
No tracking of communications in database;
- Need for a record of letters written & their subject
©2005 Tom Shriver, Columbia U, DataVisor
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Letter Writing Facility:
Thinking through the Problem
 Initially Worried About
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SIR Case Study: MNYR
Personal Ignorance of MS-Word Templates
How to “know” what kind of letter was being written
©2005 Tom Shriver, Columbia U, DataVisor
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Letter Writing Facility
Solutions
 Don’t

Use True Templates; Just copy a Base File
A PQL File Copy Subroutine;
developed years ago & used all the time
 Encode
Type of Letter in name of letter that
matches codes of tracking “action type”, e.g.
request_for_consent_02.doc
 Create
a “tracking” record when letter is written,
automatically supplying several codes
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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Letter Writing Facility
Tools Used
 PQL DISPLAY OPENBOX
 PQL Subroutine
 Many
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for Copy Procedure
PQL string functions:
To extract letter type code
To construct new letter name including:
Archive Folder, Pt_ID & Date
 PQL Subprocedure
SIR Case Study: MNYR
to pick template file
©2005 Tom Shriver, Columbia U, DataVisor
to create new Tracking Record
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Click on Picture to Set Data Values
 Impetus:
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Physicians fill out a form with checks on “Bulls-Eye”
There are 60 checkable items; internally Yes/No Vars
Data Entry Personnel didn’t want to enter into 60 fields
 Tools
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that make it Possible
PQL IMAGE control returns coordinates when clicked on
PQL Arrays to keep track of:
o Clickable regions (coordinates of diagonally opposite corners)
o Where to put check marks
o Current Yes/No settings of variables (related to regions/vars)
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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Click on Picture to Set Data Values
Practical Problems (1)
 How

to get coordinates of clickable regions
PQL Dialog with Picture
o Click top left of area & remember X1,Y1
o Click bottom right, remember X2,Y2 & write out points
 How

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to detect what user has clicked
Create IF-THEN-ELSE block with PQL program that
uses the coordinates written in above procedure
Use created if-then-else in message processing of dialog
{Examples Available}
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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Click on Picture to Set Data Values
Practical Problems (2)
 How
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Checks and Non-Checks (blank) are bitmap pictures
In GUI dialog use IMAGEs for check mark
o
o
o
o
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to Make Check Marks Appear & Disappear
Variation on previous PQL to identify location of Checkmark
A loop in GUI dialog to define IMAGEs
A loop in dialog INITIAL block to set initial state
Created IF-THEN-ELSE in MESSAGE displays check or blank
bitmap depending on current state
NOTE: GUI controls on top of each other recognize
“top” control – last one placed.
o Checks should not be on “Clickable Region”
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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Remote Control of Database:
A SIR & PQL Based “Batch Queue”
 Impetus
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for Developing Batch System
DBA is 800 miles from site
Connection via VPN & Master is “SLooooW”
o All “data” processed in PQL, Utilities has to travel back and
forth over network/internet
 Thought
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Process
Copying small files (e.g. PQL programs) is Fast
Running on the Powerful SIR server is FAST!
Question:
o How can I get the server to run my PQL?
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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Remote Control of Database: “Batch Queue”
Available Tools in SIR
 PQL
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& DBMS Command Language Flexibility
SIRBATCH.EXE for non-interactive/non-visual operations
Commands to CONNECT and DISCONNECT databases
Commands to manage SCHEMA
Commands to manage PROCFILE (PROCEDURE)
Commands to run SIR Utilities (e.g. unload, reload)
PQL commands to re-compile executable routines
PQL commands to execute other PQL: EXECUTE DBMS
 Possibility:
SIR Case Study: MNYR
One PQL Program to Control Everything
©2005 Tom Shriver, Columbia U, DataVisor
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Remote Control of Database: “Batch Queue”
System Design
 Create
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a PQL Program that waits for Work
An infinite LOOP that checks every couple of seconds
Looks for a file submitted in one folder with suffix: .PQL
When PQL file is found, main program does:
compute outf=replace(filename,’.PQL’,’.OUT’,1,0,0)
EXECUTE DBMS [‘set output “’+outf+’”’]
EXECUTE DBMS [‘include file “’+filename+’”’]
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SIR Case Study: MNYR
When submitted PQL program ends:
File Copy subroutine moves PQL to “DONE” folder
©2005 Tom Shriver, Columbia U, DataVisor
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Remote Control of Database: “Batch Queue”
Usage Considerations
 Main
PQL inherits “environment” from some
command sets
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ATTRIBUTES & GLOBALS
Default Settings, e.g. PRINT BACK
Cached Members
 User’s
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SIR Case Study: MNYR
PQL must be careful to
Properly initialize environment
Connect & Disconnect Database
Be aware of Master status for Updates
©2005 Tom Shriver, Columbia U, DataVisor
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Remote Control of Database: “Batch Queue”
Actual Usage Practices at MNYR
 Download
modified procedures to ProcFile
 Recompile
System or Selected Routines
 Nightly

Backups Run on Batch System
A Scheduled Task copies MNYR_BackUp.PQL to the Folder
 For
the Future:
End-User Submissions from Interactive Sessions
SIR Case Study: MNYR
©2005 Tom Shriver, Columbia U, DataVisor
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