SIR Case Study: MNYR ©2005 Tom Shriver, Columbia U, DataVisor 1 SIR Case Study MNYR Database Presented at SIR International Users’ Conference Columbia.

SIR Case Study: MNYR ©2005 Tom Shriver, Columbia U, DataVisor 1

SIR Case StudyMNYR Database

Presented at

SIR InternationalUsers’ Conference

Columbia UniversityNew York, N.Y.

May 2005©Tom Shriver, DataVisor

& Columbia U, 2005


Topics for the Case Study

I. Overview of the MNYR Database

II. What makes SIR/MNYR “Sophisticated”?

III. Factors Contributing to Sophisticated Applications

IV. 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

Photo: Greg Neils, Columbia U


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 theCooperative Family Registry of Breast & Colon Cancer

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


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 Answer 3-5 questionnaires Provide Blood Samples Grant Access to Medical Records


MNYR Data Collection: Detailed Data

Full Participants Provide 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


MNYR (brief) History

Six 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 created problems, DCC was consulted

DCC Recommended SIR and DataVisor in 2003


MNYR Data in a Nutshell

Family History Info about many People & Families

Questionnaire Data

Biospecimen Samples and Associated Data

Genetic Test Results

Detailed Pathology Info on Tumor Specimens

Tracking Data to Assure Collection


Metropolitan New York Registry of Breast & Ovarian Cancer Families

Database Structure

Biospecimen Data maintained in separate database (in Lab)

Non Invasive

DNA LCL

Buccal

Family

Indiv Fam Hx

Tumors

Reported Tumors

Consent

Epi / Followup

Treatment

Diet

Specimen

Registry Slides

Path Report

Blood

Biospecimens

BioSp Dispatch

Path Review

Genetic Test

Detailed Results

Invasive Details

Breast Surgery Ovarian Path

Epi Breast Surg

Vital Status

Hospitals

MNYR Staff

Mutation Names

Tracking

Memos

Reference Data Tables

Epi Ov Surg

Pregnancies

Ind Summary

Family Summary

Nutrient Summ

48 hr Qnr

Slide Box

CFR Data Dict

CFR Errors


Why Consider MNYR “Sophisticated”?

An “Sensitive” Application Database & Application mirror the MNYR world

Takes Advantage 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)


How to Create a Sophisticated Application:Application Developer Imperatives

Study & Play Review Current Tools Stay abreast of developing technology Take the time to Play with the tools

Integrate the Future into Everyday Operations Build tools you can use in other contexts Time invested today pays off tomorrow

Use the New Tools They were designed as an improvement – take a

chance


How to Create a Sophisticated ApplicationClient Factors

Listen to the Client Understand what they do & how they do it The Database & Application should model their world It has to make sense to the user

Never Say “No” “It’s a computer, it can do anything.”


Details of Some Features that Make MNYR Sophisticated

For 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


A Walk Through to Give the Overall Sense of MNYR

A Quick walk through showing how the database is used on a daily basis.

As we go, I’ll point out the features we will discuss in detail


Controlling Color & Fonts on the Main SIR Window

Impetus for Coloring Screen: The first comment in my first demo of MNYR was:

“My son does databases and his are always colorful”.

Thought 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 minutes of Study ended with a colored screen


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}


The Letter Writing FacilityThe Rationale

Impetus 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


Letter Writing Facility:Thinking through the Problem

Initially Worried About Personal Ignorance of MS-Word Templates How to “know” what kind of letter was being written


Letter Writing FacilitySolutions

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


Letter Writing FacilityTools Used

PQL DISPLAY OPENBOX to pick template file

PQL Subroutine for Copy Procedure

Many PQL string functions: To extract letter type code To construct new letter name including:

Archive Folder, Pt_ID & Date

PQL Subprocedure to create new Tracking Record


Click on Picture to Set Data Values

Impetus: 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 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)


Click on Picture to Set Data ValuesPractical 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 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}


Click on Picture to Set Data ValuesPractical Problems (2)

How to Make Check Marks Appear & Disappear Checks and Non-Checks (blank) are bitmap pictures In GUI dialog use IMAGEs for check mark

o Variation on previous PQL to identify location of Checkmark

o A loop in GUI dialog to define IMAGEs

o A loop in dialog INITIAL block to set initial state

o 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”


Remote Control of Database:A SIR & PQL Based “Batch Queue”

Impetus 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 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?


Remote Control of Database: “Batch Queue” Available Tools in SIR

PQL & 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: One PQL Program to Control Everything


Remote Control of Database: “Batch Queue” System Design

Create 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+’”’]

When submitted PQL program ends:File Copy subroutine moves PQL to “DONE” folder


Remote Control of Database: “Batch Queue” Usage Considerations

Main PQL inherits “environment” from some command sets

ATTRIBUTES & GLOBALS Default Settings, e.g. PRINT BACK

Cached Members

User’s PQL must be careful to Properly initialize environment Connect & Disconnect Database Be aware of Master status for Updates


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 1 SIR Case Study MNYR Database Presented at SIR International Users’ Conference Columbia.

Documents

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columbia u slide

datavisor columbia u

mnyr u breast ovarian

sir case study mnyr

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mnyr brief history u

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