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MY ATTEMPT TO RID THE CLINICAL WORLD OF EXCEL

MIKE MOLTER

DIRECTOR OF STATISTICAL PROGRAMMING AND

TECHNOLOGY

WRIGHT AVE

OCTOBER 27, 2016

Agenda

• Introduction to Study Designer

• Development tools

• Database

• Interface

• Brief demo (if time)

• Future of Study Designer

Technologies in Use:

• Neo4j

• Cypher

• HTML, Javascript, CSS

• Python

• Jinja2

• Google App Engine

Technologies NOT in Use:

• SAS

• Excel

What is Study Designer?

Study Designer is a web-based tool used for entering metadata (i.e. programming specs and define.xml) for a study

Signature features

• Database of CDISC data models, implementation guides, and study metadata

• Web interface that guides the user through the development of metadata by way of a study design sequence

Database

Database

Sam 10/27/16

TEMP 99.5 F

NAME DATE TEST RESULT

UNIT

Sam 10/27/16

HEIGHT

73 in

Sam 10/27/16

WEIGHT

220 lb

Sam 10/27/16

SYSBP 118 mmHg

Sam 10/27/16

DIABP 75 mmHg

Tony 10/24/16

TEMP 99.1 F

Tony 10/24/16

HEIGHT

70 IN

Tony 10/24/16

DIABP 73 mmHg

Tony 10/24/16

SYSBP 122 mmHg

Observations(records)

Properties (variables or fields)

Keys

Table

Traditional rectangular SQL database

Name :SamDate :10/27/16Test : TEMPResult : 99.5Unit : F

node Properties

Observation (node)

:VSnode label

Neo4j – Graph Database

:VS

:VS

:VS

:VS

:VS

:VS:VS

:VS

:VS:LB

:LB

:LB

:LB

:LB

:LB:LB

:LB

FirstName : TomLastName: HanksBorn: 1956

: ACTOR

[:ACTEDIN]

[:DIRECTED]

Neo4j – Graph Database

[:ACTEDIN]

Cypher – the query language of Neo4j

MATCH (tom:Person {name: "Tom Hanks"})-

[:ACTED_IN]->

(tomHanksMovies:Movie)

RETURN tom, tomHanksMovies

alternatively,RETURN tom.born, tomHanksMovies.tagline

see demo

CDISC standards in Neo4j<ItemGroupDef

Name=“AE”

other attributes>

<ItemRef ItemOID=“IT.STUDYID” Order=“1” Mandatory=“Yes”/>

<ItemRef ItemOID=“IT.AESEV” Order=“15” Mandatory=“Yes”/>

One ItemRef for each variable in the dataset

</ItemGroupDef>

<ItemDef

Name=“STUDYID”

OID=“IT.STUDYID”

STUDYID attributes>

</ItemDef>

<ItemDef

Name=“STUDYID”

OID=“IT.AESEV”

AESEV attributes>

<CodeListRef CodeListOID=“CT.SEV”>

</ItemDef>

<CodeList

OID=“CT.SEV”

<EnumeratedItem CodedValue=“MILD”>

More EnumeratedItem elements

</CodeList>

Name : AEClass : EventsPurpose:Tabulation

: ItemGroupDef

Order: 15Mandatory: Yes

: ContainsItem

CDISC standards in Neo4j


InstantiatesModel

Using Python to interact with Neo4j

from py2neo import Graph

graph = Graph()

defaults to localhost:7474

results = graph.cypher.execute(‘match (:IG)-[]->

(igd:ItemGroupDef) return igd.name,igd.class,igd.purpose’)

name class purpose

CM Interventions Tabulation

VS Findings Tabulation

AE Events Tabulation

results (a Python object called a RecordList)

Google App Engine

• A cloud computing platform for developing

and hosting web applications in Google-

managed data centers

• When downloaded and installed, a local

development server is created and listens

on port 8080.

• Comes with a Python package that allows

application developers to…

• associate web form URLs with code to

be executed

• capture and process web form input

from users

app =

webapp2.WSGIApplication([

(‘URL1’,URL1_code_class),

(‘URL2’,URL2_code_class),

(‘/’,FrontPage)

], debug=True)

class FrontPage:

def get(self):

<pre-processing code>

<code to render web form>

see demo

class FrontPage:

def get(self):

allstudies = <Cypher query to return all current

studies in the database>

<code to render web form>

self.render(webform.html, studylist=allstudies)

Jinja 2

• Templating language used for

generating dynamic HTML

• HTML generated by what is found in

the database

• Think of the SAS macro language

• Supports …

• reference of parameters passed in

from application ({{x}})

• conditional logic ({% if condition

%})

• iterative logic ({% for x in list-

name %}

HTML for dropdowns

<select name=“mydropdown”>

<option>Choose an Option</option>

<option>choice1</option>



</select>

self.render(webform.html,studylist=allstudies)


<option>Choose a study</option>

{% for x in studylist %}

<option>{{x[0]}}</option>

{% endfor %}

</select>

Capturing web form choices in Python


<option>Choose a study</option>

{% for x in studylist %}

<option>{{x[0]}}</option>

{% endfor %}

</select>

HTML World…

Back in Python Land…

chosenstudy=self.get.request(“mydropdown”)

self.get.request returns the user choice from the dropdown

USER:Enters application

URL into web browser

PYTHON:1. Execute code

based on URL (e.g. querying database)

2. Render a web form, passing parameters to build dynamic HTML

USER:1. Populates form

fields2. Clicks Submit

button

PYTHON:1. Execute code

based on URL (e.g. adding to database, querying database)

2. Render a web form, passing parameters to build dynamic HTML

Brief summary of the User input/Code Execution Cycle

In Summary

In order to replace Excel, we need• a database to house standards• a user interface

• collects information from users• interacts with the database

To connect the dots• Python code to touch the database• Python code to pass parameters to dynamic

HTML (Jinja2 templates)• Python code to capture user choices• Google App Engine to pair Python code with

URLs and provide methods for capturing user choices

The Current and Future State of Study Designer

• Custom domains

• Controlled Terminology+extensions

• define.xml

• spec.xml

• standards development

• Trial Design

• Visit Schedules

• Version control

• Dependency tracking

• protocol.xml extraction???

my attempt to rid the clinical world of excel › download › sde › rtp2016 › ... · my...

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