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An Open Source Reporting System
for Life Sciences
Magnus Mengelbier
Director
PhUSE 2010
1
Topics
PhUSE 2010
Introduction
Traditional process
Library
Analysis
Reporting
Connections
Summary
2
Tradition
Listings
Source
Derived
Tables
Graphs
Source
Listings
SDTMs
ADaMs
Tables
Graphs
Define
PhUSE 2010
3
Templates and Specifications
Specifications
SAP
Shells
Shells
Data
Sets
Data
Sets
Programs
Templates
Data Sets
Tables
Listings
Define
SAP
PhUSE 2010
4
Templates et al
PhUSE 2010
5
Library
Specifications
Shell
TLGs
Data
Sets
Data
Sets
Programs
Library
Data Sets
Tables
Listings
Define
SAP
PhUSE 2010
6
Organizing Content
Directory Trees
No restriction on the number of
levels
No restriction on naming
conventions
Contexts
Aware of parent directory
Contexts have to be consistent within a directory tree
Directory tree can be your departmental drive or network share
PhUSE 2010
7
Default Defintions
Data Sets
Tables
Listings
Graphs
PhUSE 2010
8
Definitions and Inheritance
Types of definition controlled for each level
Definitions can be inherited from parent to child levels
Report
x
Study
x
x
x
x
x
x
Indication
Project
Global
PhUSE 2010
x
x
STUDYID
AGE
x
FEDFAST
Data Set
AE
Data Set
XY
9
Specifications
Specification
Library
PhUSE 2010
A Specification is just a set of links to content in the Library
All Definitions have to be in the Library
10
A Comparison of Defintions
PhUSE 2010
11
Repository
Data Sets
Tables
Listings
Graphs
Simple Meta-Data Engine
PhUSE 2010
Model – View – Controller (MVC) design pattern
Model – Meta-data
View – Graphical and programming interface
Controller – ”Administrator” of the meta-data
Very primitive and flexible meta-data engine
12
Repository - Definitions
Defintions
Type, e.g Data Set, Table, etc.
Identified by Type and Name
References and associations to other meta-data items
Look-up
Ordered list
Versions
Increment
Construct for a unique reference to variations of the same
item
More than one version is selectable
Future plans include major/minor versions
PhUSE 2010
13
Repository – Data Set
Attribute
Value
Name
CLASS
Label
Class
Sort order
Key sequence
PhUSE 2010
Sequence
Reference
1
NAME
2
SEX
3
AGE
4
HEIGH
5
WEIGHT
Collections
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Repository – Table (1)
PhUSE 2010
15
Repository – Table (2)
Attribute
Value
Name
AGE
Label
Age (years)
Link
DM.AGE
PhUSE 2010
Attribute
Value
Attribute
Value
Name
N
Name
MEAN_SD
Label
N
Label
Mean (SD)
Format
[2]
Template
MEAN (SD)
Decimals
[0]
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Repository – Table (3)
N
MEAN_SD
MEDIAN
MIN-MAX
PhUSE 2010
N
MEAN_SD
MEDIAN
MIN-MAX
MEAN
SD
MIN
MAX
17
Analytics
Meta-data driven
Standard statistics
Statistics “meta-data” interface
Requires an analytics engine (SAS/R/S-Plus)
Code library
Code generators
PhUSE 2010
18
Analytics
Library
Specifications
Code Generator
Code
TLGs
Data
Sets
Data Sets
Data Sets
Tables
Listings
Define
Non-standard
Programs
SAP
PhUSE 2010
N
MEAN_SD
MEAN
MEDIAN
SD
MIN-MAX
MIN
MAX
19
Reporting By Elements
Reporting
Analytics
Library
PhUSE 2010
Data
Input Data Set
Select Parameter(s)
Subset
Summaries & Statistics
Compute
Append
Format
Render Table
Report structure
Format
Sort & Order
Render
20
Reporting by Elements
Analysis Data Sets
ADAE
ADLB
ADVS
…
STAE
STLB
STVS
…
Statistics Data Sets
STSUBSET
Outputs
PhUSE 2010
21
Analytics Repository
Code Generator
Code Library
Non-standard
Programs
PK Analytics
Analytics Repository
PhUSE 2010
22
Reporting Results
Code Generator
Code Library
Non-standard
Programs
PK Analytics
Analytics Repository
Tables
PhUSE 2010
Listings
Graphs
Portals
Submission files
23
Other Outputs
Data Sets
Tables
Listings
Graphs
Simple Meta-Data Engine
PhUSE 2010
Model – View – Controller (MVC) design pattern
Model – Meta-data
View – Graphical and programming interface
Controller – ”Administrator” of the meta-data
Very primitive and flexible meta-data engine
Adding an output starts with a Model, View and Controller(s)
24
Tracking and Status
Library
Code
TLGs
Data
Sets
Specifications
Code Generator
Data Sets
Non-standard
Programs
Data Sets
Tables
Listings
Define
Common Work Flow
Track status
Track and enforce dependencies
PhUSE 2010
25
Organization Revisited
Directory Trees
No restriction on the number of
levels
No restriction on naming
conventions
Contexts
Aware of parent directory
Contexts have to be consistent within a directory tree
Directory tree can be your departmental drive or network share
PhUSE 2010
26
Connections
Library
Specifications
Code Generator
Code
TLGs
Data
Sets
Data Sets
Non-standard
Programs
Data Sets
Tables
Listings
Define
Common Work Flow
Network
Subversion
SAS Server
SDD *
R
* SAS Drug Development
PhUSE 2010
27
Web Services
Library
Specifications
Code Generator
Code
TLGs
Data
Sets
Data Sets
Non-standard
Programs
Data Sets
Tables
Listings
Define
Common Work Flow
PC SAS
S-Plus / R
SAS Server
SDD *
Anything really
* SAS Drug Development
PhUSE 2010
28
Conclusion
Data Sets
Tables
Listings
Graphs
Simple Meta-Data Engine
PhUSE 2010
Model – View – Controller (MVC) design pattern
Model – Meta-data
View – Graphical and programming interface
Controller – ”Administrator” of the meta-data
Very primitive and flexible meta-data engine
Adding an output starts with a Model, View and Controller(s)
29
Conclusion
Library
Specifications
Code Generator
Code
TLGs
Data
Sets
Data Sets
Non-standard
Programs
Data Sets
Tables
Listings
Define
Common Work Flow
Network
Subversion
SAS
SDD *
S-Plus / R
* SAS Drug Development
PhUSE 2010
30
Questions & Comments
PhUSE 2010
Introduction
Traditional process
Library
Analysis
Reporting
Connections
Summary
Magnus Mengelbier
Director
Limelogic Ltd
[email protected]
+44 208 144 5701
31
THE
PhUSE 2010
END
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