Download Presentation - IMOS Consulting

farmpaintlickInternet και Εφαρμογές Web

21 Οκτ 2013 (πριν από 4 χρόνια και 18 μέρες)

91 εμφανίσεις

1

© CDISC 2012


Presented by

Kerstin Forsberg, R&D, AstraZeneca

Frederik Malfait, IMOS Consulting and Hoffmann
-
La Roche

2

Semantic Models for CDISC Based
Standards and Metadata Management

© CDISC 2012


Key Message


Things converge to create new and unique
opportunities.


The coverage and maturity of existing CDISC standards.


The establishment of these standards within the
industry.


The use of these standards as a foundation for metadata
driven systems.


The upcoming role of semantic web standards and
linked data principles.

3

© CDISC 2012


Two real world use of semantic web
standards and linked data principles

4

© CDISC 2012


Today’s Situation



Not if and when, but how
” to best adopt CDISC
based data standards is becoming the leading
question.


We see a variety of CDISC standards at different
levels of maturity,
not linked

together and
published in
different formats
.


Sponsors are faced with
challenges on all levels:
architecture, process, and application
.

5

© CDISC 2012


An Emerging Insight


The CDISC standards is all about the meaning of
what is studied in the biological and clinical reality
(often referred to as concepts).


How these concepts are represented as data
elements from protocol to submission, and beyond.


We are dealing with semantics and metadata for
biomedical and clinical research knowledge and
data.


“Put semantic into the semantic”

Use semantic web standards

and linked data principles.



6

© CDISC 2012


RDF Triples


Resource Description Framework (RDF)

A general model of how any piece of data, and
representations of knowledge, can be expressed
as so called triples.


7

subject

predicate

Stockholm

place

Stockholm

Sweden

Stockholm

Port cities in Sweden

Stockholm

“+46
-
8”

object (or value)

type

capital

subject

areaCode

“http://en.wikipedia.org/wiki/Stockholm”

primaryTopic

Stockholm

© CDISC 2012


RDF Triples


Triples can be aggregated into graphs with subject
and objects as nodes, and predicates as arcs.


8

City

Sweden

Stockholm

Port cities in Sweden

“+46
-
8”

type

capital

subject

areaCode

“http://en.wikipedia.org/wiki/Stockholm”

primaryTopic

© CDISC 2012


RDF Triples


Graphs of triples can be extended across different
sources and for different purpose.


9

City

Sweden

Stockholm

Port cities in Sweden

“+46
-
8”

type

capital

subject

areaCode

Country

type

Gothenburg

subject

CDISC

CDISC

Interchange

EU 2012

“http://en.wikipedia.org/wiki/Stockholm”

primaryTopic

© CDISC 2012


RDF Triples


RDF Schema and the RDF based Web Ontology
Language (OWL) add a typing mechanism to
classify subjects and objects into hierarchies.

10

City

Sweden

Stockholm

Port cities in Sweden

“+46
-
8”

type

capital

subject

areaCode

Country

type

CDISC

CDISC

Interchange

EU 2012

“http://en.wikipedia.org/wiki/Stockholm”

primaryTopic

Adm.Area

Place

subClass

subClass

Organization

type

Business

Event

type

Event

subClass

Thing

subClass

subClass

Gothenburg

subject

subClass

© CDISC 2012


RDF Triples


Google, Bing (Microsoft) and Yahoo use OWL
publish a joint vocabulary.

11

City

Country

Adm.Area

Place

subClass

subClass

subClass

Organization

Business

Event

Event

subClass

Thing

subClass

subClass

Exempel

http://schema.org/City

© CDISC 2012


RDF Triples


NCI use OWL to publish NCI Thesaurus (the
source for CDISC’s CT:s) in an RDF/XML format.

12

Hemoglobin

Measurement

Hematology

Test



subClass

CDISC Laboratory

Test Name

Terminology


Concept in

Subset

definition

“A quantitative measurement of the amount of

hemoglobin present in a sample.”

NCI Thesaurus

http://ncicb.nci.nih.gov/download/evsportal.jsp

CDISC Laboratory

Test

Terminology


Concept in

Subset

Laboratory

Procedure



Has NCIHD

Parent

© CDISC 2012


Linked Open Data Cloud

13



http://lod
-
cloud.net/

Richard
Cyganiak

and
Anja

Jentzsch

© CDISC 2012


Real world use


Two examples of how sponsors have started to
use semantic web standards and apply linked data
principles.


AstraZeneca:


Integrative Informatics (i2) program establishing the
components to let a Linked Data cloud grow across
AstraZeneca R&D


Roche


Implementing an internally built MDR.


14

© CDISC 2012


AZ R&D Linked Data cloud



http://research.data.astrazeneca.com/id/clinicalstudy/D5890C00003



http://research.vocab.astrazeneca.com/uDisease/DOID/2841




© CDISC 2012


Roche Biomedical MDR

16



CDISC Standards

Metadata

Management

Knowledge
Management

Schema Architecture

Production

Partial / Future

© CDISC 2012


Roche Biomedical MDR

17



Content


External content


SDTM 1.2, SDTMIG 3.1.2


NCI Thesaurus, CDISC Controlled Terminology


Integrated Data Standards, Roche and Genentech


Safety and every Roche TA, ~ 2000 data elements


Data Collection and Data Tabulation


Value level metadata


Lab measurements, Unit conversions, Questionnaires


Looking at metadata for


SDTM Conformance Checking, Biomarker (HGNC), …

© CDISC 2012


Roche Biomedical MDR

18

Information Architecture

Study
Design

Data
Collection

Data
Tabulation

Data
Analysis

Regulatory
Submission

CDISC

Data Standards

Biomedical

Domain Model

Transformation
Models

PRM

CDASH

SDTM

+++ BRIDG +++ SHARE +++ NCI Thesaurus +++ Data Element Concepts +++

ADaM

Define

Roche Global

Data Standards

Study & Project
Level Metadata

Production

Partial

Future

© CDISC 2012


Roche Biomedical MDR

19

System Architecture

Content Management

Metadata Repository

Single Point of Access

Content Publishing

© CDISC 2012


Roche Biomedical MDR

20



Value Proposition


Current


Integrated knowledge, metadata, and data standards
management


System independent information asset


Single point of access


Future


Leverage the SOA interface to create a framework for
integrated metadata driven workflow


Integrate MDR and Component Based Authoring
capabilities (study design, protocol, CSR)

© CDISC 2012


Key Message


We now see all of these things converge to create
new and unique opportunities.


The coverage and maturity of existing CDISC standards.


The establishment of these standards within the industry
at large.


The use of these standards as a foundation for metadata
driven systems.


The upcoming role of semantic web standards and
linked data principles.

21

© CDISC 2012


22



TopBraid Semantic
Modeling Workbench

© CDISC 2012


23



© CDISC 2012


24



© CDISC 2012


25



© CDISC 2012


26



© CDISC 2012


27



© CDISC 2012


28



© CDISC 2012


29



© CDISC 2012


30



© CDISC 2012


31



Roche Global Data
Standards Browser

© CDISC 2012


32



© CDISC 2012


33



© CDISC 2012


34



© CDISC 2012


35



© CDISC 2012


36



© CDISC 2012


37



© CDISC 2012


38



© CDISC 2012


39



© CDISC 2012


40



Publishing and Item
Level Versioning

© CDISC 2012


41



© CDISC 2012


42



© CDISC 2012


43



© CDISC 2012


44



Using Web Services to
Export to…

© CDISC 2012


45



© CDISC 2012


46



Oh well, if you really
want that Excel sheet

© CDISC 2012


47



© CDISC 2012


48



© CDISC 2012


49



© CDISC 2012


50



© CDISC 2012


51



© CDISC 2012


52



© CDISC 2012


53



© CDISC 2012


54



© CDISC 2012


55