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Popula'ng the i2b2 Database With
Heterogeneous EMR Data: A Seman'c
Network Approach
Sebas&an Matea, Thomas Bürklea,
Felix Köpckea, Bernhard Breilb, Bernd
Wullichc, Mar&n Dugasb, Hans-‐Ulrich
Prokoscha,d, Thomas Ganslandtd
a Chair of Medical Informa1cs,
University Erlangen-‐Nuremberg, Erlangen,
Germany b Ins1tute of Medical
Informa1cs, University of Münster,
Münster, Germany c Department
of Urology, Erlangen University
Hospital, Erlangen, Germany d Center
for Medical Informa1on and
Communica1on, Erlangen University Hospital,
Erlangen, Germany
28.09.2011, Oslo
MIE2011 full paper
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
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Introduc'on: Replacing Double Data Entry
With “Single Source” – The DPKK
Example
PSA:
EMR DPKK Partner A
PSA:
EMR DPKK Partner B
Original DPKK database
DPKK Researcher
NEW! i2b2 System
DPKK Researcher
NEW! ETL
PSA:
EMR DPKK Partner A
PSA:
EMR DPKK Partner B
EMR database EMR database
Erlangen Münster
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
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EMR in Münster: AGFA ORBIS EMR
in Erlangen: Siemens Soarian
Problem 1: How to align and
merge data from independent sources?
n Different data structures (different
vendors) n Similar informa&on (full
prostate cancer documenta&on in
EMR)
Introduc'on: Developing the Data
Integra'on Approach
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
Erlangen as an example: >
42,000 data elements (including data
element versioning)
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Problem 2: How to efficiently
access and process the huge
piles of data elements?
Introduc'on: Developing the Data
Integra'on Approach
Data:
n Structured n Uncoded
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
5
Oracle SQL Ser
ver MySQL
COGNOS
Talend JDBC ETL SQL SQ
L SQL
Tools / Data Access Layer
Data / Storage Layer
Ontology / Knowledge Base Layer
Methods: The “Ontology Layer”
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
6
Gleason3
PSA
Target Ontology Target Dataset
Gleason1 PSA:
PSA_value
Source Ontology Source System
Gleason2
n Express the target dataset with
a target ontology. n Express the
source system(s) with one or
more source ontologies. n Create a
mapping ontology to connect concepts
from the target ontology to
concepts from the source ontology.
n Some concepts can be mapped
directly, others require transforma&ons
and/or data filtering, which can
be expressed with intermediate nodes.
Methods: Approach Overview
Mapping Ontology
ADD
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
Target Ontology Mapping Ontology
Source Ontology
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Target
n To allow complex data
transforma&ons, nodes can be
cascaded into „expression trees“. n
OWL-‐to-‐SQL transla&on: For each
mapping node, an SQL statement,
which performs the
opera&on expressed by the node,
can be constructed automa&cally .
A
B
C
D
E
t=1 t=2
t=4 t=3
IF
GREATER
ADD SUBTR
processing order
Methods: Approach Overview
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
Target Ontology Mapping Ontology
Source Ontology
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Target
A
B
E
t=1 t=2
t=4 IF
GREATER
t=3 SUBTR
Methods: OWL to SQL Transla'on
ADD C
D
INSERT INTO TEMPTABLE(E, A, V) SELECT OP1.E, „Sum…“, OP1.V +
OP2.V FROM (SELECT E, A, V FROM …) OP1 FULL OUTER JOIN (SELECT E,
A, V FROM …) OP2 ON OP1.E = OP2.E WHERE OP1.V IS NOT NULL AND …
INSERT INTO TEMPTABLE(E, A, V) SELECT OP1.E, „Sum…“, OP1.V +
OP2.V FROM (SELECT E, A, V FROM …) OP1 FULL OUTER JOIN (SELECT E,
A, V FROM …) OP2 ON OP1.E = OP2.E WHERE OP1.V IS NOT NULL AND …
How to process nodes
How to access data
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
OntoExport
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OntoEdit QuickMapp i2b2
Gleason3
PSA
Target Ontology
Target Dataset
Gleason1
PSA_value
Source Ontology
Gleason2 PSA:
Source System
Mapping Ontology
ADD
Results: Developed Prototypical Tools
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
10
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
Results: Ontology Mapping for DPKK
Results in the Münster and
Erlangen Mapping
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n Described i2b2 as a target
system in OWL (incl. DPKK
dataset) n Created source ontologies
for both EMRs (Soarian and
ORBIS) n Expressed many types of
Oracle database opera'ons inside the
ontology (as it
was illustrated with the blue
“cloud”)
n Preliminary mapping results for
Erlangen and Münster (from a
total of 166 concepts):
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
12
n Re-‐implementa'on of the current
proof-‐of-‐concept n Client/server
architecture to improve administra&ve
aspects n Integra&on with other
data integra&on tools (e. g.
Talend OpenStudio)
to simplify access to mul'ple
databases
n Expression of complex and abstract
rela'onships between data elements,
e. g. between data elements at
different hierarchy levels
n Allow certain calcula&ons between
data elements from mul&ple forms
or different source systems (=>
handling of temporal aspects)
n Strong desire to export EMR
data to other systems besides
i2b2: allow descrip&on of
arbitrary target systems and database
models
Discussion Limita'ons and How to
Tackle Them: TODOs
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
13
n Abstrac'on of data records and
database opera&ons to single
ontology nodes n Simplifies data
iden&fica&on, extrac&on and
transforma&on from source
systems (e.g. EMRs) n Allows re-‐use
of created “ETL knowledge” (compared
to SQL code) n OWL format
enables easy linkage to medical
ontologies (SNOMED, NCIt, …)
n Adds the missing “easy-‐to-‐use” ETL
part to the i2b2 n
Comprehensive solu&on covers
1. Access to heterogeneous data
2. “Future-‐proof” (ontology-‐based) data
processing 3. Interac&ve
transla&onal querying of clinical
data (i2b2)
=> Step forward in implementing “secondary use / single
source”
Discussion: Benefits
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
Thank you for your aden'on!
Sebas1an Mate would like to thank
the “Arbeitskreis SoKware-‐Qualität und
–Fortbildung e. V.” (ASQF) and
the commission of computer
science of the University of
Erlangen who have awarded this
work with the 500€ ASQF diploma
prize. Thank you!
-
Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
Backup slides
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Sebas&an Mate // Chair Of
Medical Informa&cs // University
of Erlangen-‐Nuremberg [MIE2011]
