Terminology for a Centralized Biobank Information
Management System
Mary-Beth M. Joshi, MPH2, Aenoch J. Lynn1, Anita C. Walden3, and Helena J. Ellis1
References
1
Duke Biobank and Duke Translational Medicine Institute, Duke University, Durham, NC
2 Department of Surgery, Duke University, Durham, NC
3 Duke Translational Medicine Institute, Duke University, Durham, NC
Organization & Leadership
Oversight
Committee
Abstract
Method
The Duke Biobank
has
selected
LabVantage to be the enterprise-wide
biobanking
Information
Management
System to unify clinical research
biobanking
informatics.
Biobanking
terminology across Duke developed in
silos with no coordination and lacks
semantic interoperability. In order to
promote interoperability and to decrease
the probability of errors with the central
development
and
management
of
biobanks within LabVantage, The Duke
Biobank has initiated a project to develop
a standard terminology for biobanking,
sample processing, and assay result
metadata.
To facilitate interoperability across the enterprise Duke Biobank has invited a group of stakeholders
across the organization to participate in the development of the common terminology. The common
terminology will consist of data elements that include the following (Figure 1):
•
•
•
•
•
data element name
data element definition
permissible values and
definitions for permissible values
Reference - NCI and ISBER as authoritative sources/primary sources for terminology
There exists no standard terminology for
clinical or translational biobanking. The
deployment of an enterprise-wide biobank
information management system would
benefit from a standard terminology that
would be used across all biobanks and
research projects. The Duke Biobank has
begun the development of a standard
terminology which will be used in the
implementation of LabVantage for the
enterprise-wide biobanking platform.
Informatics Leads
Committee
Group 1
Group 2
Group 3
Group 4
Group 5
Sample
Collection &
Storage
Non-Chemical
Handling,
Tracking
Chemical
Handling &
Derivatives
Complex Data
Clinical Data
Working Groups
Stakeholders are encouraged to identify terminology from existing standards, systems, initiatives and
publications then come to a consensus on a common name and definition.
Figure 2. Project Organization Structure
2. Mead, C.N. (2006) ‘Data
interchange standards in
healthcare IT –
computable semantic
interoperability: Now
possible but still difficult,
do we really need a
better mousetrap?’,J.
Healthc. Inf. Manag., Vol.
20, No. 1, pp.71–78.
Results
DE ID
#
Category
Data Element Name
Background
The lack of standards leads to ambiguous
exchange and hinders understanding and
interpretation of information within clinical
research 1,2. Implementing a consensus
developed semantic set of data elements
into the biobank will hopefully improve
data, management, exchange and reuse
across the organization. A methodology
based on previous data standards project
is being followed for creating therapeutic
or domain specific data elements3.
Facilitators
Committee
A Facilitator and
Informatics Lead is
Part of Each Working
Group
1. Ewen, E.F., Zhao, L.,
Kolm, P., Jurkovitz, C.,
Fidan, D., White, H.D.,
Gallo, R. and Weintraub,
W.S. (2009) ‘Determining
the in-hospital cost of
bleeding in patients
undergoing
percutaneous coronary
intervention’, J. Interv.
Cardiol., Vol. 22, No. 3,
pp.266–273.
1
2
SAMPLE COLLECTION
ACQUISITION PROCEDURE
INSTITUTIONAL
APPROVALS IRB PROTOCOL STATUS
3 ACQUISITION SPECIMEN COLLECTION TIME
4
SAMPLE COLLECTION
ACQUISITION PROCEDURE
Data Element Definition
Permissible Values
Mechanism describing how a sample or
a single unit from one specimen was
obtained.
the condition or state of the research
plan submitted to an IRB for review.
surgical resection, venipuncture,
autopsy, fine needle aspiration, organ
procurement, etc.
The value that represents the time
which a specimen is collected.
BRISQ
CaDSR; Duke IRB;
ACTIVE, CLOSED, SUSPENDED, PENDING C25688
An expression of both date and time
that an event has happened or will
happen. [Explanatory comment: The
preferred exchange format is DateTime;
See permissible values & definitions of
DATE TIME]
CTEP; CaDSR
Mechanism describing how a sample or surgical resection, venipuncture,
a single unit from one specimen was autopsy, fine needle aspiration, organ
obtained.
procurement, etc.
Figure 1. Sample Draft Biobank Data Elements
Reference
BRISQ
The biobanking domain was divided into 5
categories and each one was assigned to a working
group to identify and develop data elements and
their associated definitions (Figure 2).
• Working Groups consist of 4-6 members drawn
from clinical researchers and biobankers across
Duke that meet weekly or bi-weekly for the last 6
months.
• Facilitators and Informatics Lead provide project
management and technical assistance for working
groups in the development of the content.
• The Oversight Committee provides the
governance, leadership and monitors the overall
project.
Conclusion
Duke will vet the drafted terminology with a broader
set of stakeholders during a public comment periond
before incorporating it into the biobanking system.
3. Nahm, M., Walden, A.,
McCourt, B., Pieper, K.,
Honeycutt, E., Hamilton,
C., ... & Hammond, W.
(2010). Standardising
clinical data elements.
International Journal of
Functional Informatics
and Personalised
Medicine, 3(4), 314-341.
Acknowledgements:
The project described is
funded in part by the
National Center for
Advancing Translational
Sciences (NCATS) a
component of the National
Institutes of Health.
Clinical and Translation
Science Award (CTSA)
grant
For more information
on Duke Biobank
please visit us online:
biobank.duke.edu
A governance and maintenance process will be
developed to ensure the terminology is current and
meets the needs of the enterprise and stakeholders.