May 2010

LIMS Integration Framework

Model
Dr. Partha Mukherjee


LIMS Integration Framework Model | May 2010

Contents
Abstract

Market Trend

Target Audience

Problem statement

Solution

Conclusion

References

About the Author

ABOUT HCL

10

Abstract
Todays LIMS business applications rarely live in isolation.
The LIMS users expect instant access to all the LIMS business
functions an enterprise can offer, regardless of which LIMS system
the functionality may reside in. This requires disparate LIMS
applications to be connected into a larger, integrated solution. This
integration is usually achieved through the use of some form of
middleware. Middleware provides the plumbing such as data
transport, data transformation, and routing.
The integration of the Laboratory Information Management System
(LIMS) is a major challenge in the industry. In a pharmaceutical
company which has multiple versions of LIMS or a single version
of LIMS, the integration within the LIMS products is still under
research. Here, the ideal solution would be a systematic LIMS data
integration and cleansing of the unstructured data management
and the information management that allows storing the data
from the various LIMS operational system to a common single
LIMS repository system, from where, the user can retrieve the data
for the reporting. The proposed framework model is designed in
such a way that any type of LIMS product can be plug-in with
the proposed integration model. Here, the intelligent and generic
adaptors will help in the data push/pull operation for the seamless
integration between the different types of LIMS applications. These
adaptors can be plug-in with any types of LIMS.
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LIMS Integration Framework Model | May 2010

Market Trend
The revenues in the laboratory information management systems
(LIMS) market have received a huge boost with the growing use
of these systems in various applications in mature sectors such as
pharmaceuticals, manufacturing, and IT. They are also used in
emerging sectors such as biotechnology and food and beverage. This
increased usage can be attributed to the launch of innovative LIMS
technologies and products, especially in the biotech industries. The
adoption of LIMS and the biotech companies are likely to expand
simultaneously. As biotech enterprises become successful and begin
to mimic pharmaceutical companies, they will have greater need for
LIMS integration so that they can get one common platform and
repository for all.
The Frost & Sullivan research service examines the key trends in
the LIMS market and observed that lots of research work is still
required for the LIMS integration. As the LIMS software is more
expensive to install, low research funding has become a huge
concern among LIMS companies. Most of the solution framework
of the available LIMS products in the market is based on old
technologies and the laboratories do not obtain adequate funds for
managing their data and up-gradation of LIMS, and therefore have
to manage with systems having lesser compatibility. Since these old
technology systems lack in beneficial and flexible operations, they
will reduce the efficiency of work. So for an organization it is just
impossible to maintain the multiple versions of LIMS and business
is searching for some solution for the seamless LIMS integration so
that business can integrate the multiple version of LIMS to a single
version LIMS.

Target Audience
The target audiences are from the following industries,
Pharmaceutical industry & Biotech Industry
Petrochemicals & Chemicals
Contract Research Organization
Clinical Lab
Food Industry
Others

Problem statement
Global life science organizations are under increasing pressure
to harmonize and integrate their asynchronous types of LIMS
business processes and are searching for ways to standardize on
mission-critical computing solutions for an integration of multiple
types of LIMS to a single version LIMS. The integration of LIMS
is a real challenge in industry because most of the LIMS products
which are available in the industry are the propitiatory systems.
Lots of challenges are involved in the integration of the different
LIMS business processes because the data format is different and also
unstructured works in asynchronous mode. Most of LIMS which
are available in the market are based on the old technologies and
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LIMS Integration Framework Model | May 2010

most of them are also stand alone systems. It is very much difficult
to align the multiple types of source LIMS with a single target
LIMS because of unstructured data exchange and data formats. The
business is in pressure to integrate their multiple versions of LIMS
to a single version LIMS where master data as well as the transaction
data plays a major role.

Solution
Architecting LIMS integration solutions is a complex task. There are
many conflicting LIMS process rule engines and even more possible
right solutions. Most integration vendors provide methodologies
and best practices, but these instructions tend to be very much geared
towards the vendor-provided tool set and often lack treatment of
the bigger picture, including underlying guidelines, principles and
best practices. Asynchronous messaging architectures have proven
to be the best strategy for enterprise integration because they allow
for a loosely coupled solution that overcomes the limitations of
remote communication, such as latency and unreliability. The
trend towards asynchronous messaging has manifested itself in a
variety of EAI (Enterprise Asynchronous Integration) suites as
well emerging standards for reliable, asynchronous web services.
Many of the assumptions that hold true when developing single,
synchronous applications are no longer valid. What is needed
is vendor-independent design guidance and framework model
on building robust LIMS integration architectures based on
asynchronous messaging.
The LIMS integration layer of the proposed solution focused on the
Data Virtualization, discussed in section 5.1 and the data integration
techniques discussed in section 5.2.

LIMS Integration Framework Model

Data integration is a difficult proposition, but help is coming in
the form of a relatively new approach to information management
called data virtualization. The typical enterprise today runs multiple
types of LIMS, where the data integration within the LIMS is a real
challenge. Data integration is getting harder all the time, and we
believe that the data volumes and the unstructured data format is the
major issues here which are continuing to grow. The data integration
is really needed because it represents the value to the business, to
the consumers and to the partners. Customer wants quality data
to be able to make better business decisions. Data virtualization,
also referred to as Information-as-a-Service and Data-as-a-Service,
promises to ease the impediments to data integration by decoupling
data from applications and storing it on the middleware layer. Data
virtualization can essentially be thought of as a service-oriented
architecture (SOA) for data, according. But where the traditional
SOA approach has focused on business processes, data virtualization
focuses on the information that those business processes use.
The features of a LIMS Integration become challenges from a
data integration perspective. There are three key data integration
challenges involved with the LIMS Integration, which are:

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LIMS Integration Framework Model | May 2010

Completeness of the LIMS life cycle information that deals with

the unstructured data format
Correctness of the LIMS information that deals with the data
accuracy and the data quality
Criticality of information that deals with on-time availability.
These challenges become more prominent with the expectation
that the level of data integration with the unstructured data format
which are complete and the requirement that multiple views of data
should not lead to inaccuracy while blending them with data from
external sources. In order to address these issues, big vendors in the
market started promoting industry-specific data integration models
that can be implemented with some customization to fit the needs
of the enterprise. However the challenges specific to the integration
of unstructured data sources go beyond these generic data models.

Fig.-1: LIMS Integration and Migration

In the proposed Integration layer the LIMS unstructured or
structured data formats from the different types of LIMS are pulled
by an intelligent software devise called the Pulled Adapter. The
function of this Pull Adaptor is to extract the data from the different
types of LIMS to a single location where the meaningful LIMS data
but in different data format are transformed to a single data format.
Once the meaningful data formats from the different versions of the
LIMS are transformed to a single version then the transformed data
will be pushed to a common repository. The Common repository
will contain a single version of LIMS which will be extracted from
different types of LIMS. The data integration framework for the
unstructured data is based on the ESB ( Enterprise Service Bus) and
MoM (Message Oriented Middleware). The Pull/push adaptors are
the integrator encapsulated within the MoM. An enterprise service
bus (ESB) is a software architecture middleware that provides
fundamental services for more complex integration architectures.
Messaging tends to concentrate on the reliable exchange of messages
around a network; using queues as a reliable load balancer and
topics to implement publish and subscribe. An ESB typically
tends to add different features above and beyond messaging such
as orchestration, routing, transformation, adapters and mediation.
The adaptors are generic in nature and it can be plug-in with any
types of LIMS Product.
In the proposed paper we are providing two types of LIMS
integration scenarios. The first is the LIMS integration and the
migration that can be done between the two or more types of source
LIMS products with a single version of target LIMS, where after the
migration and integration the old version of the source LIMS can be

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LIMS Integration Framework Model | May 2010

decommissioned and the new version of target LIMS can continue.

Another scenario, where we can extract and integrate the data from
the various types of source LIMS to a single common repository
from where we can generate various types of reports with respect to
the multiple version/types of source LIMS. This type of integration
holds good for the LIMS Analytics.

Data Integration Techniques

There are various types of middleware generally used for the
integration methodologies like,
1. Remote procedure calls
2. Message-oriented middleware
3. Message brokers
In the proposed system we are using the MoM (Message-oriented
middleware) as shown in Fig.-3. The proposed integration system
is based on the ESB framework where for the seamless data
integration the Message-Oriented Middleware (MOM) is created.
Here, MOM is also able to guarantee that Data& Messages will
reach their destination, even when the destination is not available
(asynchronous mode). The root pattern hierarchy is based on the
messaging technologies where the creation of the message channels
are dependent on the message deployment time, what and how many
channels will be involved and what will be the channel direction. In
the proposed system as data exchange and data integration is required
in both the directions like source LIMS to Target LIMS and again
Target LIMS to the source LIMS so it should be bi-directional. The
structure of the channel adaptors will be created as per Fig.-2.

Fig.-2: Two different LIMS Applications with different

data formats
Here the source applications LIMS A and LIMS B are the two
different source LIMS applications where the data formats for
LIMS-A is A with message and the data format for the LIMS-B is
B with message, which is different. Here we are considering only
one process like the Sample Life Cycle. As an example we can say
that the LIMS-A= Sapphire and the LIMS-B= Labware, where
the Sapphire database is in RDBMS where as the Labware database
is in DBMS. As the Labware database is in DBMS so all the data
integrity are designed at the business layer where as in sapphire it
has been designed at the database layer. If we have to transform the
data from both of these LIMS product to a third target LIMS, where
the Database is in RDBMS, then we can follow the proposed steps

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LIMS Integration Framework Model | May 2010

and the canonical data model. The different data formats will be
translated through the source translator which will be mapped to
the target data formats C athrough the target translator and finally
the resultant data will be transformed as per the format of the target
LIMS-X. The integration and the transformation will be performed
via the canonical data model between source to the target application
so that seamless data exchanged can occur between the source LIMS
to the target LIMS. The basic steps for the above mentioned LIMS
integration are as follows:
Step-1: Data Synchronization (data mapping) between the source
LIMS to the
Step-2: Data Migration from source LIMS to the Target LIMS
Step-3: Process Integration between the source LIMS to the target
LIMS
Step-4: Data Integration between the source LIMS to the target
LIMS
Step-4: Data build-up (following Incremental & Iterative process)
The proposed protocol for the integration layer will be SOAP
(Simple Object Access Protocol).

Fig.-4: Application Integration with Different data format

The asynchronous data mapping allows the application to continue
processing through the message channel after making a middleware
service request with different data format extracting from different
types of LIMS Products. The message is dispatched to the queue
manager, which makes sure that the message is delivered to its final
destination LIMS. The message transformation layer understands the
data format of all messages being passed among the applications and
transforms those messages while they move. The massage channels
are handling the canonical data model where it can handle the
unstructured data format for different types of LIMS applications.

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LIMS Integration Framework Model | May 2010

Conclusion
In the proposed integration framework model, the system will be
flexible enough to add more source LIMS as and when required.
This would also help in adding new LIMS business line in future.
The target LIMS will hold both the transactional level information
at the lowest level as well as the master data so there will be no bottle
neck in generating operational or Adhoc nature reports from a single
source as and when required. The migration process will take care
the data migrate by incremental method which would bring down
the data loading time to a great extent. The proposed design acts a
single unified source of reporting for optimal performance. Due to
the integration, the licensing cost will be reduced considerably. The
number of physical servers will reduce; this would bring down the
recurring hardware and maintenance cost. So using this frame work
we can also optimize the cost to a great extent.

References
1. Worldwide Regulatory Compliance Issues in Life Science
(IDC #32690,December 2004)
2. 1Q05 Leading Indicators in Life Science s IT Spending Survey,
an IDC Report
3. Knowledge Management in Drug Discovery R&D 3rd
Millennium, Inc. February 2003
4. Laboratory Automation: Smart Strategies and Practical
Applications Donald S. Young1, University of Pennsylvania
Medical Center, 3400 Spruce St., Philadelphia, PA 19014-4283
5. Laboratory Information Management System Outlook,
Five year market analysis and technology forecast through 2008
Arc Advisory Group
6. Laboratory Automation and Information Management 32 (1996)
7-22
7. A Revolution in Agility: Business Integration Through
Service-Oriented Architecture : An Oracle White Paper Updated
August 2008
8. Enterprise Integration Patterns: Mr. Eva Shon , Software &
Systems Engineering Seminar

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LIMS Integration Framework Model | May 2010

About the Author

Dr. Partha Mukherjee is engaged as a Project
Manager at LIMS COE, Kolkata, HC L Technologies
Ltd. He has around16 years of IT experience. Last
10 years he has been engaged with HCLT in the
area of Business Intelligent and data warehouse
technology. Partha has specializes in the area of BI,
LIMS Integration, LIMS Analytics and Master Data
Management. Partha has done his doctoral research
on Multimedia Database Management System
and BI from the CSE Department, Jadavpur
University, Kolkata and he had published multiple
research papers in the international IEEE Journals
and Conferences.

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10
LIMS Integration Framework Model | May 2010

ABOUT HCL
HCL Technologies

HCL Technologies is a leading global IT services company, working

with clients in the areas that impact and redefine the core of their
businesses. Since its inception into the global landscape after its
IPO in 1999, HCL focuses on transformational outsourcing,
underlined by innovation and value creation, and offers integrated
portfolio of services including software-led IT solutions, remote
infrastructure management, engineering and R&D services and BPO.
HCL leverages its extensive global offshore infrastructure
and network of offices in 26 countries to provide holistic,
multi-service delivery in key industry verticals including Financial
Services, Manufacturing, Consumer Services, Public Services and
Healthcare. HCL takes pride in its philosophy of Employee First
which empowers our 58,129 transformers to create a real value for
the customers. HCL Technologies, along with its subsidiaries, had
consolidated revenues of US$ 2.6 billion (Rs. 12,048 crores), as on
31st March 2010 (on LTM basis).

About HCL Enterprise

HCL is a $5 billion leading global Technology and IT Enterprise

that comprises two companies listed in India - HCL Technologies
& HCL Infosystems. Founded in 1976, HCL is one of Indias
original IT garage start-ups, a pioneer of modern computing, and
a global transformational enterprise today. Its range of offerings
spans Product Engineering, Custom & Package Applications, BPO,
IT Infrastructure Services, IT Hardware, Systems Integration, and
distribution of ICT products across a wide range of focused industry
verticals. The HCL team comprises over 64,000 professionals of
diverse nationalities, who operate from 26 countries including
over 500 points of presence in India. HCL has global partnerships
with several leading Fortune 1000 firms, including leading IT and
Technology firms. For more information, please visit www.hcl.in.
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