Chemistry infrastructure serves as a backbone of pharmaceutical discovery informatics. In last two year, we have implemented and migrated most of our applications and systems using ChemAxon technology as our core chemistry infrastructure platform. During this evolutional migration, we encountered challenges in legacy systems, technology adaption, and data curation. An effective organization and business engagement are crucial for the success.

1. Zhenbin (Benjamin) Li and Edith Richter
IT RD&M
Challenges and Approach in Migration
of Chemistry Infrastructure for Systems
and Applications

2. Historical/background Information about Chemistry
Infrastructure Migration in BI
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
2013 - 2015
System and Application
Migration Projects
Migration of systems and applications to
ChemAxonTechnology
2011 - 2012
Chemistry
Infrastructure Project
Experimented and Piloted ChemAxon in BI
environment
2008
MDL Alternatives
Project
Evaluated ChemAxon, Accelrys Accord, Symyx
MDL, CambridgeSoft
ERMS with ChemAxon JChem to fulfill a
strategic user requirement (2010), presented
in 2011 UGM
ERMS with ChemAxon JChem cartridge
implementation as pilot (2012), presented in
2012 UGM

3. Historical/background Information about Chemistry
Infrastructure Migration in BI
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

4. • Reliability
• Extensibility
• Compatibility and
integratability
• Enterprise
architecture
• User friendliness
• Clear path for
migration
• Consulting
• Support
• Expertise
• Agility of
enhancement
• Customization
• New upgrade
according to
customers’ needs
• License model
• Negotiation power
• Short-term cost
cut
• Long-term
financial gain
• Company stability
• Size
• Culture/work
ethics
• Familiarity with
global
pharmaceutical
industry
Chemistry Infrastructure Selection Criteria
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

5. Roadmap of Chemistry Infrastructure Migration
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
Business
intention
Market options
Preliminary
evaluation
Business approval
In-depth
evaluation
Pilot
implementation
Negotiation
Financial
commitment
Acquire licenses
Consulting
In-depth system
analysis
Implementation
planning
Data migration
System migration
Testing
Completion

6. Waterfall
● Clear license cutoff time
● Resources (including external
consulting) are more focused on the
migration projects
● Potentially short time to complete the
whole migration
● Requires clear understanding of
existing systems and interrelations
● Need of established expertise
● May have nonadjustable deadline
● Less tolerant to failure
● Resources may have to reduce other
responsibilities
Evolutional
● Migration takes it own path
● Flexible resource and time planning
● Skills and knowledge accumulating
as it goes so that later projects benefit
from the experiences of previous
projects
● It takes a long time to complete whole
migration
● Requires license co-existing period
(perpetual license model)
● Structures may be interpreted differently
in different technology. Internal
standardization process or common
understanding may be needed
Migration Approach
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

7. System Interdependency Analysis
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

8. Migration Planning
Time 2012 2013 2014 2015
System Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1-Q4
System A
System B
System C
System D
System E
System F
System G
System H
 Migration planning was based on the interdependency of systems and applications as well as
available resources.
 The pilot project provided benchmark for the estimation of time needed for each system. The
estimation should include the migration of data, application, interfaces, and logistics.
 Each additional system migration served as additional benchmark for the other systems in order to
further modify and optimize the estimation.
 Learning curve effects are considered
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

9. General Challenges and Approach
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
Organizational change management
IS global alignment
System/service global harmonization
Numerous new application releases or
upgrades
More strict IS project management and QA
processes
Windows operation system upgrade
Users’ reluctance to adapt new technology
Low exposure to ChemAxon technology
among IS colleagues
Created a Molecular Structure and Reaction
Service:
An advisory committee formed by experts in
chemistry informatics from different OPUs to
provide centralized and harmonized service,
consulting, training, and tutoring as well as
system QA for IS developers, system leaders
as well as end users.
Non-stop service Using evolutional migration and globally
coordinated projects.
Packaging for user deployment (internal
process)
Continual improvement of BI global IS
service
Challenges Approach

10. Technical Challenges
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
Our Experiences Pain Points Opportunities for ChemAxon
Support is great, able
to reproduce the error
and sometimes add
into the next version
Sometimes the new fix introduced
other bugs
Better quality assurance and
quality control mechanism
Frequent version
changes/updates
Tracking detailed information of
the upgrades that are relevant to BI
environment. We have to create
database to track changes
Track changes in database so that
customers can compare different
versions or upgrades to
understand the potential benefits
or threats to their environment
(change management)
Great customer-centric
service
Not sure about the roadmap and
future direction
Forming an advisory committee
represented by delegates from
industry, and more frequent
communications with key clients

11. Technical Challenges (continue)
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
Our Experiences Pain Points Opportunities for
ChemAxon
Marvin technology can
handle many chemistry
representations(mol,
smarts etc)
Special features in MarvinSketch need to be
coded in application. But if application only
uses the default, then user will see their own
default, causing different settings for
different users
Implementation of
application defaults for
special features
Integration of Marvin
technology with Java
Swing is easy to do
Web applications hosted with Tomcat are
difficult to integrate, especially when there is
no clear instruction about which jars to be
included. Sometimes specific configuration
inTomcat is needed to allow certain files pass
through. At one time, Java 1.7 had some
integration problem so we had to go back to
1.6
More clear instructions
and cookbook of web
application integration.

12. Technical Challenges (continue)
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
Our Experiences Pain Points Opportunities for
ChemAxon
JChem Java APIs are
very powerful and
flexible.
.Net APIs are less ideal (may be not as mature
as Java APIs) and time-consuming. We cannot
use the latest version.This may be due to
some of our third-party components.
Maybe better
documentation or
training for .Net APIs.
Database cartridge set
up is straightforward.
When database password changes (for
compliance purpose) or database reboots, we
have to re-enable the cartridge. Sometimes
JChem server is stuck and not responsive.
A streamlined process
to check and re-
initiate all databases
that use ChemAxon
cartridge
Domain indexing is a
bit long, but
reasonable. Structural
search is quickly
implemented.
ChemAxon cartridge apparently is more strict
than MDL cartridge for Markush and R-group
structures. Interpretation of ‘X’ is different.
Solution is to capture error in error table
during indexing and make correction by
business (those structure will be in database,
but not searchable).
NA?

13. Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014
Structure
Checking
(Spell Checking)
searches the
chemical structure
for issues and
reports the
problems found
Structure
Checking &
Fixing
(Autocorrection)
searches the
chemical structure
for issues and
corrects them if
possible
Standardizing
(Translation)
Transforms the
structures to
customized,
canonical, and
consistent
representations
Approach of Data Curation and Data Qaulity

14. Workflow of Data Curation and Data Quality
Provide GlobalTemplates for Cartridge/Interface
Implement Customized Checkers with ChemAxon
Decide about Standardizing and Structure Checking
Review and Discuss Existing Rules
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

15. Templates for Databases
• Provide functions for single- and multistep checks and fixings
• Provide functions for automated checks
Packages
• Store the default checker and standardizing configuration
• Store customized result messages for checks
• Store dedicated structures for tests
DatabaseTables
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

16. Used Types of Checkers
• As Abbreviated Group / Pseudo Atom etc.
Basic Checkers
• Working with SMARTS defined substructures
• Can be set individually
• Very flexible approach
Substructure Checkers
• Provided as consultancy projects
• Good experiences by now
• Easy to implement both for DB Cartridge and for MarvinTools
Customized Checkers
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

17. Conclusions
• This is a decision and investment for next decades and requires
commitment from business and IS.
• Evolutional approach can reduce the complexity of the migration.
• Multiple migration projects may be needed.
• System interdependency analysis is a key step.
• Globally aligned and harmonized service is a great platform.
• Generally the migration was smooth.
• Data curation effort should not be underestimated.
• Effective mechanisms for data curation require IS and business
engagement.
• Strong support from users, especially from key stakeholders, is
crucial [success = (process improvement) x (customer acceptance)].
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014

18. Acknowledgement
• Members of Molecular Structure
and Chemical Reaction Service
• Members of Content
Management in BI Research
• System Leaders in BI IS RDM
• Infrastructure Service Leaders
• ChemAxon support and
consulting
Z. Li and E. Richter, Boehringer Ingelheim, ChemAxon UGM, September2014