A user’s story on a successful transition into the modern era: Niels Clauson-Kaas A/S, a small contract research and development organisation, created a reaction database in 1990. The database program ChemBase was chosen as the platform and were considered very sophisticated for that time and we were fully able of doing both structure and substructure searches. Efforts were made to archive all the reactions done since 1956, where the company was founded, into the database, and today the database consists of more than 58 years of accumulated knowledge. Time passed, the standard formats for storing chemistry electronically developed, and dos as an operating system disappeared. Today we are forced to use a DOS emulator in order to keep accessing and maintaining the database, using standard Windows operating system – this is not an ideal solution, but it works. Attempts over the years to transform the ChemBase database into something more modern failed, as the knowledge on how to translate the electronically stored information was lost. The Database, now consisting of more than 8000 reactions, was maintained in DOS until recently, where ChemAxon took on the challenge to migrate the data to Instant JChem, and was successful.

1. Migrating a legacy platform from the
“DOS age” to Instant JChem
- easier than expected
 Brian Kreiser
 Project Manager
 Niels Clauson-Kaas A/S (Denmark)
 Péter Cseh
 Product Owner (Core & IO)
 Chemaxon Ltd (Hungary)

2.  Agenda
 About Niels Clauson-Kaas A/S
 The Chemical Database
 Transformation from DOS to Windows
 Conclusion
 Technical Details (Péter Cseh, Chemaxon Ltd)

3. - with 58 years’ experience
Small molecule API provider

4. The founder of our company, Dr Niels Clauson-Kaas, started
his career at the universities in Copenhagen, Zürich and
Haifa. In 1949 he was offered a position as head of an
industrial organic synthesis laboratory in Denmark.
In 1956 he decided to start his own company focused on
research and development in organic synthesis, providing
contract services to the chemical industry.
THE STORY SO FAR…
In 1983, a foundation was established to facilitate the
buyout of Niels Clauson-Kaas.
The objective was evident: To build a sustainable company,
and continue to have an inspiring work environment.
INDEPENDENT COMPANY

5.  58 Years’ Experience
in Synthetic Organic Chemistry
 Process Development / Up-Scaling
 Lab to Pilot Scale Syntheses
 API Manufacturing according to cGMP
 Analytical Development and Validation
 Stability Studies
 Genotoxic Impurities / Method Development
 Technology Transfer
 Approx. 50% of our projects over a 5 years period
are for oncology therapeutics
- a technology based company
OUR FOUNDATION

6. Discovery
Pre-Clinical Phase 1 Phase 2a-2b
Early clinical trialsToxicology First-in-man Full clinical trials Launch
CLIENT CLIENTNIELS CLAUSON-KAAS A/S
Phase 3 On-Going Production
- your new potential drug were to enter the development stage..
Imagine if…
..you will need a trustful CMC partner who can support, guide and
 structure a project to meet the various milestones
 provide the right solution in high quality
 supply the world’s best track record

7. ORGANISATION
- Project management involvement

8. - in a well-organized matrix organisation, with..
NCK offers projects
 a unique project management system
 clear line of communication through project management
 with seamless progression throughout project milestones
CEO
Process Dev.
12 people
Pilot Plant
2 people
Anal. Dev. / QC
4 people
QA
3 people
Adm. & Service
5 people
Sales, Marketing & HR
1 person

9.  Work on the reaction Database
was initiated in 1990
 One of the best choices of
database software in the ”DOS
age” was ChemBase
 > 8,000 Reactions were stored in
the database, which was
maintained until recently
DATABASE SETUP

10. CHEMBASE

11. NCK ISSUES WITH CHEMBASE
 Only few people in the company
are comfortable using DOS today
 Important chemical know-how not
fully exploited as the project
managers do not check our
reaction database
 The DOS platform is obsolete
 The data could not be exported
into a new windows based
chemical database

12. DATABASE TRANSFORMATION
 ChemAxon offered to test our
ChemBase data, free of charge
 A pilot project was performed on a
small part of the database – with
success
 The full ChemBase database was
converted to Instant JChem

13. INSTANT JCHEM

14.  Successful transfer of the
ChemBase database
 Project Managers are now actively
searching the database for
information
 Project Managers are able to add
new reactions to the database
 Access to historical reaction data
now preserved for the future
CONCLUSION

15. Clauson-Kaas database migration
Technical details
Péter Cseh

16. First bits of information
“I do have one challenge for you on
which the engineers at
CambridgeSoft could not manage.”
• Binary data
• Some kind of text export,
but “the export routine is
faulty and you lose info”

17. Ideas for migration
Image
recognition
Manual
check
Add
properties
Database
import

18. Ideas for migration
Current
import
Draw arrows
Fix structures
Database
import

19. Towards the solution
• MDL Information Systems, 1999
• ChemBase uses CPSS-type Rxn file, obsolete
• All the information is there, let’s extract it!
Reactions
Import to
relational
database
Intermediates
Custom
converter

20. Small issues along the way
• Intermediate products of reactions
• Relational database
• Invalid entries of the original database
• database clean-up before the conversion
• Issues with character encoding
• Handling of free text fields
• E.g. “salt form”, “solvent”
• Date conversion with Y2K problem
• 04.05.113 -> 04.05.2013

21. Results
• Conversion without information loss
• Free text fields became searchable
• Possibility to develop infrastructure further
• In budget, on time
• The converter is reusable

22. Thank you!

23. Ideas for migration
D2S
Manual
check
Add
properties
Import Draw arrows Fix structures
Database
import