Many research teams are facing chemistry data migrations in the coming months due to legacy system retirements and/or the opportunity to move to new informatics platforms. Some approaches, case studies, and experiences will be shared on migrating chemistry data between vendor technologies, with a focus on moving to ChemAxon cartridge technology.

1. Great Migrations!
Approaches to Moving your Chemistry
Michael Dippolito – 2013 ChemAxon UGM Budapest

2. 2013 ChemAxon UGM Budapest
DeltaSoft – Migrations ‘R’ Us
Accelrys
Accord
Accelrys
Direct
ChemAxon
JChem
Perkin Elmer
CSCartridge
OpenEye
Cartridge
ChemCart
Query, Browse, Update,
Report, Analyze
ChemCart
Choose your
chemistry

3. 2013 ChemAxon UGM Budapest
Migration Drijvers
Technology retirement
Mergers and Acquisitions
Competitive Advantage
Cost Savings

4. 2013 ChemAxon UGM Budapest
Chemistry Oracle Cartridges
ChemAxon JChem
Accelrys (formerly Symyx, MDL, ISIS) Direct
Accelrys Accord
PerkinElmer CambridgeSoft Cartridge
OpenEye Cartridge
Daylight DayCart
InfoChem ICCartridge
IDBS ChemXtra
Scitouch (GGA) Bingo
Dotmatics Pinpoint
Digital Chemistry Torus
Scillegence MolSQL
Biochemfusion Proteax
EBI OrChem
Custom Cartridge

5. 2013 ChemAxon UGM Budapest
Older technologies
ISIS/Host, ISIS/Base
ChemFinder
Spreadsheets
etc…

6. 2013 ChemAxon UGM Budapest
Chemistry Format ‘Standards’
• Molfile
• V2000 – The ‘original’ molfile
• V3000 – Extended molfile capabilities
• SDFile – Molfile + Data
• SMILES
• INCHI
• many others…

7. 2013 ChemAxon UGM Budapest
Chemical structure indexing
Oracle Cartridge Domain Index provides
chemical operators for Oracle
• JChem cartridge indexes a number of formats directly
• Migration needed for some propietary formats
• Many options are possible for migration
• A few approaches and case studies will be shared…

8. 2013 ChemAxon UGM Budapest
Tools of the trade
Cartridge operators
• Accessing chemistry
JChem MolConvert
• Converting chemical formats
Structure Standardizer
• Clean up and standardize
SQL scripts
• Easily automate migration and testing
Cloud servers
• Great staging, test, and work environment

9. 2013 ChemAxon UGM Budapest
Migration Approach 1
SDFile or SMILES export / import
• Fairly simple
• Best for older technologies or small databases
• Less practical for large databases
• Requires
• Tool or script for import / export
• Field mapping

10. 2013 ChemAxon UGM Budapest
Case Study #1
ISIS / Base  ChemAxon JChem
• Small local ISIS database
• Export SDFile from ISIS
• Create Oracle table with SDFile fields
• Map and import SDFile using ChemCart SDFile import

11. 2013 ChemAxon UGM Budapest
Migration Approach 2
One Table, Two Cartridge
• Install JChem cartridge in same instance
• Add additional field for new structure
• Use cartridge operators to populate new structure
field (molfile or smiles)
• Ex: update moltable set newstructure = molfile(oldstr);
• Create JChem domain index on new structure field
• Least movement of data, fastest for large datasets

12. 2013 ChemAxon UGM Budapest
Case Study #2
• Accord  JChem conversion
• Large Accord cartridge database
• Added new field for JChem structure
• Convert and insert newstructure
• Update structure_table set JChem_struct =
Accord.convertout(oldstruct, ‘MDL Molfile’)
• Remove old structure field
• > 99% conversion
• Manual remediation of ‘bad’ structures

13. 2013 ChemAxon UGM Budapest
‘Convert to JChem’ button

14. 2013 ChemAxon UGM Budapest

15. 2013 ChemAxon UGM Budapest
Migration Approach 3
Two Table, Two Cartridge
• Install JChem cartridge in same instance
• Add new table with new structure field
• Use cartridge operators (or JChem molconvert) to
populate new structure table and field (molfile or
smiles)
• Ex: insert into moltable2.newstructure (select molfile(oldstr)
from moltable)
• Create JChem domain index on new structure field

16. 2013 ChemAxon UGM Budapest
Case Study #3
CambridgeSoft  ChemAxon JChem conversion
• Registry and ELN conversion
• Molecules and reactions converted using JChem
molconvert
• Data reformatted to new table structures
• Some manual remediation needed

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Migration Approach #4
Two instance
• Install JChem cartridge in 2nd instance
• Convert structure using cartridge tools in 1st instance
• Export schema from Oracle instance 1
• Import schema into Oracle instance 2

18. 2013 ChemAxon UGM Budapest
Case Study #4
Accelrys Direct  ChemAxon JChem
• Registry database
• Molfile column added to structure table
• Populated using Direct cartridge tools
• Export complete schema
• Import to 2nd instance
• Create JChem domain index

19. 2013 ChemAxon UGM Budapest
Validation & Verification
Automated checks
• SQL scripts
• Search each structure with exact match to ensure it returns
• Search each structure with substructure search to ensure it is
contained in the hits
• Timings – before and after migration
Manual checks
• Searching
• Registration

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Ideally invisible to the user
Before After

21. 2013 ChemAxon UGM Budapest
Summary
• Chemistry migrations are likely in your
future.
• Several good approaches are possible.
• With proper planning you can experience a
painless and Great Migration!