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

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1 Great Migrations! Approaches to Moving your Chemistry Michael Dippolito

2 DeltaSoft Migrations R Us ChemCart ChemCart Choose your chemistry Query, Browse, Update, Report, Analyze Accelrys Accord Accelrys Direct ChemAxon JChem Perkin Elmer CSCartridge OpenEye Cartridge

3 Migration Drijvers Technology retirement Competitive Advantage Mergers and Acquisitions Cost Savings

4 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 Older technologies ISIS/Host, ISIS/Base ChemFinder Spreadsheets etc

6 Chemistry Format Standards Molfile V2000 The original molfile V3000 Extended molfile capabilities SDFile Molfile + Data SMILES INCHI many others

7 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 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 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 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 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 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 Convert to JChem button

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15 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 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

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

18 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 2 nd instance Create JChem domain index

19 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

20 Ideally invisible to the user Before After

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