The document discusses how Novartis Institutes for Biomedical Research (NIBR) implemented the Instant JChem (IJC) platform to replace their previous system and improve data sharing and collaboration. Key points include: IJC was introduced in 2011 and legacy data was imported; plugins were developed for tasks like batch registration, calculating properties, and retrieving data from warehouses; shared databases and projects allow scientists to access large collections and commercial databases; and the system has improved team collaboration and made data previously stored in documents searchable and accessible.

1. Anna Pelliccioli
Novartis Institutes for Biomedical Research (NIBR) Informatics
Budapest, 20 May 2014
Building on the Instant JChem platform at NIBR

2.  Introduced at NIBR in 2011 to replace ISIS
 Data exported from legacy databases and imported via IJC
into local and shared Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only2
JChem
Cartridge
Shared DBs
SDF,RDF
Local DBs
Scientists
IJC at NIBR – the beginning

3. The IJC Platform
Deployment via Java WebStart
Shared Projects
Groovy
Scripting
Java Plugin
Development
NIBR-specific features
for the whole user
community
Centrally configure access
to databases
Easy, global distribution of
software without packaging
Personal DBs
ad-hoc customization
for single projects
3 | ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only

4. The IJC Platform
Java WebStart
Deployment
Personal
DBs
Shared
Projects
Groovy
Scripting
Java
Plugins
Team Collaboration   
Share large structure
collections
 
Access commercial
databases
 
Retrieve data from the
Data Warehouse
   
Batch registration   
Calculate QSAR Model
Values and other Structure
properties
  
4 | ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only

5. Team collaboration and sharing
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only5
From office documents to shared, searchable databases
 Prep Lab databases (hydrogenation, carbonylation...)
 Analytical Data and related Structures
 Radioactive Compound Inventory
 Building Block Archive
 Chiral Separation Database
 NIBR IP Priority Database
JChem
Cartridge
Scientists
ChemAxon’s Markush
Search Plugin

6. JARA - Radioactive Compound Inventory
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only6
Groovy scripts used to create a custom application
 Replaces previous ISIS-based application
 Custom interface to add bottles/batches
 Tracking of deliveries to other labs and waste disposal
 Reports to check that amounts stay within allowed limits

7. Large Structure Collections
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only7
Databases useful to a large community that do not ‘fit’ into the data WH
 Vendor Sample Database (> 10 Mi. Structures)
 Legacy Combinatorial Chemistry Library Collections
JChem
Cartridge
Scientists
Data Adminstrator

8. Commercial Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only8
ACD
 Access to Accelrys’ ACD + CPI databases
JChem
Cartridge
Shared DBs
Scientists
Data Adminstrator

9. Commercial Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only9
ACD - the set up: optimal performance on all sites
Project created once and then transferred to other ERM instances
ERM DB
Basel
ERM DB
Cambridge
ERM DB
Emeryville
ERM DB
Shanghai
ERM DB
Singapore
Sciquest ERM IJC
ChemAxon’sTest to
Production
Metadata Migrator
Shanghai
Singapore
Cambridge
Emeryville
Basel

10. Commercial Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only10
Accelrys’ Metabolite – work in progress
 Data available as RDF
from Accelrys
 ChemAxon helping us
import the data into
Oracle and build the
User Interface
 Will be deployed as
other Shared
Databases

11. | ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only11
In-house, Java Plugin Development
IJC NIBR Extensions
11
Bulk Registration
Calculations
Assay Data

12. | ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only
12
In-house, Java Plugin Development
Retrieve Assay Data from Data Warehouse
12
JChem
Cartridge
Shared ProjectLocal DBs
Scientists
NIBR Data
Warehouse
Dart+DW services
 Retrieve assay data based on DART URL
 Create Forms, annotate data DART

13. Batch Registration
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only13
In-house, Java Plugin Development
 Validate data against Registration
service: highlight errors, fix data in
Grid view
 Register from within IJC and get
back identifiers
13
SDF
Scientist
Structure
Repository
Registration
service
CRO
SMR

14. Calculate QSAR Model Values and other Structure properties
In-house, Java Plugin Development
14
Scientist
CiX services
 Using same Framework currently
accessed by Spotfire and Knime
 Consistency with values
displayed by other applications
SMILES/Compound Nr.
clogP, PSA,
QSAR Model predictions.
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only

15. 15
JChem
Cartridge
Shared DBs
SDF,RDF
Local DBs
Scientists
IJC at NIBR - Summary
NIBR Data
Warehouse
Structure
Repository
DW
services
CiX services
Registration
service
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only

16. Acknowledgements
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only16
NIBR IT
 Benoit Hensinger
 Gregory Landrum
 Manuel Schwarze
 Sadik Keshwani
ChemAxon
 Attila Szabo
 Mihály Medzihradszky
 Petr Hamernik
 Tim Dudgeon
 IJC Support Team