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Instant JChem (IJC) was first introduced at NIBR as a replacement for a number of legacy applications. Driven by the very positive response from our chemistry community, we have fully integrated IJC into NIBR’s application and data landscape via a collections of Java plugins and Groovy scripts. This presentation will describe how IJC is currently used for a number of different purposes ranging from team collaboration, to accessing commercial databases, retrieving data from the data warehouse and registering compounds.
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Anna Pelliccioli
Novartis Institutes for Biomedical Research (NIBR) Informatics
Budapest, 20 May 2014
Building on the Instant JChem platform at NIBR
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 Only 2
JChem Cartridge
Shared DBs
SDF,RDF
Local DBs
Scientists
IJC at NIBR – the beginning
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
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
Team collaboration and sharing
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 5
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
JARA - Radioactive Compound Inventory
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 6
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
Large Structure Collections
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 7
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
Commercial Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 8
ACD
Access to Accelrys’ ACD + CPI databases
JChem Cartridge
Shared DBs
Scientists
Data Adminstrator
Commercial Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 9
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
Commercial Databases
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 10
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
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 11
In-house, Java Plugin Development IJC NIBR Extensions
11
Bulk Registration
Calculations
Assay Data
| 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 Project Local DBs
Scientists
NIBR Data Warehouse
Dart+DW services
Retrieve assay data based on DART URL
Create Forms, annotate data
DART
Batch Registration
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 13
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
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
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
Acknowledgements
| ChemAxon UGM 2014 | Anna Pelliccioli | 20 May 2014 | Building on the IJC Platform at NIBR | Business Use Only 16
NIBR IT
Benoit Hensinger
Gregory Landrum
Manuel Schwarze
Sadik Keshwani
ChemAxon
Attila Szabo
Mihály Medzihradszky
Petr Hamernik
Tim Dudgeon
IJC Support Team
