Created in september 2003, the “Chimiothèque Nationale” (CN) – French Academic Compound Library – has for mission to federate collections of synthesis products, natural compounds and natural extracts available in French academic laboratories and to promote their scientific and industrial valorisation. Information concerning available molecules and extracts are contained in two databases (synthesis products, natural compounds and natural extracts), accessible through a web portal (http://www.chimiotheque-nationale.org/). The compounds database currently refers about 50,000 molecules coming from 30 French academic laboratories. The chemical compound database is built on Oracle database and IDBS tools (ActivityBase and ChemXtra). Chemaxon tools are also integrated in the CN information system : Marvin applet and calculator plugins. For several reasons (including software maintenance costs and evolutivity), we decided recently to evaluate the possibility to move to Chemaxon tools (Jchem, Jchem Cartridge and Standardizer). I will show you the present and future (expected) use of Chemaxon tools in the CN information system.

1. French Academic Compound Library
Chimiothèque Nationale
UGM Budapest – 28th may 2013 Philippe Jauffret and Kiet Tran
Chimiothèque Nationale

2. Chimiothèque Nationale
Outline
1- Introduction : French academic compound library
2- Current information system : data model, database, web architecture
3- Why a new information system based on chemaxon tools?
4- Prospects
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3. Chimiothèque Nationale
Chimiothèque Nationale [CN]
1- Consortium of academic chemical laboratories
(40 labs participating)
2- Double aim : - preserve the French academic chemical patrimony
- promote its biological evaluation
Key dates:
 2003 : launch of the project
 2005 : opening of Information System
(www.chimiotheque-nationale.org)
 2007 : creation of a service Unit of CNRS
 2010 : partner of EU-Openscreen project
Recent scientific results (2008-2011)
 53.000 compounds  200 collaborative projects
 15.000 natural extracts  200 validated hits
 5% growth/year  100 publications
 350 users (biologists)  8 licenced patents
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4. Chimiothèque Nationale
CN’s organization overview
national
database
Requests
treatment
laboratory
national
server
biologist
local database
DiffusionData merging
Collaboration
Legal
validation
GIS
members
GIS
members
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5. Chimiothèque Nationale
Architecture of the information system
(2005-2013)
National
SDF File
CFusion tools
Chemaxon
Administration Server
APACHE (https) + PHP
+ SSH
Backstage National Server
National Database
(ORACLE
ActivityBase + ChemXtra)
WEB Browser
Administration Client
SDF
File
Local Library
Database
Local Management
Isis/Draw MarvinSketch MarvinSketch
Isis/Base L-g Chimio IJC other…
other…
Secured
Connexions
WEB Browser
+ Sketch (JME/Marvin)
Query Client
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6. Simplified Data Model
(IDBS-CN)Chimiothèque Nationale
structure
substance
batch
Laboratory
basket
Order
User
Access Log
Has structure
Is in
Provides
Provides
Direct to
Direct to
Has selected
or ordered
Has ordered
Has item
Has
accessed to
Structure_id
idbs
molfile
Smilescode
Molecular_mass
Delete Status
Substance_nat_id
Substance_local_id
Packaging
Quantity
Purity
Nature_substance
Date_creation
Date_update
Delete Status
lot_nat_id
lot_local_id
Delete Status
Structure descriptors:
-LogP, HBD, HBA, Lipinsky (Chemaxon)
- Herg, Mutagen (Isida) 6

7. Online query module
Chimiothèque Nationale
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8. Online query module-
similarity searchChimiothèque Nationale
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9. Online query module-
batch viewChimiothèque Nationale
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10. Instant Jchem -
Storage and query data screeningChimiothèque Nationale
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11. Simplified Data Model
(Chemaxon-CN)Chimiothèque Nationale
structure
substance
batch
Laboratory
basket
Order
User
Access Log
Has structure
Is in
Provides
Provides
Direct to
Direct to
Has selected
or ordered
Has ordered
Has item
Has
accessed to
Cd_id
Structure_id
cd_ smiles
Cd_molecular_mass
Molfile
Inchi
Descriptors
Delete Status
Substance_nat_id
Substance_local_id
Packaging
Quantity
Purity
Nature_substance
Date_creation
Date_update
Delete Status
lot_nat_id
lot_local_id
Delete Status
Structure descriptors:
-LogP, HBD, HBA, Lipinsky (Chemaxon)
- Herg, Mutagen (Isida)
screening
Is tested
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Why use Jchem?

12. New web architecture
(Chemaxon-CN)Chimiothèque Nationale
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National
SDF File
CFusion tools
Chemaxon
Administration Server
APACHE (https) + PHP
+ SSH
Backstage National Server
National Database
(ORACLE +
Jchem Cartridge)
WEB Browser
Administration Client
SDF
File
Local Library
Database
Local Management
Isis/Draw MarvinSketch MarvinSketch
Isis/Base L-g Chimio JChemBase other…
other…
Secured
Connexions
WEB Browser
+ Sketch (Marvin)
Query Client

13. New query by name
(May 2013-…)Chimiothèque Nationale
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14. State of project and prospectsChimiothèque Nationale
1- Data model (OK)
2- Installation and configuration : Oracle Linux, Oracle, Jchem (OK)
3- Compounds loading ( in progress)
4- Query module
5- Data merging
6- Test
7- End of 2013 … : launch of the new information system
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15. DiscussionChimiothèque Nationale
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16. Marvin 03140315382D
13 14 0 0 0 0 0 0 0 0999 V2000
2.2043 0.1758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4898 0.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4898 1.4133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7754 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0609 0.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6536 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3680 0.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0825 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0825 -0.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3680 -1.0617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6536 -0.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0609 -1.0617 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7754 -0.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
6 7 2 0 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
9 10 1 0 0 0 0
10 11 2 0 0 0 0
6 11 1 0 0 0 0
11 12 1 0 0 0 0
12 13 1 0 0 0 0
4 13 1 0 0 0 0
M END >
> <bulk> (1)
3000
> <plate> (1)
lot1
> <id_local> (1)
LPS1877
> <purity> (1)
90
$$$$
Sdf File : the exchange fileChimiothèque Nationale
Mandatory fields Optional fields:
-substance nature
- purity analysis method
- observations
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17. Data Model of natural extracts
Chimiothèque Nationale
organism
Organism_part
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