Daylight/Oracle Chemistry Cartridge
Using the Chemistry Cartridge

Alberto Gobbi

Novartis Crop Protection

Why do we need it?

Daylight is a great Chemical Information System!

But not a perfect database system!


Data Modeling: How do we Create Data Models?

_S<SMILES notation, primary identifier in the Daylight system>
_D<The uniquified SMILES notation is the primary key to all data in the Daylight Chemical Information System. See the Daylight Software Manual for a comple
te description.>
_M<System, Structure, Lookup, Common>
_S<Indirect reference for keyword data, used in Spresi datatypes JA and PAT>
_C<Spresi datatype>
_V<Ave molecular weight>
_B<Ave MW>
_S<Average molecular weight using isotope distribution in nature>
_D<Average molecular weight using isotope distribution in nature>
_M<System, Medchem, Measured>

hview nci3d

comment This is the Hview for the NCI-3D 94.1 database with MODEL over MOL.
comment 11/16/94

tree mol
device maccsdb
database nci3d:
tname mol
rename mol>(molclass) to <hide>
rename mol>(molskeys) to <hide>
rename mol>(molname) to <hide>
tinfo key molregno

tree model basedon mol
tname model
rename model>(molregno) to (2d_regno)
rename model>(modelname) to <hide>
tinfo fieldtype source model.source flatten text
tinfo key modelregno

link model model>(molregno) over mol (molregno)

Data Modeling: How is your Data Model?

Data Modeling: A Relational Model

Why? For Data Modeling!

SELECT s.Structure FROM Structures s, Neighbors n WHERE = n.Neighbor AND n.Compound = 3578;

SELECT s.Structure FROM Structures s, Salts sa WHERE = sa.salt AND sa.BaseCompound = 1001;

Application Development:
A 100% Daylight Database Example

  • Easy Fullstructrue Search.
  • No enforcement of relationships in the database.
  • No consistency checks in the database.
  • Complicated navigation through the data hierarchy.
  • No link to biological data.
  • No transactions.
  • No data aware controls (Java Beans, ActiveX).

Application Development:
An Oracle 7/Daylight Toolkit Example.

  • No substructure search.
  • Complicated SMILES canonization.
  • Complicated structure normalization.
  • No tautomer search.
  • No hash lookup.
  • No similarity search.

Application Development:
An Oracle 8I Example.

  • Includes Daylight SSS.
  • Includes similarity search.
  • Implementation effort: 5H
  • Easy SMILES canonization.
  • Callouts for structure normalization.

Why? For Application Development

Why? For Database Management

First Experience: Not Perfect but Alive!

Do we need more?

DayBlob is Alive!

It is not perfect but a large step ahead!


Norah MacCuish

Dave Weiniger


Sam Defazio

Johnny Petersen

Cathleen Trezza

M. Visscher


Paul Gatewood

Matthias Ochs

Dieter Poppinger

Bernd Rohde

CP_IT Department