Daylight/Oracle Chemistry Cartridge
Finally a Chemical Database

Alberto Gobbi

Novartis Crop Protection

This is a Marketing Presentation

• I have not seen the cartridge yet.
• But I will tell you all about the features.
• Everything sounds great!
• I will not tell you any delivery dates.
• I will not mention any prices.

Why do we Need it?

• For data modeling.
• For application development.
• For database management.

Data Modeling: How do we Create Data Models?

$D<"$SMI">_
V<Structure:SMILES>
_B<SMILES>
_N<USMILES MAKEGRAPH>
_P<*>
_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 complete description.>
_M<System, Structure, Lookup, Common>
TS<199707081541.19>
|
$D<"$ISW">
_V<"indirect/keywords;keywords">
_B<"$ISW/id;$ISW/data">
_S<Indirect reference for keyword data, used in Spresi datatypes JA and PAT>
_P<>
_C<Spresi datatype>
_M<Indirect>
_O<mjollnir@daylight.com>
TS<199707081541.19>
|
$D<AMW>
_V<Ave molecular weight>
_B<Ave MW>
_N<NUMERIC>
_P<>
_S<Average molecular weight using isotope distribution in nature>
_D<Average molecular weight using isotope distribution in nature>
_M<System, Medchem, Measured>
TS<199707081541.19>
|

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
      password
      rename mol>(molclass) to <hide>
      rename mol>(molskeys) to <hide>
      rename mol>(molname) to <hide>
      tinfo key molregno

   tree model basedon mol
      tname model
      password
      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!

• Get all the nearest neighbors of ?

  SELECT s.Structure FROM Structures s, Neighbors n WHERE
  s.id = n.NeighborAND n.Compound = 3578;

• Get all salts of ?

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

• All salts with same BaseCompound.
• Different depiction (display formats) for different users?
• Link biological, toxicological, physical or Spectroscopic data
• Update Neighbors table by triggers.
• 

Application Development: A 100% Daylight Database Example

Easy Full Structure Search. No enforcement of relationships in the database. No consistency check 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 Example.

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

Why? For Application Development

• Enforce data consistency.
• Enforce relationships.
• Allow for transactions.
• Simple query and update of any fields via SQL.
• Easy link do any other data in house.
• Standard Client Server interfaces (JDBC, ODBC).
• Data aware controls (Java Beans & ActiveX).
• Fullstructure, substructure, tautomer and similarity search.

Why? For Database Management

• Current structural input of 500 000 compounds per year.
  • TPO Third Party database 2 000 000 records.
  • Screening Database 500 000++ entries.
• Future input 1 000 000++ compounds per year.
• Cartdridge advantages:
  • Maintenance by professionals.
  • No 2 GB file size limit.
  • Partitioned backup.
  • On-line backup.
  • Parallelization?
• Scaleable?

Our Plans: The Chemical Repository CHEST

• Centralization of storage for structures.
  • Store structures in one place.
  • Enforce corporate normalization roles.
• Unify Access to structures
  • Provide one single API which can be used from any applications.
• Leave database management be done by professionals.

What Do we Need? Finally a Chemical Database!

• Requirements:
  • Canonization of SMILES in the database.
  • Conversion function from and to SMILES and MOL-Files in the database.
  • Check for corporate structural rules in the database (API).
  • Substructure Search in the database.
  • Bugfix in SMILES canonization.
• Nice to have:
  • Similarity search.
  • Direct MERLIN load from database.
  • Update of MERLIN pool via database triggers.
• Daylight on HP-UNIX.

Contributions