Motivation

Chemical structure databases have been traditionally stored in non-relational systems. Biological data has traditionally been stored in relational systems. With the emergence of ORDMSs (Object Relational Database Management Systems), we have investigated the possibility of using an ORDBMS to integrate these two kinds of data.

Object Relational Database Management System versus a Relational Database Management System- What's the difference?

RDBMS-

Limited number of datatypes- char, decimal, integer, date, ..

Data stored in tables has to have a format that is one of the standard datatypes

Limited number of functions- equals, less than, greater than, ...

Functions are restricted to SQL-92 standard functions

ORDBMS-

Ref: Michael Stonebraker Object-Relational DBMSs The Next Great Wave,Morgan Kaufmann Publishers, Inc., San Francisco, CA, 1996.

Extended Datatypes- clob (character large object), blob(binary large object), opaque datatypes, multi-rep types. Database Administrators can define their own "types"
Extended Functions- function overloading (Equals, less than, greater than, etc.), server understands new functions in SQL queries. DBAs can define their own "functions"
This technology gives us the ability to define a "molecule" type (tmol), and chemical query functions, e.g. day_findsassub.

ORDBMS SQL Example:

create table chemtable(molecule tmol);

load from 'medchem97.smi' delimiter '|' insert into chemtable(molecule);

select molecule from chemtable
where day_findassub('c1ccccc1',molecule);

Why not use commerically available products or proprietary custom applications?

Current approaches for integration:

Commercial Products-

RS3- Oxford Molecular has added chemical storage and searching capabilities to Oracle 7
ISIS Host Gateway to Oracle, client application is ISIS

Proprietary Applications-

Cousin (Pharmacia-Upjohn)

With the current rate of data acquisition due to combinatorial chemistry and High Throughput Screening (HTS), Information Technology groups are constantly faced with the challege of custom data integration applications. Can we use Daylight and ORDBMS to generate a database which allows for flexible application interfaces to be built on the order of weeks instead of months?

EuroMug'98, 6-7 October 1998 Cambridge, England

Daylight Chemical Information Systems, Inc.
info@daylight.com