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?
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
Ref: Michael Stonebraker Object-Relational DBMSs
The Next Great Wave,Morgan Kaufmann Publishers, Inc., San Francisco,
Why not use commerically available products or proprietary
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
select molecule from chemtable
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
RS3- Oxford Molecular has added chemical storage and searching
capabilities to Oracle 7
ISIS Host Gateway to Oracle, client application is ISIS
EuroMug'98, 6-7 October 1998 Cambridge, England
Daylight Chemical Information Systems,