Daylight CGI interface

David Weininger
Daylight Chemical Information Systems, Inc.
Santa Fe, New Mexico

Daylight Common Gateway Interface (DCGI)

The World Wide Web has caused a revolution in the way information is exchanged in the last few years. Starting from humble beginnings (distribution of static documents), it has grown to embody most computational user interface functions. One can easily argue that the Web has fundamentally transformed the ideas of "publishing", "computer", "database" and "user interface".

One of the most powerful Web concepts is the Common Gateway Interface (CGI), a mechanism to deliver computational results and a meta-GUI to an end user over the net. Given CGI-capable servers and clients, the "Web" becomes a what we used to think of as a "computer" and computers become more like abstract "computational resources".

The Daylight Common Gateway Interface (DCGI) is a chemical information interface which operates using Web technology. Such technology can be used on an isolated machine, in a secure network, or in the global WWW environment. The Web provides a great framework and many general purpose utilities but was not designed to deliver chemical information interactively and is deficient in this respect. DCGI provides tools, utilities, and meta-interfaces required to successfully deliver chemical information in the Web environment.

A brief history of chemical information interfaces

Single-machine architecture

Database interfaces were terminal-based programs which directly accessed databases which were simple files. Data integrity was dependent on the quality of interface programs. Access to data was limited by the need to connect directly to the computer on which the data was stored. User interfaces were extremely machine-specific, e.g., only terminals for which the system was developed worked reliably. Such database systems are expensive to build, debug, maintain, improve, and purchase.

Client-server architecture

Databases are accessed by a single "server" process which provides all services required by one or more "client" processes via a network. TCP/IP becomes the defacto network standard.. Client-server systems are able to provide high data integrity, concurrency, access control and high-volume data delivery. Database application programs become distinct from database systems, e.g., they could operate on completely different platforms.

In theory, user-interface programs should have become less precious since maintaining data integrity is now a server responsibility. In fact, this simplification was more than offset by the added complexity required to create a reliable, event-driven GUI. Such systems remained expensive largely due to the added effort required to build complex client interfaces.

World Wide Web architecture

The need for information delivery in other fields leads to the widespread availability of very capable, high-quality information browsers. HTML (Hypertext markup language) servers, HTML browsers, IP (Internet Protocol) and the Internet itself combine to form a defacto standard for information exchange. Because HTML servers now provide a meta-GUI as well as data, the whole job of data delivery can be done with servers.

This architecture should result in major improvements in the availability and cost of chemical information access. Since the entire information delivery interface is provided "free" to the developer, a system based on a "zero-cost seat" should be possible. Remaining issues include access control, high-volume data delivery and handling the special requirements of chemical information.

Key features

Advantages of the DCGI approach

Disadvantages of the DCGI approach

DCGI Architecture

Secure DCGI system

wdi -- a minimalistic interface

The wdi HTML interface is a special-purpose interface to Derwent's World Drug Index. It is designed to deliver essential information quickly and reliably to users who do not need to be chemical information specialists.

acd -- a special-purpose interface

The acd HTML interface is a special-purpose interface to MDL's Available Chemical Directory. This interface is designed for ACD users who purchase chemicals (who are typically not chemical information specialists).

savant -- a special-purpose interface

Savant is a special-purpose interface to the Spresi database which is designed to provide chemists with a synthetic literature survey as painlessly as possible. Given a structure, the user is presented with references to papers which describe the synthesis of the given structure (if available) and similar structures.

hyperthor -- a general-purpose database browser

Hyperthor is a general-purpose HTML browser for Thor databases.

wizard -- a general-purpose EDA interface

Wizard is a general HTML interface to Merlin, an exploratory data analysis tool. The wizard interface is quite different from others described here: it is basically a programming tool for MCL (Merlin Control Language).

DCGI "Toolkit"

Grins in v4.5 and beyond

The version of Grins available in MUG '96 is the 4.42 version, suitable for input of generic organic structures only. There is only one control panel in this version:

The initial version of the 4.5x Grins prototype is very similar:

Additional capabilities (chirality and reaction specification) are provided by a second panel which is available by selecting the "More" control:

If reaction specification is prohibited the panel looks like this:

Are the functions of the smiley faces clear? Can anyone suggest better icons?)

It is tempting to write a version of Grins in Java. Maybe we'll try it out and see. In any event, the basic HTML-Grins capabilities will be available in DCGI.

Outstanding issues

Daylight Chemical Information Systems, Inc.