Bioinformatics: The New Software Patent Frontier

Originally Published in the National Law Journal (Vol. 23, No. 8) on October 16, 2000, at B10.

Automated instrumentation used to conduct biotechnology experiments is generating unprecedented amounts of experimental data. Experimental data from automated High Content Screening systems, High Throughput Screening systems and other automated systems using micro-arrays or bio-chips is being used for genome sequencing, drug discovery and genetic analysis to help select better pharmaceutical targets and to help cure diseases.

New bioinformatic techniques are being developed to collect, store and manipulate such experimental data. In general, such bioinformatic techniques relate to the systematic development and application of informatic methods and data mining techniques for processing, storing, analyzing and displaying experimental data obtained from automated instrumentation, automated modeling and database searching to make observations about biological processes. Many of these bioinformatic techniques can be protected with patents.

Patents could always be used to protect novel aspects of bioinformatic inventions

Only a small number of biotech companies have attempted to protect their bioinformatic inventions with patents. If bioinformatic inventions have been protected with patents at all, the focus of the protection has been limited mostly to instrumentation hardware and to databases systems, databases and database structures used to store experimental data generated by automated screening systems.1

The holdings of the State Street Bank2 and AT&T3 cases have allowed the biotech industry to begin to pursue methods of doing business patents including those related to the Internet. The State Street Bank and AT&T cases have also heightened the awareness of the biotech industry to the importance of protecting bioinformatic inventions with software patents. For example, the IBM Corporation has recently formed a new life sciences business unit and is investing $100 million to develop new bioinformatic related technologies.4

However, many executives in the biotech industry and even many biotech patent practitioners have mistakenly concluded that the holdings of these cases have only now provided the opportunity to seek patent protection for bioinformatic inventions with software patents. Yet, most bioinformatic inventions, such as including those inventions related to software methods, software systems, data structures, the Internet and other software features were capable of receiving patent protection with software patents long before the State Street Bank and AT&T cases were decided under U.S. patent law.5

In addition, software patents have been used for many years in the computer industry and other industries to protect novel features similar to those now being developed in connection with bioinformatic inventions. For example, bioinformatic inventions may include such novel features such as a graphical user interface ("GUI"), application programming interfaces ("API"), libraries of functions, data protocols and data pathways.

A GUI provides a visual environment to represent information with graphical icons, menus, dialog boxes and other graphical entities that can be selected and manipulated by a user with a mouse or a keyboard. An API is a programming interface to a set of software routines, such as a library of...