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 functions, which can be used by an application program to accomplish a desired set of tasks. Libraries of functions include a set of software routines to accomplish a desired set of tasks that are stored in a specialized format. A data protocol is a set of messages with pre-determined layouts that are used to allow devices to communicate on a computer network. A data pathway includes a route through a structured collection of information such as a logical route through nodes of a tree data structure resulting in some type of conclusion, inference or new knowledge.

These features are just a few examples of the type of novel features that may be part of a bioinformatic invention that have already been protected with software patents. There are numerous examples of patent claims in issued software patents6 from a variety of industries that can and should be used to help biotech patent practitioners protect similar novel features in bioinformatic inventions.

Preparing and prosecuting bioinformatic patent applications may require collaboration

Most bioinformatic inventions include a blending of complex biotech concepts along with complex computer science concepts. On the biotech side, bioinformatic requires an understanding of biological or chemical constructs and their interaction with other biological or chemical constructs, as well as a sense of how biotech experiments are designed, conducted and analyzed. If the bioinformatic invention includes innovations including nucleotide sequencing, metabolic pathways and other topics, the biotech concepts may require PhD level expertise in biology.

On the computer science side, bioinformatic requires an understanding of the design, development and implementation computer programs, computer algorithms, data structures and other software and hardware constructs. Depending on the invention, the computer science concepts typically require computer science expertise far beyond that held by any biologist. Very few patent practitioners have the appropriate expertise in biology and computer science to effectively draft bioinformatic patent applications to adequately protect bioinformatic inventions.

Since it may be difficult for either a biotech patent specialist or a software patent specialist alone to understand and appreciate all possible novel aspects of a bioinformatic invention, collaboration between such specialists can be very effective in preparing a bioinformatic patent application. In many instances, a bioinformatic inventor may be interviewed by a team comprising a biotech patent specialist and a software patent specialist. Each patent specialist asks the appropriate questions to determine the novel aspects of the bioinformatic invention in his/her area of expertise. This type of collaboration helps ensure that all of the novel aspects of a bioinformatic invention will be properly identified and addressed before a bioinformatic patent application is drafted.

Collaboration is also effective during the review and prosecution of a bioinformatic patent application. Regardless of which patent specialist actually drafts the bioinformatic patent application, the invention is going to include both biotech and software aspects. In such a collaboration, a biotech patent specialist reviews the biotech-related information, and a software patent specialist review the software-related information, to check for accuracy, un-necessary limitations and help overcome rejections by the patent office. This type of collaboration provides a better overall protection for a bioinformatic invention.

Bioinformatic inventions can be very important to the success or failure of a biotech company

In numerous segments of the biotech industry, bioinformatic inventions are still commonly viewed as far less important than biotech inventions. However, in many instances bioinformatic inventions may actually help determine the success of failure of a biotech company.

For example, visual display of biotech data with bioinformatic techniques is now recognized as being "necessary" for biotech research.7 Bioinformatic techniques used to create visual display tools such as a specialized GUI allow creation of complex views of large amounts of inter-related data. A specialized GUI may be created to provide a visual environment that is used to display a new nucleotide sequence discovered in a biotech experiment. The specialized GUI is used to compare the new nucleotide sequence to multiple known nucleotide sequences using multi-colored graphics or provide three-dimensional viewing.

Bioinformatic techniques included in the specialized GUI can be used to visually analyze new nucleotide sequences to quickly and efficiently determine the most promising and valuable new drug targets from the hundreds or thousands new nucleotide sequences discovered. The most promising drug targets can then be turned into pharmaceutical products, quicker and with less expense, giving the biotech company a competitive advantage in the marketplace. The bioinformatic techniques used to visually analyze the new nucleotide sequences and thus may be as important competitively to a biotech company as discovering the new nucleotide sequences themselves.

Patented bioinformatic inventions can provide a competitive advantage to a biotech company

A biotech company can use patents for bioinformatic inventions as an offensive weapon against competitors who are using bioinformatic technologies covered by a patented bioinformatic invention. Bioinformatic patents can be used to help maintain or even a gain a competitive advantage. A patent owner can prevent a competitor from making, using, selling or importing8 patented bioinformatic technologies and may decide not to license the patented invention. Without the offer a license to use the patent bioinformatic invention, a competitor who is relying on bioinformatic techniques covered by the patent would be forced to spend considerable time and resources designing around the asserted patent or risk millions of dollars in patent infringement litigation costs as well as the potential for treble damages9 for willful infringement.

Patented bioinformatic inventions may also be used defensively. For example, bioinformatic patents can be used for cross-licensing with competitors who also hold bioinformatics patents. They may also be used to prevent a competitor from trying to patent bioinformatic techniques invented by a biotech company. For example, if a biotech company chooses to conceal a bioinformatic invention (e.g., as a trade secret) and not pursue patent protection, it may lose the right to patent the bioinformatic invention to a competitor. In such a scenario, the competitor as a second inventor/first filer, may be able to bar the biotech company as a first inventor/second filer from using its own bioinformatic invention because of the concealment.10

Patented bioinformatic inventions can also provide an additional revenue stream to a biotech company

Many biotech companies often find themselves operating at a loss or operating with limited revenue as it typically takes many years for biotech companies to reach profitability. Biotech companies that find themselves strapped for cash should consider the value of patented bioinformatic inventions as a source of revenue. Although most biotech companies are typically not in the business selling or transferring patented bioinformatic technologies such as software, this is a business alternative all biotech companies with bioinformatic inventions should at least consider, especially when the bioinformatic invention is protected with a patent.

For example, software or other technologies including a patented bioinformatic invention can be licensed for an up-front payment and/or royalty payments over the life of the patent. Such a license on a patented bioinformatic invention can provide a revenue stream for the life of patent, not to exceed 20 years from its date of filing. However, many patented bioinformatic inventions including software or other computer technologies will have significantly shorter life cycles. Licensing can also accelerate the acceptance of bioinformatic inventions and may significantly increase the size of the market for such a patented product.

An innovative and patented bioinformatic invention developed by a biotech company can also be marketed, licensed and/or sold to other biotech companies, either to competitors or non-competitors, especially when a comparable product is not available. In this scenario, a patented bioinformatic invention may be licensed or sold for a first price to by non-competitor who is not using the bioinformatic invention to compete with the biotech company in a core business area. The patented bioinformatic invention may also be licensed or sold at a second, much higher price, to a competitor that does not desire to invest the time or resources to create technology including the bioinformatic invention, but competes with the biotech company in a core business area.

Many biotech companies should also consider packaging bioinformatic inventions with their biotech inventions. For example, a biotech company may sell or license automated instrumentation including patented biotech methods, laboratory robots, databases and computer hardware and software for genome sequencing or cell screening. A patented bioinformatic invention, including for example, a GUI and bioinformatic software to aid collection and analysis of experimental data may add significant value and justify a higher purchase price for such automated instrumentation.

Conclusion

Patent protection has been available for many years and should be sought for bioinformatic inventions. In light of the blending of complex biotech and computer science concepts, collaboration among biotech and software patent specialists may be the most effective way to prepare and prosecute bioinformatic patent applications. Patented bioinformatic inventions can also be effectively used for providing a competitive advantage, providing additional revenue streams or determining the ultimate success or failure of a biotech company.

FOOTNOTES

  1. Colin G. Sandercock and Qin Shi, "Database Systems Evolve in a Biotechnology Arena," Nat'l. L.J., March 27, 2000, at C8.
  2. State Street Bank & Trust Co. v. Signature Financial Group, 149 F.3d 1368 (Fed. Cir. 1998).
  3. AT&T v. Excel Communications, Inc. 172 F.3d 1352 (Fed. Cir. 1999).
  4. "Other News to Note," BioWorld Today, Aug. 17, 2000, at 3.
  5. See, e.g., Diamond v. Dehr, 450 U.S. 175 (1981), In re Freeman, 573 F.2d 1237 (CCPA 1978), as modified by In re Walters, 618 F.2d 758 (CCPA 1980) and In re Abele, 684 F.2d 902 (CCPA 1982), Arrhythmia Research Tech. V. Corazonix Corp., 958 F.2d 1053 (Fed. Cir. 1992), In re Lowrey 32 F.3d 1579, (Fed. Cir. 1994), In re Alappat, 33 F.3d 1526 (Fed. Cir. 1994), and the Manual of Patent Examining Procedures (MPEP), §2106, Patentable Subject Matter - Computer Related Inventions, USPTO.
  6. See, e.g., issued software patents in the free patent databases available on the Internet at www.uspto.gov or www.ibm.com/patents by searching for the software constructs described above.
  7. Dmitrij Frishman, et al., "Comprehensive, Comprehensible, Distributed and Intelligent Databases: Current Status," Bioinformatics Rev., vol. 14, no. 7, 1998, at 551, 557.
  8. 35 U.S.C. §271.
  9. 35 U.S.C. §284.
  10. 35 U.S.C. 102(g).

Copyright © 2000 by Stephen Lesavich, PhD. All rights reserved

 

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