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Improving the IP Search

By David Warshawsky

May 12, 2005 | The issues of what constitutes a new, patentable invention and what is protected by an issued patent are continuously being redefined and tested in the marketplace and in the courts. Effective resources to draft, prosecute, and examine patent applications, such as sophisticated data sources, will benefit all sides involved in the biotech patents arena.

To obtain the best possible patent coverage, and to ensure that issued patents represent novel inventions, it is essential to use sophisticated IT tools as well as traditional search mechanisms and methodologies. Such resources can effectively complement the traditional means used by IP professionals to perform prior art searches, to draft effective patent applications, and to successfully prosecute patent application.

The Challenge
Gene-related and biotech patents have seen turbulent times over the past decade. A few years ago, companies and non-profit research institutions were filing large patent applications, sometimes including thousands of DNA sequences. Assertions of utility were often based on negligible evidence. Over time, patent examiners became more demanding, seeking strong rationale for utility claims.

The U.S. Supreme Court and the U.S. Court of Appeals for the Federal Circuit have recently made the drafting and prosecution of patent applications even more challenging with their decisions in Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., Ltd., 234 F.3d 558, 586 (Fed. Cir. 2000) (en banc), reversed in part, by Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., Ltd., 535 U.S. 722 (2002).  The Festo cases significantly limited the doctrine of equivalents, which had been used by patent owners to expand the scope of their patents to cover infringers who were outside the literal scope of their patent claims. 

In Festo, the Supreme Court held that an amendment made during prosecution that narrows a claim creates a presumption that the applicant has surrendered any subject matter between the original claim and the amended claim, thus limiting the scope of the claim to its literal interpretation. Although the patentee may rebut the presumption by showing that “at the time of the amendment one skilled in the art could not reasonably be expected to have drafted a claim that would have literally encompassed the alleged equivalent,” in practice, this can be difficult to show at trial.

One approach to dealing with the Festo decisions calls for “filing with narrow claims that should be allowable without any need for amendments; filing continuation applications after the allowance of narrow claims in order to prosecute broader claims; explaining why amendments to the claims do not narrow their scope when amendments become necessary; and studying the prior art before drafting claims to avoid the necessity of amendments to overcome rejections based on the art.”

Peter Fasse, Esq., a principal with Fish & Richardson, suggests a somewhat different approach to preparing the first application, especially for clients with limited funds. Rather than starting with narrow claims, he drafts the claims as broadly as the prior art allows, and prosecutes the claims to obtain the broadest possible protection. On the theory that even if your claims are amended during prosecution, the literal scope may be broader than any equivalent one could obtain for a narrow claim that was never amended, Fasse believes one should not file claims that are too narrow just to avoid possible Festo issues.

Another example that highlights the challenges facing both patent applicants and the patent offices is the case of Myriad Genetics Inc.’s BRCA1 patent. Due to discrepancies between the sequence described in Myriad’s 2001 patent and the sequence in Myriad’s original 1994 application (the updated sequence exactly matched the one in the issued patent, but it was provided only after the patent was published and hence deemed prior art), the European Patent Office (EPO) decided in January that the contested patent could be maintained only in amended form. The patent now covers detection of specific mutations in the BRCA1 gene, but not diagnostic methods. To date the U.S. Patent and Trademark Office has not announced a decision to reject or revoke this patent. The National Academies of Science has urged greater care in approving gene sequence patents.

These examples show how crucial it is to file accurate, detailed descriptions and claims (and of course to attempt to generate broad coverage as well). Patent applications are examined for novelty and non-obviousness relative to prior art. Thus, they should also be drafted with the prior art in mind. Hence, it is essential to determine the novel aspects of a potential invention, and to file the application after considering all known relevant information. Given the explosion in the amount and complexity of prior art, the challenges facing intellectual property (IP) professionals performing such tasks has become formidable. 

The Solution
The examples above and the overall state of patenting in the biotech field clearly demonstrate the need for advanced and comprehensive tools that enable IP professionals to perform searches of the current knowledge base. Ease of use is key, too, since IP professionals conduct a large number of searches. Effective tools are essential for both preparing and examining patent applications. First, applicants must conduct efficient prior art searches to determine if a potential invention can be patented, and retrieve relevant information to support application drafting and patent prosecution. Second, examiners need efficient and comprehensive search tools to perform examinations.

Traditional methods for prior art search and for identifying relevant information regarding a potential invention rely on searching databases of trade and professional publications as well as seminar reports and patent databases.

In addition to these resources, many databases about genes and their products exist. Fortunately, as the field of gene-related patenting evolved, so did the software tools and databases that relate to genes and their products. However, to be effective for IP professionals, a data source needs to integrate data from many sources in order to provide complete data and to overcome the challenges imposed by data format heterogeneity (e.g., the use of multiple synonyms for a given gene). Since most data sources either focus on a subset of gene-based data or rely mostly on their particular organization’s view of the data, they do not always answer the needs of IP professionals.

One tool that effectively deals with these needs is GeneCards, which was developed by a bioinformatics team at the Weizmann Institute of Science in Israel. GeneCards is a compendium of human genes and their encoded proteins, with major focus on functional genomics and medical aspects, including involvement in diseases. The tool extracts and integrates a carefully selected subset of the gene information obtained from major data sources, overcoming barriers of data format heterogeneity. GeneCards is unique in both its user-friendly interface and the organization and display of links and detailed information.

Drawing on information from many data sources, GeneCards is an effective way to perform prior art searches likely to reveal any existing art. Because it is comprehensive, it can help ensure that the patent applicant identifies all potential utilities using sound rationale as well as potential compositions (i.e., DNA and/or protein sequences) that are related to the subject matter of the patent at hand.

While popular with many biotech and pharmaceutical companies for research and development, GeneCards is also extremely useful for IP professionals engaged in patent prosecution and examinations. The EPO, for example, queries GeneCards in the review and approval of patent applications in life sciences, as a key component in the process of approving biotech patent applications. Patent examiners from the EPO access GeneCards to conduct prior art research and help determine whether an invention is patentable, and to retrieve relevant information to support their patent-related activities. The EPO also uses LION Bioscience’s SRS system, which will soon be available as an integrated system with GeneCards for review and approval of patent applications. The EPO will use GeneCards via SRS upon integration by LION. The use of systems such as GeneCards and SRS by the EPO emphasizes the need for such advanced tools to improve prior art searching. l

David Warshawsky is CEO of Xennex Inc. based in Cambridge, Mass. Email: The author thanks Peter Fasse, Esq. (Fish & Richardson P.C., email:, for his assistance and insight in writing this article.

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