Michael P. Woodward Supervisory Patent Examiner, Art Unit 1631 (703) Bioinformatics & §101

NonStatutory Subject Matter Claims to bioinformatics-related inventions that are clearly nonstatutory fall into the same general categories as nonstatutory claims in other arts.

Case Law Impacting Bioinformatics In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994) (claim to data structure stored on a computer readable medium and that increases computer efficiency held statutory subject matter) In re Warmerdam, 33 F.3d 1354, 31 USPQ2d 1754 (Fed. Cir. 1994) (claim to data structure per se held nonstatutory subject matter where data structure did not cause functional change in computer)

Functional Descriptive Material Consists of data structures and computer programs which impart functionality when employed as a computer component.

Data Structure Defined “a physical or logical relationship among data elements, designed to support specific data manipulation functions.” (The New IEEE Standard Dictionary of Electrical and Electronics Terms 308 (5 th ed. 1993))

Nonfunctional Descriptive Material Includes but is not limited to music, literary works and a compilation or mere arrangement of data

Neither type of “descriptive” material is statutory when claimed as descriptive material per se

Merely claiming nonfunctional descriptive material stored in a computer-readable medium does not make it statutory.

Case Law Impacting Bioinformatics In re Gulack, 703 F.2d 1381, 1385, 217 USPQ 401, 404 (Fed. Cir. 1983) (when descriptive material is not functionally related to the substrate, the descriptive material will not distinguish the invention from the prior art in terms of patentability).

A Common Situation a process that differs from the prior art only with respect to nonfunctional descriptive material that cannot alter how the process steps are to be performed to achieve the utility of the invention.

Obviousness and Non-Functional Descriptive Material If the difference between the prior art and the claimed invention is limited to descriptive material stored on or employed by a machine, Office personnel must determine whether the descriptive material is functional descriptive material or nonfunctional descriptive material. Functional descriptive material is a limitation in the claim and must be considered and addressed in assessing patentability under 35 U.S.C. 103.

Obviousness and Non-Functional Descriptive Material (Cont.) Thus, a rejection of the claim as a whole under 35 U.S.C. 103 is inappropriate unless the functional descriptive material would have been suggested by the prior art. Nonfunctional descriptive material cannot render nonobvious an invention that would have otherwise been obvious.

A Virtual Life Example A method of determining the most hydrophilic peptide in a polypeptide comprising a sequence of at least six amino acid residues which method comprises: (a) determining the amino acid sequence of said polypeptide; (b) assigning relative hydrophilicity values to each sequenced amino acid; (c) determining the repetitive local average of hydrophilicity values on the basis of said assigned values of each residue of at least six amino acids sequentially along said polypeptide; (d) comparing said repetitive local averages and selecting the peptide of at least six amino acid residues corresponding to the greatest local average hydrophilicity..

Pending Claim 1. A method of determining the most hydrophilic peptide in a polypeptide comprising a sequence of at least six amino acid residues which method comprises: (a) inputting SEQ ID NO:2; (b) assigning relative hydrophilicity values to each sequenced amino acid; (c) determining the repetitive local average of hydrophilicity values on the basis of said assigned values of each residue of at least six amino acids sequentially along said polypeptide; (d) comparing said repetitive local averages and determining the peptide of at least six amino acid residues corresponding to the greatest local average hydrophilicity.

Conclusion Because the specifically recited SEQ ID NO: 2 is mere data and does not alter the actual process steps the claim would be rejected as obvious over the reference disclosure.

Tips for Bioinformatics Applicants Applicants should be increasingly aware of overlapping biotech and computer technologies To the extent that an invention overlaps into the computer arts, biotech attorney should become familiar with the Examination Guidelines for Computer-Related Inventions Consult MPEP for information on the submission of computer programs and/or flow charts. htm

Tips for Bioinformatics Applicants Avoid claims to a computer readable media with sequence data on it. These claims are drawn to non statutory descriptive matter. However, a claim to a software program on a disk may be statutory.

Tips for Bioinformatics Applicants Take care to distinguish clearly between manipulation of molecules and sequence information, e.g., software that deletes flanking vector sequences from insert sequences after sequencing a clone. Do not phrase the claim to recite deletion of nucleic acids from the vector nucleic acid, if you really intend to refer to sequence data or information.

Tips for Bioinformatics Applicants Come in for Interviews: Clarity of and support for claim language has been a central issue. Claims tend to be extremely broad and actual embodiments are frequently difficult to understand which has led to confusion. Both applicants and their representatives have been wonderfully cooperative in having interviews and explaining their inventions.

Tips for Bioinformatics Applicants Consider both the biotechnology aspects and the computer software aspects of the invention; make sure the disclosure is ample for both. Trap: citing an example of a computer program which you assert can be adapted to perform the computer aspects of the invention. During prosecution you may become aware of the fine points of the computer components which may render the claims patentable but the specification may provide inadequate support for a specific computer.

Tips for Bioinformatics Applicants Assert a practical utility and disclose how it is realized in the specification. Submit an IDS, especially foreign patents and NPL to assist examiner. Provide the most relevant prior art in usable form and information on the state of the art. Disclose and claim clearly what is the real invention.

Tips for Bioinformatics Applicants Provide more information regarding the significance of art recognized terminology used in the patent application. Define such terms in the specification. –These terms may be hard to search. –It may not be clear how broadly these terms are being applied. –Be especially clear as to how the invention differs from the prior art as many statistical techniques and mathematical elements are prior art but are difficult to find in searches.

Tips for Bioinformatics Applicants Pay attention to the sequence rules, especially formal matters pertaining to references to sequences