Michael P. Woodward Supervisory Patent Examiner Art Unit 1631 (703) 308-4028...

Michael P. WoodwardSupervisory Patent Examiner

Art Unit 1631(703) 308-4028

[email protected]

SNiPpetS & BytesSNiPpetS & [email protected]

What is Bioinformatics?What is Bioinformatics?

Computational Biology:• Use of computational methods to

solve biological problems

• Involves storage, retrieval and analysis of biological data

• Will aid in gene discovery, molecular modeling, mutagenesis

BioinformaticsBioinformatics

• Involves methods reciting significant data processing steps directed to inventions in areas such as gene sequencing, nucleic acid hybridization, protein structure prediction, X-ray crystallography, pharmacology, receptor-ligand modeling, and immunology.

Bioinformatics:Bioinformatics:Challenges For USPTOChallenges For USPTO

• Creating appropriate classification systems for bioinformatics inventions - establishing definitions of what these applications comprise

• Processing and examination of the inventions and the voluminous data - implementing search infrastructure for analysis of large data sets

• Searching the bioinformatics prior art

• Staffing and training for examination of bioinformatics

• Legal issues pertaining to bioinformatics

Bioinformatics:Bioinformatics:Prior Art SearchingPrior Art Searching

• Developing collections of bioinformatics-related patents to serve as initial search resources:

– Searching publications of assignees pursuing this technology

– Patents currently in Class 702/subclasses 19-32 which are directed to bioinformatics

– Sequence alignments

– 3D modeling

– Motif/pattern searching

– DNA on a chip technology

BioinformaticsBioinformaticsArt Unit 1631Art Unit 1631

• Inventory of 275 "informatics" patent applications pending; 123 filed after October 1, 2000

• Projection: Over 300 applications this year

• Coordinates with TC 2100 and TC 2600(computer-related inventions) with regard to examination practice to maintain consistency

• Encourage interviews so both parties can better understand the invention and how it should be claimed

Bioinformatics: Bioinformatics: Examiner TrainingExaminer Training

• Specialized training with respect to 35 USC §112, first paragraph, including ESTs, 35 USC §101 with regard to biotechnology and computer based inventions and 35 USC §112, sixth paragraph.

• How to search the prior art for algorithms and other mathematical issues

• Currently available bioinformatics software packages

• Seminars and interactive sessions with representatives from firms and universities actively involved in bioinformatics

Case Law Impacting Case Law Impacting BioinformaticsBioinformatics

• State Street Bank & Trust Co. v. Signature Financial Group Inc.

• AT&T Corporation v. Excel Communications, Inc.

– Are part of a favorable legal climate for private research and development of bioinformatics

– Provide a framework for patent protection for inventions involving mathematical algorithms and business methods, e.g., 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)


• 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).

Non-functional Descriptive Non-functional Descriptive MaterialMaterial

• Mere arrangements or compilations of facts or data, stored so as to be read or outputted by a computer without creating any functional interrelationship, either as part of the stored data or as part of the computing processes performed by the computer.

A Common SituationA 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 Obviousness and Non-Functional Descriptive MaterialDescriptive 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 Obviousness and Non-Functional Descriptive Material (Cont.)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 ExampleA 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 ClaimPending Claim1. 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.

ConclusionConclusion

• 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 ApplicantsTips 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 2106.01-2106.02 for information on the submission of computer programs and/or flow charts.

• http://www.uspto.gov/web/offices/pac/dapp/oppd/patoc.htm


• 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.


• 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.


• 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.


• 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.


• 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.


• 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.


• Pay attention to the sequence rules, especially formal matters pertaining to references to sequences

Definition of SNPDefinition of SNP

• Single Nucleotide Polymorphism -

• A single base difference in a DNA sequence among individuals.

Issues/Prior ArtIssues/Prior Art• Would a single base difference over the

prior art have been obvious?

• Absent a teaching, suggestion, or motivation to modify the nucleic acid sequence at a particular location found in the prior art or in the knowledge generally available to one skilled in the art, such a difference would not have been obvious.

SNPs and UtilitySNPs and Utility

• A specification setting forth a specific, substantial and credible utility for a SNP would satisfy the utility requirement.

William “Gary” JonesSupervisory Patent Examiner

Art Unit 1655(703) 308-1152

[email protected]

SNiPpetS SNiPpetS [email protected]

Michael P. WoodwardSupervisory Patent Examiner

Art Unit 1631(703) 308-4028

[email protected]

SNiPpetS & BytesSNiPpetS & [email protected]

Michael P. Woodward Supervisory Patent Examiner Art Unit 1631 (703) 308-4028...

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