Ex Parte Kincaid et alDownload PDFPatent Trial and Appeal BoardFeb 26, 201610403762 (P.T.A.B. Feb. 26, 2016) Copy Citation UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 10/403,762 03/31/2003 22878 7590 03/01/2016 Agilent Technologies, Inc, in care of: CPA Global P. 0. Box 52050 Minneapolis, MN 55402 FIRST NAMED INVENTOR Robert Kincaid UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www .uspto.gov ATTORNEY DOCKET NO. CONFIRMATION NO. 10020714-2 6328 EXAMINER SIMS, JASON M ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 03/01/2016 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address( es): IPOPS.LEGAL@agilent.com Agilentdocketing@cpaglobal.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte ROBERT KINCAID and ADITY AV AILA YA Appeal2013-007930 Application 10/403,762 1 Technology Center 1600 Before RICHARD M. LEBOVITZ, JEFFREY N. FRED MAN, and JACQUELINE T. HARLOW, Administrative Patent Judges. LEBOVITZ, Administrative Patent Judge. DECISION ON APPEAL This appeal involves claims directed to a system comprising a memory that stores an ordered data matrix, a display, a pointer, and a processor that reorders the data matrix. The Examiner has finally rejected the claims as obvious under 35 U.S.C. § 103(a). We have jurisdiction under 35 U.S.C. § 134. The Examiner's rejections are affirmed. STATEMENT OF CASE Appellants appeal from the Examiner's final rejection of claims 62, 63, 67, 70-77, and 84--89. The claims stand finally rejected by the Examiner as follows: 1 "The '762 Application." Appeal2013-007930 Application 10/403,762 1. Claims 62, 71, 74--76, 85, 88, and 89 under 35 U.S.C. § 103(a) as obvious in view of Warrington, 2 Rusterholz, 3 Balaban '5 61, 4 and Tamura. 5 2. Claims 70, 72, 73, 84, 86, and 87 under 35 U.S.C. § 103(a) as obvious in view of Warrington, Rusterholz, Balaban '561, and Tamura as applied to claims 62, 71, 74--76, 85, 88, and 89, and further in view of view of Bal ab an et al.,' 5 0 1, 6 Ootomo, 7 and Ram et al. 8 3. Claims 63, 67, 77, and 81under35 U.S.C. § 103(a) as obvious in view of Warrington, Rusterholz, Balaban '561, and Tamura as applied to claims 62, 71, 74--76, 85, 88, and 89, and further in view of view of Schadt. 9 There are two rejected independent claims, claims 62 and 76. Claim 62 is reproduced below (brackets with numbers have been added to distinguish the different limitations in the claims): 62. A system comprising: [ 1] a memory that stores an ordered data matrix compnsmg: [ 1 a] a plurality of values representing a plurality of different physical measurements performed on a plurality of samples, [ 1 b] a plurality of sample descriptive values corresponding to each sample, each sample descriptive value characterizing a corresponding sample independent of said measurements, and [ 1 c] a plurality of measurement descriptive values corresponding to each physical measurement, each 2 US 6,884,578 B2, issued April 26, 2005. 3 US 5,864,838, issued January 26, 1999. 4 US 6,185,561 Bl, issued February 6, 2001. 5 US 2002/0021299 Al, published February 21, 2002. 6 US 2003/0028501 Al, published February 6, 2003. 7 US 6,269,261 Bl, issued July 31, 2001. 8 US 2003/0009411 Al, published January 9, 2003. 9 US 7,035,739 B2, issued April 25, 2006. 2 Appeal2013-007930 Application 10/403,762 measurement descriptive value characterizing a corresponding type of measurement or measurement condition, independent of said samples; [2] a display comprising a two dimensional detail display having a plurality of cells, each cell corresponding to one of said values in said data matrix, said display providing a view of a portion of said data matrix that is defined by a base location in said data matrix; [3] a pointer that selects one of said cell in said display and [ 4] a processor that reorders said data matrix based on a measure of similarity of values corresponding to one of said samples or physical measurements, said one of said samples or physical measurements being indicated by said pointer, said processor causing said display to display a new portion of said data matrix based on said re-ordering. REJECTION 1 The Examiner found that Warrington describes an n x m matrix stored in a database, meeting the claim limitation of a [ 1] "a memory that stores an ordered data matrix." Final Rej. 4. The Examiner also found that Warrington's system comprises a [2] "display." Id. at 4--5. The Examiner stated that Warrington does not teach a [ 4] "a processor that reorders said data matrix," but found that Rusterholz and Balaban '561 describe methods for reordering a matrix of data. Id. at 5. The Examiner also cited Tamara for displaying data that had been reordered. Id. at 6. The Examiner concluded that it would have been obvious to one of ordinary skill in the art to reorder and display reordered data as described by Rusterholz, Balaban '561, and Tamura in Warrington's method "because it can be more effective and is a goal of the researcher to be able to visualize 3 Appeal2013-007930 Application 10/403,762 and manipulate data in customizable ways in order to be able to more effectively interpret experimental data." Id. Appellants contend that Warrington does not describe [ 1 a] "a plurality of different physical measurements" nor [ 1 c] "a plurality of measurement descriptive values corresponding to each physical measurement" as required by the claims. Appeal Br. 8; Reply Br. 3. Appellants' arguments are not supported by a preponderance of the evidence. Warrington, as found by the Examiner, describes a relational database comprising "reference samples": Those skilled in the art will recognize that in a preferred embodiment, the expression profiles from the reference samples will be input to a database. A relational database is preferred and can be used, but one of skill in the art will recognize that other databases could be used. A relational database is a set of tables containing data fitted into predefined categories. Warrington; co 1. 12; 11. 41--4 7. Contrary to Appellants' assertions, Warrington also describes [ 1 a] "a plurality of different physical measurements performed on a plurality of samples." Warrington discloses: The database is assembled with a plurality of different samples to be used as reference samples. An individual reference sample in one embodiment will be obtained from a patient during a visit to a medical professional. The sample could be for example a tissue, blood, urine, feces or saliva sample. Information about the physiological, disease and/or pharmacological status of the sample will also be obtained through any method available. This may include, but is not limited to, expression profile analysis, clinical analysis, medical history, and/or patient interview. Id. at col. 12, 1. 58 to col. 13, 1. 1 (emphasis added). 4 Appeal2013-007930 Application 10/403,762 The individual sample, as indicated above, can be characterized by its "physiological" and "pharmacological" status, each which would involve "different physical measurements" as required by the claim. Specifically, Warrington teaches that physiological state "refers to any normal biological state of a cell or organism." Id. at col. 3, 11. 28-30. Warrington teaches: Preferably several indicators of physiological state will be used to categorize a reference sample. Methods to determine the physiological state of a sample include but are not limited to measuring the abundance and/or activity of cellular constituents (expression profile, genotyping), morphological phenotype, or interview of the subject. Id. at col. 3, 11. 38--43. Expression profile, genotyping, and morphological phenotype are physical characteristics of the sample and thus constitute "different physical measurements." Warrington further teaches that the "pharmacological state of a sample relates to changes in the biological status following drug treatment." Id. at col. 4, 11. 19-20. Warrington describes measuring the biological state with methods "not limited to measuring the abundance and/or activity of cellular constituents, characterizing according to morphological phenotype or a combination of the above methods." Id. at col. 4, 11. 35-39. Warrington also discloses that the "biological status of a sample can be measured or observed by interrogating the abundances and/or activities of a collection of cellular constituents." Id. at col. 4, 11. 40--42. The latter measurements, i.e., "abundance and/or activity of cellular constituents," "morphological phenotype," are clearly "physical measurements" as required by the rejected claims. 5 Appeal2013-007930 Application 10/403,762 In sum, the disclosures from Warrington quoted above provide clear evidence that Warrington describes a "plurality of different physical measurements performed on a plurality of samples," including expression profiles, genotypes, morphological phenotypes, and abundance and/or activity of cellular constituents. The plurality of physical measurements are present in an "ordered data matrix" as required by rejected claims 62. Warrington describes a table in which physiological status is "further categorized according to disease and pharmacological status." Id. at col. 13, 11. 19--31. Warrington also describes at column 16, lines 14--30 "a database of reference samples wherein the samples could be comprised of expression profiles from many different individuals and the samples themselves can be derived from tissue at different stages and tissues subjected to a variety of perturbations." Answer 12. In others words, a single table or matrix can comprise the plurality of physical measurements, including measurements from physiological status, pharmacological status, and expression profiles. [le] "a plurality of measurement descriptive values corresponding to each physical measurement, each measurement descriptive value characterizing a corresponding type of measurement or measurement condition, independent of said samples" Appellants contend that Warrington does not describe "measurement descriptive values" as recited in limitation [ 1 c]. Reply Br. 3. Appellants state: "there is no column in the tables taught in Warrington that specifies the type of physical measurement in the row in question as would be necessary if there was more than one type of physical measurement." Id. 6 Appeal2013-007930 Application 10/403,762 The claim defines "measurement descriptive value" as a "type of measurement or measurement condition." Appellants direct our attention to paragraph 7 5 of the Specification for this limitation, but we do not find a clear definition at this location of what is meant by the claim terms. Appeal Br. 3. As best as we understand it, a measurement descriptive value could be specifying that the measurement was: of RNA or DNA when an expression profile is used ("type of measurement"); of abundance units or intensity units of the sample ("type of measurement)"; when or at what stage the sample was taken ("measurement condition"); or, the physiological or disease status of the patient ("measurement condition"). See also Answer 12. The disclosure identified by the Examiner at column 16 provides evidence that Warrington describes "a plurality of measurement descriptive values corresponding to each physical measurement." The pertinent passage is reproduced below: In one aspect, a database of reference samples could be comprised of expression profiles from endometrial samples and data points identifying the physiological, pharmacological and/or disease state of the samples. These reference samples would be from many different individuals representing many different physiological, pharmacological and/or disease states. The reference samples can be derived from for example: normal tissue at different stages of development and differentiation, tissues affected with a variety of pathological conditions, including but not limited to, premenstrual syndrome, PMDD, stress urinary incontinence, polycystic ovarian disease, endometriosis, endometrial cancer, infertility, hormone imbalance, and tissue subjected to a variety of perturbations including but not limited to hormone replacement therapy, or chemical contraception. In one preferred embodiment, reference samples will be taken from individuals 7 Appeal2013-007930 Application 10/403,762 during routine doctor visits. In one embodiment the reference samples would represent different physiological states of the menstrual cycle including but not limited to the secretory and proliferative stages of the endometrium. Warrington, col. 16, 11. 14--34 (emphasis added). As described above, Warrington discloses taking samples from different "stages of the endometrium" and determining their physiological state, the latter which would involve physical measurements such as the expression profile, morphological phenotype, and activity and/or abundance of cellular constituents. The different "stages of the endometrium" would represent different periods of the menstrual cycle, constituting a "measurement condition" of a "measurement descriptive values" because it describes at what stage the sample was taken ("measurement condition"). Warrington also mentions taking samples from different "pathological conditions," which would represent the disease status of the patient and would serve as a "measurement condition" describing the sample. Warrington teaches making a "database of reference samples" from this information which meets the claim requirement of [ 1] an ordered data matrix. Based on this disclosure from Warrington, we find there is sufficient evidence that Warrington describes system with a memory comprising elements of [la] and [le] as required by the rejected claims. The Examiner expressly identified this disclosure at column 16 in the Answer at page 12. Appellants in their Reply Brief did not identify a flaw in the Examiner's finding that such disclosure meets the claim limitations. 8 Appeal2013-007930 Application 10/403,762 [ 4] "a processor that reorders said data matrix based on a measure of similarity of values corresponding to one of said samples or physical measurements " Appellants contend that Balaban '561 does not sort data or reorder data as required by limitation [ 4 ], noting that "query that selects all records having a particular property does not order or sort the target table(s), it generates a new table having the indicated portions of the selected records from the table(s)." Appeal Br. 10. With respect to Tamura, Appellants acknowledge that "Tamura teaches displaying hybridization data based on similarity of the probe sequences used in the hybridization experiments." Id. However, Appellants argue that the Examiner has not identified data in Warrington that would be subject to a computation of a similarity score. Id. Appellants also challenge the Examiner's findings regarding Rusterholz, but the deficiency in Rusterholz is not evident from their argument. Id. at 9--10. To begin, the Examiner gave a logical reason for applying the methods of Rusterholz, Balaban, and Tamura to Warrington: "to be able to visualize and manipulate data in customizable ways in order to be able to more effectively interpret experimental data." Final Rej. 6. In the Answer, the Examiner further explains that the publications "teach known methods for manipulating data when performing analysis." Answer 14. The Examiner notes that, like the '762 Application, each of "Warrington, Balaban '561 and Tamura teach analysis of gene expression data." Id. Thus, the Examiner found it obvious to have applied the methods of Balaban '561 and Tamura to Warrington since one of ordinary skill "in the art of 9 Appeal2013-007930 Application 10/403,762 informatics" would have consulted "known data manipulation techniques such as sorting, re-ordering, and displaying data, such as those taught by the cited references for use in a system designed for data analysis." Id. Moreover, the Examiner found that Warrington at column 13, lines 32-36, referenced U.S. Patent Application Serial No. 09/354,935 as an example of a processing system in which its invention may be embodied. Serial No. 09/354,935 is the application which matured into the Balaban '561 patent. Based on this express disclosure by Warrington of Balaban '561, we find Appellants' argument that the skilled worker would not have consulted Balaban '561, as well as other prior art processing systems, to have little merit. With respect to the arguments about selecting and reordering data, we conclude that there is sufficient evidence that cited publications describe this limitation as it appears in the rejected claims. Balaban '561, as found by the Examiner, describes making a query and then visualizing the results of the query, where the visualizing draws data from a larger group and shows only those genes having a specific expression value. Balaban '561, col. 3, 11. 1-15. Appellants contend that such a step of making a query is not "reordering" as required by the claim. Appeal Br. 10. However, selecting out genes from a larger list is putting them into a different order. The selection of data from a larger set reorders the data because it places the data in a different order, e.g., ifthe data set had a 100 entries from 1-100, and entries 2 and 99 were selected, then the result would have 2 and 99 adjacent to each other in contrast to their consecutive numerical order in the original set of 1-100. 10 Appeal2013-007930 Application 10/403,762 The claim further requires "said processor causing said display to display a new portion of said data matrix based on said re-ordering." This step is met by Balaban '561 which has extensive disclosure on visualization techniques to understand the results of data mining which involves making queries and selecting subsets of data from larger sets. Balaban '561, col. 2, 11. 50-55; col. 14, 11. 33--43; col. 15, 11. 10-30. With respect to Tamura, Appellants argue that there is no data in Warrington that would be computed to have a similarity score as in Tamura. Appeal Br. 10. Specifically, Appellants contend that Tamura teaches "reordering hybridization data based on the similarity scores for the probes used in the microarrays." Reply Br. 5. Appellants attempt to distinguish Warrington, arguing that the "reordering is not done in response to the user identifying one probe and the system reordering with respect to the similarity score between that probe and the other probes" and that "Warrington does not store the hybridization data ... but rather the expression profiles obtained from a number of such experiments after clustering analysis has been performed on the hybridization data." Id. The rejection is based on the combination of Warrington and Tamura. Appellants acknowledged that Warrington describes hybridization data. Tamara describes displaying information about hybridization levels and similarity scores side by side to determine whether unexpected hybridization reaction has taken place. Tamura, i-fi-f 12-17. The similarity score is calculated from the probe nucleic acid base sequence. Id. at i-f 12. Warrington, like Tamura, utilizes nucleic acid probes in its expression profiles. Warrington, col. 5, 11. 5-15. Consequently, we do not find Appellants' assertion that no data in Warrington that would be subject to a 11 Appeal2013-007930 Application 10/403,762 computation of a similarity score (Appeal Br. 10) to be supported by evidence in the record. In sum, the Examiner's position that it would have been obvious have applied Tamura's method to Warrington's hybridization data for the reasons taught by Tamura to be supported by a preponderance of the evidence. The application of known data analysis methods to Warrington for their established function would have been obvious to one of ordinary skill in the art. In KSR Intern. Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007), the Supreme Court wrote that the "combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results." To make this determination, the Court explained "it will be necessary ... to look to interrelated teachings of multiple patents ... and the background knowledge possessed by a person having ordinary skill in the art, all in order to determine whether there was an apparent reason to combine the known elements in the fashion claimed by the patent at issue." Id. at 418. The Court further instructed: [I]f a technique has been used to improve one device, and a person of ordinary skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond his or her skill ... a court must ask whether the improvement is more than the predictable use of prior art elements according to their established functions. Id. at 417 (internal citation omitted). Warrington discloses various method by which its data can be analyzed and visualized, providing reason to have consulted Rusterholz, Balaban '561, and Tamura. See Warrington, col. 13, 11. 32-56; col. 14, 11. 12 Appeal2013-007930 Application 10/403,762 20-59. Appellants' own specification makes reference to other known systems that can be employed as visualization tools. Spec. i-f 71. Claims 71 and 85 Dependent claims 71 and 85 recite that the physical measurements are displayed as graphical symbols. While the Examiner generally pointed to column 12, lines 4--67 and columns 13-14 for this feature (Answer 7), the Examiner also found that Balaban '561 teaches "histograms and graphical display of data" (id. at 18) which include X-Y plot, ... bar charts, graphs, pie-charts and the like" (Balaban, col. 15, 11. 29-31) which are either graphical symbols or would suggest ones. Tamura also discloses patterns to represent similarity between probes. Tamura i-f 12. Consequently, despite Appellants' arguments (Appeal Br. 10-11), we find the evidence in the record is sufficient to support the obviousness of using graphical symbols, such as bar and pie charts, and patterns to represent physical measurements. Claims 74, 75, 88, and 89 Dependent claims 74 and 88 further recite that "said processor further performs statistical analysis on portions of said data matrix, said portions depending on said ordering of said data matrix." Appellants contend that this subject matter, and that of dependent claims 75 and 89, are not described in Warrington. Appeal Br. 11. However, the Examiner explained: Warrington et al. discloses performing data analysis, expression profile analysis as described above and would motivate a skill artisan to use statistical analysis on a portion of the database as the expression profile analysis described by Warrington et al. is modified for performing analysis on particular portions of the data. Balaban et al. teach, in Fig's 7 J and 7K, histograms and 13 Appeal2013-007930 Application 10/403,762 graphical display of data. Graphing and charting are statistical functions. Balaban et al. explicitly teach, as part of their data mining, performing normalization and other transformative functions in col. 10, lines 11-18 and 45-50. Normalization and scaling, at least, are forms of statistical analysis. Answer 18. The Examiner also identified a reason to conduct the analysis depending on ordering of the data matrix. Id. at 19. Appellants contend that the Examiner has not pointed to any teaching or reasoned argument that "would cause someone of ordinary skill in the art to modify Warrington to use statistical analysis on a portion of the database that depends on the ordering of the data matrix." Appeal Br. 11. However, the Examiner states that Warrington's teachings about separating differential gene expression data would have given the skilled worker reason to perform data analysis, such as the statistical analyses of Balaban, on a portion of said data matrix depending on its ordering. Answer 19. The Examiner's reasoning is based on teachings from Warrington and Balaban. Appellants have not identified a defect in the Examiner fact-finding nor reasoning. Summary The rejection of claims 62, 71, 74--76, 85, 88, and 89 as obvious is affirmed. To the extent claims were not argued separately, they fall with claims 62 and 76. 37 C.F.R. 41.37(c)(vii). REJECTION2 Claims 72 and 86 depend on the claims that require the data to be displayed as a graphical symbol, and further recite that the symbol "comprises a color and/or intensity of color that is a function of said value." Claims 73 and 87 further require that "graphical symbol comprises a 14 Appeal2013-007930 Application 10/403,762 partially filled symbol characterized by a fraction of said symbol that is filled, said fraction being a function of said value." The Examiner cited the combined teachings of Balaban '501, Ootomo, and Ram for these specific claim limitations, finding that such features were commonly used for displaying data. Answer 9--11. Appellants argue that the Examiner has not identified a reason as to why one of ordinary skill in the art would have utilize graphical symbols in Warrington. Appeal Br. 13. Appellants' argument is not persuasive. The Examiner explicitly found that graphical display of data is commonly used for displaying data. Answer 9-11. For example, Balaban '501 utilizes bar graphs and pie-charts. Balaban '501, i-fi-166---69. Tamura uses patterns and colors for data display. Tamura, i-f 12. Both Balaban '501 and Tamura analyze gene expression data as does Warrington. It is obvious to use a known technique to improve a known method for its established function, which in this case is to display and visualize data. See KSR, 550 U.S. at 417. Claims 70 and 84 further recite that the "display comprises an overview window that provides an ordered display of said data matrix including portions of said data matrix that are not shown in said detail display and wherein said base location is specified by selecting a point in said navigation display." The Examiner found the Balaban '501 suggests such limitation "to be able to mine data to provide a user with more helpful and better organized data and visualized data, which suggests displaying different size tables of information." Final Rej 10. The Examiner also cited paragraphs 56-69 and Figs. 5-10 of Balaban '501. Id. 15 Appeal2013-007930 Application 10/403,762 Appellants contend that the Examiner's argument is "conclusionary with no reasoned analysis that would lead someone of ordinary skill in the art to make the suggested changes." Appeal Br. 13. As indicated above, the Examiner cited express teachings in Balaban '501 and reasoned why they would suggest the claim limitation. Final Rej. 10. Thus, Appellants' arguments are not supported by the record. The rejection is affirmed. REJECTION3 Claims 63 and 77 recite that the measure of similarity comprises "calculating a Euclidean distance between said physical measurements corresponding to said selected physical measurement across a select set of samples and each of said corresponding physical measurements across said selected set of samples." The Examiner found that Warrington describes using GENECLUSTER which performs data analysis "that involves clustering data such as hierarchical clustering, Bayesian, and k-means clustering wherein these types of clustering methods calculating a distance based on a Euclidean distance is commonly used and well known methods." Final Rej. 13. The Examiner further cited Schadt for its description of using Euclidian distance as a known statistical method in the art. Id. Appellants contend that the Examiner has not provided "any factually based arguments that would lead someone of ordinary skill in the art to make the necessary modifications in Warrington absent the present application as a guide." Appeal Br. 15. 16 Appeal2013-007930 Application 10/403,762 This argument is not persuasive. As explained above, the Examiner made explicit findings that Euclidian distance is commonly used in data analysis. Furthermore, the Examiner reasoned that it would have been obvious to have used this method since it is a known method for manipulating data. Final Rej. 13. Thus, contrary to Appellants' argument, the Examiner provide factually based arguments and a reason to have modified Warrington to have arrived at the claimed subject matter The rejection is affirmed. TIME PERIOD No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(l )(iv). AFFIRMED 17 Copy with citationCopy as parenthetical citation