DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 01/07/2026 has been entered.
Claims 21-40 remain pending in this application.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 21-40 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Step 1:
Claims 21-37 are drawn to a system which is within the four statutory categories (i.e. machine). Claim 38 is drawn to a system/kit (product), which is within the four statutory categories (i.e. machine). Claims 39-40 are drawn to a method, which is within the four statutory categories (i.e. process).
Step 2A, Prong 1:
Claims 21, 38, 39 recite:
“for a disease of interest at a higher level in a disease hierarchy, retrieving gene-disease associations of genes associated with diseases at a given level in the disease hierarchy from a disease association database…;
for each gene associated with the diseases at the given level, applying a weight to the strength parameter for each gene-disease association to form a weighted strength parameter of the gene-disease association,
adding the weighted strength parameters of the gene-disease associations to form a rank score for the each gene associated with the diseases at the given level;
applying a threshold to the rank scores to select the rank scores having values greater than or equal to the threshold to form selected rank scores, wherein a number of the selected rank scores is less than an initial number of the rank scores;
ranking the genes associated with the diseases at the given level based on the values of the selected rank scores, wherein the genes are ranked from a highest selected rank score to a lowest selected rank score, to provide ranked gene information;
assigning a rank order index to each ranked gene based on the value of the selected rank score for the ranked gene;…
and selecting at least one of the ranked genes from the table of ranked genes for the set of genes in the gene panel in response to a selection of the disease of interest by a user.”
These steps correspond to certain methods of organizing human activity (e.g. This is a method of managing interactions between people, such as user following rules or instructions). The mere nominal recitation of a generic processor and database does not take the claim out of the methods of organizing human interactions grouping). Thus, the claims recite an abstract idea.
The processor described in the current specification as a generic processor (i.e. [0059] of the specification recites “The processor can be any custom made or commercially available processor,…”).
Claim limitations of “for each gene associated with the diseases at the given level, applying a weight to the strength parameter for each gene-disease association to form a weighted strength parameter of the gene disease association, adding the weighted strength parameters of the gene-disease associations to form a rank score for the each gene associated with the diseases at the given level; applying a threshold to the rank scores to select the rank scores having values greater than or equal to the threshold to form selected rank scores, wherein a number of the selected rank scores is less than an initial number of the rank scores; ranking the genes associated with the diseases at the given level based on the values of the selected rank scores, wherein the genes are ranked from a highest selected rank score to a lowest selected rank score, to provide ranked gene information; assigning a rank order index to each ranked gene based on the value of the selected rank score for the ranked gene;…”correspond to mathematical relationships, which falls within the “mathematical concept” grouping of abstract ideas.
Accordingly, the claims recite an abstract idea.
Depending claims also recite abstract idea of certain methods of organizing human activities, such as, “use the rank scores for gene-disease associations at a lower level of the disease hierarchy to provide the rank scores for the diseases at a plurality of higher levels of the disease hierarchy where there is a hierarchical relationship between the disease at the lower level with the diseases at the higher levels”-claim 32, “use the ranked gene information for the gene-disease associations at a lower level of the disease hierarchy to provide the ranked gene information for the diseases at a plurality of higher levels of the disease hierarchy where there is a hierarchical relationship between the disease at the lower level with the diseases at the higher levels”-claim 33, “determine an order of values of the strength parameters for the gene-disease associations at the given level from a highest value to a lowest value, and assign an order index to each of the strength parameters based on the order of values, wherein the weight applied to each strength parameter is based on an inverse of its order index”-claim 34, “group the genes into gene clusters based on correlations of the rank scores of the genes associated with the diseases at a level of the disease hierarchy”-claim 36 and “apply a principal component analysis to the rank scores corresponding to the genes of each gene cluster to determine principal component vectors for the gene clusters”-claim 37. These limitations correspond to certain methods of organizing human activity (e.g. This is a method of managing interactions between people, such as user following rules or instructions).
After considering all claim elements, both individually and in combination and in ordered combination, it has been determined that the claims do not amount to significantly more than the abstract idea itself.
Claims 22-37, and 40 are ultimately dependent from claims 21, 39 and include all the limitations of claims 21, 39 Therefore, claims 22-37, and 40 recite the same abstract idea. Claims 22-37, and 40 describe a further limitation regarding the basis for ranking the genes linked with the disease of interest. These are all just further describing the abstract idea recited in claims 21, 39, without adding significantly more.
Step 2A, Prong 2:
This judicial exception is not integrated into a practical application. In particular, the current claims recite the additional elements of “a disease association database”, “a processor”, “a graph database system”, “disease/gene nodes”, and using the processor to perform: retrieving, applying a weight, adding the weighted strength parameters to form a rank score…, applying a threshold to the rank scores, ranking the genes and assigning a rank order, which are hardware or software elements, these limitations are not enough to qualify as “practical application” being recited in the claims along with the abstract idea since these elements are merely invoked as a tool to apply instructions of the abstract idea in a particular technological environment, and mere instructions to apply/implement/automate an abstract idea in a particular technological environment and merely limiting the use of an abstract idea to a particular field or technological environment do not provide practical application for an abstract idea (MPEP 2106.05(f) & (h)). The processor is described in the current specification as a generic computing device, the specification recites “Examples of hardware elements may include processors, microprocessors, input(s) and/or output(s) (I/O) device(s) (or peripherals) that are communicatively coupled via a local interface circuit, circuit elements (e.g., transistors, resistors, capacitors, inductors, and so forth), integrated circuits, application specific integrated circuits (ASIC), programmable logic devices (PLD), digital signal processors (DSP), field programmable gate array (FPGA), logic gates, registers, semiconductor device, chips, microchips, chip sets, and so forth.” in par. 59.
Claims also recite other additional limitations beyond abstract idea and these limitations, including functions such as retrieving/storing data from/to a database and these are insignificant extra-solution activities (see MPEP 2106.05 (g)), which do not provide a practical application for the abstract idea.
Accordingly, these additional elements do not integrate the abstract idea into a practical application because they do not impose any meaningful limits on practicing the abstract idea. The claims are directed to an abstract idea.
Step 2B:
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to integration of the abstract idea into a practical application, the additional element of using a processor to perform the “applying weights, applying a threshold to rank scores, rank the genes an assigning a rank order” steps amounts to no more than mere instructions to apply the exception using a generic computer component. Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept.
Therefore, claims are nonetheless rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 01/07/2026 have been fully considered but they are not persuasive. Applicant’s arguments will be addressed below in the order in which they appear.
Applicant argues that claims recite “store in the memory a table of ranked genes linked with the disease of interest at the higher level in the disease hierarchy, the table including, a disease identifier for the disease of interest, gene symbols for the ranked genes corresponding to the selected rank scores, the selected rank scores and the rank order index, wherein the table of ranked genes based on the selected rank scores is stored using a lower amount of the memory than a table of ranked genes based on the initial number of the rank scores”, and a significant data reduction is achieved by storing the table of ranked genes and a computational reduction is achieved for the ranked gene information, reducing search times for selecting genes for gene panel design.
In response, Examiner submits that neither the claims nor the current specification recites any technological improvement. In particular, claims recite storing data using a lower amount of memory, since the calculated table of ranked genes (data) corresponds to less data, than the unranked data. The current specification recites “In some embodiments, the GSA module 120 applies a threshold to the rank scores prior to ranking the genes based on rank scores. The GSA module 120 selects rank scores with values greater than or equal to the threshold and ranks those genes having the selected rank scores. Applying the threshold has advantages of reducing computations for ranking genes having below-threshold rank scores and reducing memory size or storage requirements for the tables of ranked genes generated for the levels of the disease hierarchy.” And applying a threshold to the ranked scores, therefore, ranking selected rank scores is directed to organizing (classifying) data, which result in less data to store. The feature of “storing in the memory a table of ranked genes…” corresponds to insignificant extra-solution activities (see MPEP 2106.05 (g)), which do not provide a practical application for the abstract idea.
Applicant argues that the current claims are similar to the claims of Enfish, that the current claims recite elements reduce the amount of memory required to store the table of ranked genes.
In response, Examiner submits that the Enfish claims provide a specific improvement to the way computer operate, embodied in the self-referential table. The decision includes:
**Here, the claims are not simply directed to any form of storing tabular data, but instead are specifically directed to a self-referential table for a computer database.
The present invention improves upon prior art information search and retrieval systems by employing a flexible, self referential table to store data.
The specification also teaches that the self-referential table functions differently than conventional database structures.
In sum, the self-referential table recited in the claims on appeal is a specific type of data structure designed to improve the way a computer stores and retrieves data in memory. The specification’s disparagement of conventional data structures, combined with language describing the “present invention” as including the features that make up a self-referential table, confirm that our characterization of the “invention” for purposes of the § 101 analysis has not been deceived by the “draftsman’s art.” Cf. Alice, 134 S. Ct. at 2360. In other words, we are not faced with a situation where general-purpose computer components are added post-hoc to a fundamental economic practice or mathematical equation. Rather, the claims are directed to a specific implementation of a solution to a problem in the software arts. Accordingly, we find the claims at issue are not directed to an abstract idea.**
In the current application, there is no indication of non-conventional data structures or any non-conventional operations that provide an improvement to the functioning of the computer. The current claims and the specification is directed to organizing (classifying) data, which result in less data to store, may be resulting the usage of lower amount of memory.
Therefore, the arguments are not persuasive and claims are rejected under 35 U.S.C. §101 as being directed to non-statutory subject matter.
Conclusion
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/DILEK B COBANOGLU/Primary Examiner, Art Unit 3687