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 .
Response to Amendment
The amendment filed 5/26/2026 has been entered. Claims 1, 2, 6, 7, and 13 stand amended. Claims 1-11 and 13-17 stand pending.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-11 and 13-17 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kincaid in US Patent Application Publication № 2004/0061702, hereinafter called Kincaid.
In regard to claim 1, Kincaid teaches a method comprising:
storing, in a storage element of a computer system, an ordered data matrix including a plurality of values, each value, from the plurality of a values, representing phenomena (“The term "cell", when used in the context describing a data table or heat map, refers to the data value at the intersection of a row and column in a spreadsheet-like data structure or heat map; typically a property /value pair for an entity in the spreadsheet, e.g. the expression level for a gene.” Paragraph 0043);
providing a two-dimensional graphic on a display of the computer system, the graphic having a plurality of cells, each cell corresponding to a pair of values, from the plurality of values, in the ordered data matrix (“A "heat map" or "heat map visualization" is a visual representation of a tabular data structure of gene expression values, wherein color-coding are used for displaying numerical values. The numerical value for each cell in the data table is encoded into a color for the cell. Color encodings run on a continuum from one color through another, e.g. green to red or yellow to blue for gene expression values. The resultant color matrix of all rows and columns in the data set forms the color map, often referred to as a "heat map" by way of analogy to modeling of thermodynamic data.” Paragraph 0053)
rendering, via a computer processor of the computer system, on the electronic display, a heat map on the two-dimensional graphic including a vertical axis and a horizontal axis orthogonal to the vertical axis, the plurality of cells being arranged in a plurality of rows and columns on the heat map initial grid along the vertical and horizontal axes (“The resultant color matrix of all rows and columns in the data set forms the color map, often referred to as a "heat map" by way of analogy to modeling of thermodynamic data.” Paragraph 0053;also “Likewise, the column of clinical data containing the cloneID (i.e., "Clone") 44 for the CDNA having been deposited on the microarray with respect to each individual microarray reading is linked to the particular row of experimental data that it describes and moves with that row when the row is repositioned” paragraph 80), wherein each cell of the plurality of cells on the heat map displays indicia selected from the group consisting of a color, a pattern and a combination thereof (“FIG. 1 shows an example of a portion of a conventional heat map visualization 200 that is currently available to users. A standard heat map visualization such as visualization 200 is a static visual representation of a tabular data structure of gene expression values, wherein color coding are used for displaying numerical values. The numerical value for each cell 202 in the data table is encoded into a color for the cell, although the colors are not apparent in the figs. of this application in order to comply with figure drafting rules generally requiring black and white figs.” Paragraph 0077), indicative of an associated pair of values, from the plurality of values, including (i) a first data value within a first data range and (ii) a second data value within a second data range,
selecting, via the computer processor, one of a single column selected for sorting or a single row selected for sorting, from the plurality of rows and columns on the heat map in the initial grid (“For example, FIG. 3 shows the results of a column sort that was conducted with regard to column 20 of the experimental data. In this example, the cells in column 20 have been sorted according to the cell with the highest degree of up-regulation (which is color-coded red according to the normal heat map visualization schema), with subsequent cells in descending order of expression value down to the lowest value” paragraph 0088);
sorting the plurality of cells of the selected single column selected for sorting or the single row selected for sorting based solely on an ordering of the displayed indicia (note that the displayed indicia, i.e. color, is taught to be an encoding of the value, “A standard heat map visualization such as visualization 200 is a static visual representation of a tabular data structure of gene expression values, wherein color codings are used for displaying numerical values. The numerical value for each cell 202 in the data table is encoded into a color for the cell…” paragraph 0077, and accordingly a sort by the value is logically equivalent to a sort by the encoded value, i.e. a sort by the color, “For example, FIG. 3 shows the results of a column sort that was conducted with regard to column 20 of the experimental data. In this example, the cells in column 20 have been sorted according to the cell with the highest degree of up-regulation (which is color-coded red according to the normal heat map visualization schema), with subsequent cells in descending order of expression value down to the lowest value” paragraph 0088),
the sorting generating a generated global mapping order that is independent of similarity metrics, correlation calculations, or distance calculations (“For example, FIG. 3 shows the results of a column sort that was conducted with regard to column 20 of the experimental data. In this example, the cells in column 20 have been sorted according to the cell with the highest degree of up-regulation (which is color-coded red according to the normal heat map visualization schema), with subsequent cells in descending order of expression value down to the lowest value” paragraph 0088, wherein “As each of the cells in column 20 are rearranged according to the sort order determined, the entire row of experimental data assumes the same row placement as that of the reordered cell of column 20. Also, the non-experimental data and identification data in the left side of the visualization remains linked with the respective rows that it originally pertained to, and is rearranged according to the sort order of the cells in column 20.” Paragraph 0088);
sorting each remaining column of the initial grid or each remaining row of the initial grid respectively, in its entirety according to the generated global mapping order without recalculating individual similarity relationships for the remaining rows or columns (“As each of the cells in column 20 are rearranged according to the sort order determined, the entire row of experimental data assumes the same row placement as that of the reordered cell of column 20.” Paragraph 0088; note that, as the claim is recited in the alternative, either a sort by row or column meets the broadest reasonable interpretation of the claim)
and rendering a revised grid that preserves relative positional correspondence across all rows or columns, via the processor, according to the generated global mapping order that presents a reordered visual pattern on the display. (“FIG. 4 shows the display order resulting after a row sort that was performed after the column sort described above with regard to FIG. 3.” Paragraph 0090).
In regard to claims 7 and 13, they are substantially similar to claim 1 and accordingly are rejected under similar reasoning.
In regard to claim 2, Kincaid further teaches that (i) each row of the initial graphical grid is displayed in an order sorted according to the generated global mapping order, or (ii) each column of the initial graphical grid is displayed in an order sorted according to the generated global mapping order (“As each of the cells in column 20 are rearranged according to the sort order determined, the entire row of experimental data assumes the same row placement as that of the reordered cell of column 20.” Paragraph 0088); and wherein sorting is from an initial order to one of an ascending order and a descending order (“Upon selecting the ath row, as described, each experimental data value (i.e., cells one through n of the ath row, noted as cells 1, a through n,a in step S19 )) are compared to perform a new sorting order, whether the cells are to be arranged in descending order of value or ascending order of value.” Paragraph 0101; alternatively or additionally, “In this example, the cells in column 20 have been sorted according to the cell with the highest degree of up-regulation (which is color-coded red according to the normal heat map visualization schema), with subsequent cells in descending order of expression value down to the lowest value. Of course, the present invention is not to be limited to sorting from highest up-regulated cell, as a reverse sorting order could be performed.” Paragraph 0088).
In regard to claims 8 and 14, they are substantially similar to claim 2 and accordingly are rejected under similar reasoning.
In regard to claim 3, Kincaid further teaches accepting via a sorting widget a user signal indicative that the sorting should be one of the ascending sort order and the descending sort order (“The user interaction for performing a sub-sorting procedure is effectively the same as described above with regard to various methods of similarity sorting, except that upon selecting a row or column, the user chooses the sub-sort function, and specifies a row-based or column based sub-sort, whereby the selected row/column maintains its present location and the subsequent rows/columns are reordered based upon similarity calculations carried out” paragraph 0136; alternatively or additionally, the selection of rows to sort in paragraph 0090, wherein the selection is taught to include either ascending or descending sort).
In regard to claims 9 and 15, they are substantially similar to claim 3 and accordingly are rejected under similar reasoning.
In regard to claim 4, Kincaid further teaches that the indicia is further selected from an icon (i.e. symbol) in addition to the group consisting of a color, a pattern, and a combination thereof (“FIG. 1 shows an example of a portion of a conventional heat map visualization 200 that is currently available to users. A standard heat map visualization such as visualization 200 is a static visual representation of a tabular data structure of gene expression values, wherein color coding are used for displaying numerical values. The numerical value for each cell 202 in the data table is encoded into a color for the cell, although the colors are not apparent in the figs. of this application in order to comply with figure drafting rules generally requiring black and white figs.” Paragraph 0077; additionally, “The BNS_Symbol column 48 contains symbols which identify the particular gene in that row that the expression data is being presented for.” Paragraph 0081. Note that, absent any further technical limitation, a symbol is within the broadest reasonable interpretation of an icon).
In regard to claims 10 and 16, they are substantially similar to claim 4 and accordingly are rejected under similar reasoning.
In regard to claim 5, Kincaid further teaches that the value order of one of the pair of values is determined according to at least one of a legend of the data indicia, and a user-indicated ordering of the data indicia (“The present invention supports both row and column sorting, as described above, as well as limited column and row re-ordering. This limited column and row reordering may be accomplished manually by the user. To accomplish manual reordering, the user can drag-and-drop rows and columns.” Paragraph 0094).
In regard to claims 11 and 17, they are substantially similar to claim 5 and accordingly are rejected under similar reasoning.
In regard to claim 6, Kincaid further teaches that generating the generated global mapping order comprises determining an association between cells in the initial grid and cells in the revised grid (i.e. a sorting, (“Upon selecting the ath row, as described, each experimental data value (i.e., cells one through n of the ath row, noted as cells 1, a through n,a in step S19 )) are compared to perform a new sorting order, whether the cells are to be arranged in descending order of value or ascending order of value.” Paragraph 0101).”; alternatively or additionally, the rows are taught to be re-ordered in the same way as the column in paragraph 0088).
Response to Arguments
Applicant's arguments filed 5/26/2026 have been fully considered but they are not persuasive.
Regarding applicants’ argument that the heat map which uses color-coding taught by Kincaid (see applicants’ remarks, pages 8-9), examiner notes that, absent any specific limitations recited in the claim regarding the type or manner of color coding, the express recitation of a ‘heat map’ which encodes numerical information into color information is sufficient to meet the broadest reasonable interpretation of the claim language. Additionally, Kincaid clearly describes the application of color to create a heat map in conjunction with the figures, and further, examiner notes that this description is relied upon in the rejection. Accordingly, the argument that Kincaid fails to teach a heat map because the figures in isolation do not expressly show color information is not persuasive.
In regard to applicants’ arguments that the instant claims have been amended to exclude similarity-based and distance-based sorting, and accordingly the ordering taught by Kincaid is excluded (see applicants’ remarks, pages 9-11), acknowledgement is made that the instant amendments are made, however, the teachings of Kincaid include non-similarity-based and non-distance-based sorting. Kincaid teaches ordering in strictly increasing or deceasing value order (“For example, FIG. 3 shows the results of a column sort that was conducted with regard to column 20 of the experimental data. In this example, the cells in column 20 have been sorted according to the cell with the highest degree of up-regulation (which is color-coded red according to the normal heat map visualization schema), with subsequent cells in descending order of expression value down to the lowest value.” Paragraph 0088, “Like the column sort described above, this row sort was performed according to an order displaying the highest up-regulated cell (9rl) first (i.e., the left most cell of the row), with the second cell having the next highest expression level and so forth, down to the lowest expression value in column 31 of row R9. Once again, it is noted that the present invention is not to be limited to sorting from the highest up-regulated cell, as the sort could be based on the lowest expression level, and arranged in an ascending expression level order, for example” paragraph 0090), which does not appear to require similarity-based or distance-based sorting. Additionally, the indicia (i.e. color) is taught to be expressly based upon the value of the cells (“The numerical value for each cell 202 in the data table is encoded into a color for the cell,” paragraph 0077), and accordingly, absent any particular technical limitation as to the nature of the sort based on indicia, a sort by value is logically equivalent to a sort by the value encoded in color.
Further, in regard to applicants’ arguments regarding a global sort order, a sort order of the entire set of rows and columns appears to be taught by Kincaid to be derived from this mapping order (“As noted above, the row sort was performed on the basis of the expression values in row R9 (i.e., Melan-A gene). As each of the cells in row R9 are rearranged according to the sort order determined, the entire column of experimental data assumes the same column placement as that of the reordered cell of row R9. Also, the non-experimental data and identification data in the top portion of the visualization remains linked with the respective columns that it originally pertained to, and is rearranged according to the sort order of the cells in row R9. In this way, the identifying information/non-experimental data in the cells of rows Rl-R4 remains in the same row relative to the experimental data after re-ordering, thereby maintaining the accuracy of the normalization scheme. The non-experimental data on the left side of the visualization 100 remains locked, as it is normalized with respect to the rows of experimental data, which were not reordered in this manipulation.” Paragraph 0091).
Further, in regard to applicant’s assertion that reordering taught by Kincaid is fundamentally recalculated based on similarity metrics, in particular as taught by Kincaid in paragraphs 0107-0117, 0123-0133, (see applicants’ remarks, page 11-12), note that Kincaid separately teaches a simple ascending or descending sort based on values encoded into color indicia, as in paragraphs 0088 and 0090. The cited portions of Kincaid are not relied upon in the instant rejection, and accordingly the arguments are not persuasive.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/AJAY M BHATIA/ Supervisory Patent Examiner, Art Unit 2156
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