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 .
DETAILED ACTION
This action is response to the communication filed on September 30, 2025 Claims 1-12 are pending.
Response to Arguments
Applicant’s arguments filed on September 30, 2025 have been considered but are moot in the view of new ground of rejection.
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 1-12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Regarding the claim 1, it recites acquiring protein information represented by an encoded amino acid sequence from a data file on a first storage device in which the protein database is stored, the protein database including the data file that stores the protein information and an index file that stores name, offset, and length for the amino acid sequence; selecting between at least a first function corresponding to lossless compression function and a second function corresponding to an identity mapping based on a compression policy that defines a whether a compression ratio of the protein information satisfies a predetermined threshold; generating a compressed data file including a compression code indicating a selected function and compressed protein information resulted from the selected function; generating a new index file including the name, a new offset, a new length and the uncompressed original length of the amino acid sequence corresponding to the compressed protein information, and the compression code; registering the compressed data file and the new index file in a second storage device that is capable of accessing data at higher speed than the first storage device; and when a similarity search request is received, accessing the compressed data file and the new index fine from the second storage device to decompressing the compressed protein information registered in the compressed data file based on the compression code to accelerate the similarity search.
The claim recited the limitation of “selecting between at least a first function corresponding to lossless compression function and a second function corresponding to an identity mapping based on a compression policy that defines a whether a compression ratio of the protein information satisfies a predetermined threshold” as drafted, is a process that, under its broadest reasonable interpretation, covers performance of the limitation in the mind. User can mentally select a function between two functions as claimed which is a mental process. Further, the limitations “generating a compressed data file including a compression code indicating a selected function and compressed protein information resulted from the selected function” as drafted, is a process that, under its broadest reasonable interpretation, covers performance of the limitation in the mind. User can mentally generate a compression code for a data file which is a mental process. Similarly, the limitation “generating a new index file including the name, a new offset, a new length and the uncompressed original length of the amino acid sequence corresponding to the compressed protein information, and the compression code” as drafted, is a process that, under its broadest reasonable interpretation, covers performance of the limitation in the mind. User can mentally generate index as claimed. Hence, the limitation is mental process. If necessary, use can use physical aid (paper and pencil). See MPEP 2106.04(a)(2) III, B, If a claim recites a limitation that can practically be performed in the human mind, with or without the use of a physical aid such as pen and paper, the limitation falls within the mental processes grouping, and the claim recites an abstract idea. See, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674 (noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."). Therefore, the limitation is a mental process.
The claim recites four additional elements: acquiring, registering compressed data file, and access the compressed data file …. to decompressed protein information. The steps acquiring and accessing as recited amounts to mere data gathering for use in the compressing step, which is a form of insignificant extra-solution activity, (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information)). Further, the limitation the limitation registering compressed data file step can be done with well under routine the conventional computing component which is a form of insignificant extra-solution activity. Similarly, the compressing and decompressing as recited in the claim are nothing but data organizing which is a form of insignificant extra-solution activity. Accordingly, even in combination, 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 claim is directed to the abstract idea.
The claim does 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 acquiring, registering, compressing, and when access to the storage is received, decompressing steps amounts to no more than mere instructions to apply the exception using a generic computer component. The courts have recognized these functions as well‐understood, routine, and conventional as they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d) II, Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information)). Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept. The claim is not patent eligible.
Claim 2 is dependent on claim 1 and includes all the limitations of claim 1. Therefore, claim 2 recites the same abstract idea of compressing and decompressing of acquired information. The claim recites the limitations of wherein the compression policy defines a plurality of lossless compression functions for which the compression ratio is different, and in the compressing of the protein information, a lossless compression function that has a highest compression ratio when the protein information is compressed is selected, and the protein information is compressed based on a selected lossless compression function, which can be done mentally with or without the use of a physical aid (e.g., pen and paper) or with a generic computer and is not an inventive concept that meaningfully limits the abstract idea. Therefore, the limitation is a mental process.
Claim 3 is dependent on claim 2 and includes all the limitations of claim 2. Therefore, claim 3 recites the same abstract idea of compressing and decompressing of acquired information. The claim recites the limitations of wherein the compression policy defines that deflate compression is to be executed when the compression ratio is equal to or greater than a threshold and identity mapping is to be executed when the compression ratio is less than the threshold, and in the compressing, the deflate compression or the identity mapping is selected and the protein information is compressed, which can be done mentally with or without the use of a physical aid (e.g., pen and paper) or with a generic computer and is not an inventive concept that meaningfully limits the abstract idea. Therefore, the limitation is a mental process.
Claim 4 is dependent on claim 1 and includes all the limitations of claim 1. Therefore, claim 4 recites the same abstract idea of compressing and decompressing of acquired information. The claim recites the limitations of wherein the compression policy defines a plurality of lossless compression functions with different time taken when the protein information that has been compressed is decompressed, and in the compressing of the protein information, a lossless compression function with shortest time taken when the protein information that has been compressed is decompressed is selected and the protein information is compressed based on a selected lossless compression function, which can be done mentally with or without the use of a physical aid (e.g., pen and paper) or with a generic computer and is not an inventive concept that meaningfully limits the abstract idea. Therefore, the limitation is a mental process.
As to claims 5-12, they have similar limitations as of claims 1-4 above. Hence, they are rejected under the same rational as of claims 1-4 above.
Claim Rejections - 35 USC § 103
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-12 are rejected under 35 U.S.C. 103 as being unpatentable over Mirandola et al. (Pub. No. : US 20220310200 A1) in the view of Song et al. (Pub. No. : US 20200294629 A1)
As to claim 1 Mirandola teaches a non-transitory computer-readable recording medium storing a compression program for causing a computer to execute a process comprising:
acquiring protein information represented by an encoded amino acid sequence from a data file on a first storage device in which the protein database is stored, the protein database including the data file that stores the protein information and an index file that stores name, offset, and length for the amino acid sequence (paragraph [0071], [0108]: receive an input amino acid sequence from a sequence acquisition interface and retrieved by an algorithm associated with an SAI from a NCO Protein database);
generating a new index file including the name, a new offset, a new length and the uncompressed original length of the amino acid sequence (paragraphs [0093,] [0096]: amino acid sequence (e.g., gene name), offset value, index value);
Mirandola does not explicitly disclose but Song teaches the compressed protein information, and the compression code (paragraph [0034]: compressing a most approximate position p of the read sequence R in the reference genome and the reversible computing result that serve as two data streams) selecting between at least a first function corresponding to lossless compression function and a second function corresponding to an identity mapping based on a compression policy that defines a whether a compression ratio of the protein information satisfies a predetermined threshold; (paragraphs [0006], [0034], [0040]-[0051]: comparing the read sequence R with the reference genome to obtain the most approximate position p thereof from the reference genome, so as to obtain the most approximate equal-length gene character sequence CS of the read sequence R and compressing the most approximate position p of the read sequence R in the reference genome and the reversible computing result that serve as two data streams, and outputting the compressed data streams);
generating a compressed data file including a compression code indicating a selected function and compressed protein information resulted from the selected function (paragraph [0034]: compressing a most approximate position p of the read sequence R in the reference genome and the reversible computing result that serve as two data streams, and outputting the compressed data streams);
registering the compressed data file and the new index file in a second storage device that is capable of accessing data at higher speed than the first storage device (paragraph [0002]: storage management); and
when a similarity search request is received, accessing the compressed data file and the new index fine from the second storage device to decompressing the compressed protein information registered in the compressed data file based on the compression code to accelerate the similarity search (Paragraphs [0025]-[0031], [0110]: the one or more amino acid sequences may be tested in order to identify and/or provide analogs that have one or more improved properties compared to the predetermined amino acid sequence and decompressing and reconstructing the read sequence R.sub.c to be decompressed to the most approximate position p in the reference genome and the reversible computing result CS1 with the length of Lr bit).
It would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to modify Mirandola by adding above limitation as taught by Song to improve the compression ratio of the gene sequencing data (Song, paragraph [0034]).
As to claim 2 Mirandola together with Song teaches a non-transitory computer-readable recording medium according to claim 1. Song teaches wherein the compression policy defines a plurality of lossless compression functions for which the compression ratio is different, and in the compressing of the protein information, a lossless compression function that has a highest compression ratio when the protein information is compressed is selected, and the protein information is compressed based on a selected lossless compression function (paragraph [0034]).
As to claim 3 Mirandola together with Song teaches a non-transitory computer-readable recording medium according to claim 2. Song teaches wherein the compression policy defines that deflate compression is to be executed when the compression ratio is equal to or greater than the threshold and identity mapping is to be executed when the compression ratio is less than the threshold, and in the compressing, the deflate compression or the identity mapping is selected and the protein information is compressed (paragraph [0043]).
As to claim 4 Mirandola together with Song teaches a non-transitory computer-readable recording medium according to claim 1. Song teaches wherein the compression policy defines a plurality of lossless compression functions with different time taken when the protein information that has been compressed is decompressed, and in the compressing of the protein information, a lossless compression function with shortest time taken when the protein information that has been compressed is decompressed is selected and the protein information is compressed based on a selected lossless compression function (paragraph [0007]).
As to claims 5-12, they have similar limitations as of claims 1-4 above. Hence, they are rejected under the same rational as of claims 1-4 above.
Examiner's Note: Examiner has cited particular columns and line numbers or paragraphs in the references as applied to the claims above for the convenience of the applicant. Although the specified citations are representative of the teachings of the art and are applied to the specific limitations within the individual claim, other passages and figures may apply as well. It is respectfully requested from the applicant in preparing responses, to fully consider the references in its entirety as potentially teaching of all or part of the claimed invention, as well as the context.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
The prior art made of record, listed on form PTO-892, and not relied upon, if any, is considered pertinent to applicant's disclosure.
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/MD I UDDIN/Primary Examiner, Art Unit 2169