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 May 06, 2026 Claims 1-12 are pending.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 May 06, 2026 has been entered.
Response to Arguments
Applicant’s arguments regarding art rejection filed on May, 2026 have been considered but are moot in the view of new ground of rejection. The argument regarding 101 rejection is not persuasive.
Regarding 101 rejection applicant argues the claimed process, as a whole, describes an unconventional system that improves the overall throughput of a similarity search by orchestrating a dual storage hierarchy, a sophisticated compression policy, and efficient memory management. This is not an abstract idea but a practical application that results in a measurably faster and more efficient computer system.
In response examiner respectfully disagree. The limitations selecting plurality of predefined and distinct compression functions ---, generating a compressed data file ---, generating a new index file --- as drafted, is a process that, under its broadest reasonable interpretation, covers performance of the limitation in the mind. The additional limitations of acquiring, registering compressed data file, and access to the protein information, and retrieving the compressed data file are insignificant extra solution activity. 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 compressed data file, and access to the protein information, and retrieving the compressed data file 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.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-12 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The second limitation of claim 1 recited “the selecting is being based on a compression policy that defines a technical trade-off between reducing a data size of the amino acid sequence to fit within a capacity of a second storage device and minimizing a processing time required for decompression” Applicant specification fails to disclose that the compression policy that defines a technical trade-off. Appropriate correction is required.
The third limitation of claim 1 recited “the compressed data file including a compression code indicating the selected function and a resulting data payload”. Applicant specification fails to disclose a resulting data payload. Appropriate correction is required.
The fourth limitation of 1 recited “generaton a new index file”, “the resulting data payload”, and “on-the-fly decompression”. As to applicant specification it discloses FFindex which is a tab-delimited file (see applicant specification [0088] as published). The “index file” as claimed is not disclose. Applicant disclosure further fails to disclose “the resulting data payload”, and “on-the-fly decompression”. Note that “on-the-fly” limitation also recited in the last limitation of claim1. Appropriate correction is required.
All independent claims are rejected as recited similar limitation as claim 1. All dependent claims are rejected based on their respective dependency.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. As to claim 1, it is not clear by the claimed limitation “technical trade-off”, “resulting data payload”. Ordinary meaning of the limitation “index file” does not fit to the claim context. The specification recited “FFindex file is a tab-delimited file in which names, offsets (including ‘\0’), and lengths of proteins (including ‘\0’) are listed for each line”. Appropriate correction is required.
All independent claims are rejected as recited similar limitation as claim 1. All dependent claims are rejected based on their respective dependency.
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 of a protein database, the protein database including a data file that stores the encoded amino acid sequences and an index file that stores name, an offset, and a length for each amino acid sequence; for each amino acid sequence, selecting plurality of predefined and distinct compression functions including at least a first function corresponding to a lossless compression function and a second function corresponding to an identity mapping, the selecting is being based on a compression policy that defines a technical trade-off between reducing a data size of the amino acid sequence to fit within a capacity of a second storage device and minimizing a processing time required for decompression; generating a compressed data file by applying the selected function to the amino acid sequence, the compressed data file including a compression code indicating the selected function and a resulting data payload; generating a new index file including the name, a new offset, a new length and the resulting data payload, the compression code, and uncompressed original length of the amino acid sequence, the uncompressed original length being configured to enable pre-allocation of a memory buffer of a precise size for on-the- fly decompression; 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 in response to a similarity search request that requires access to the protein information, retrieving the compressed data file and the new index file from the second storage device, and for each protein information required by the search, dynamically decompressing the resulting data payload using a decompression function corresponding to the compression code retrieved from the new index file, thereby improving overall throughput of the similarity search by balancing faster data retrieval from the second storage device against on-the-fly decompression overhead.
The claim recited the limitation of selecting plurality of predefined and distinct compression functions ---, generating a compressed data file ---, generating a new index file --- 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 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 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 to the protein information, and retrieving the compressed data file. The steps acquiring, accessing and retrieving 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 compressed data file, and access to the protein information, and retrieving the compressed data file 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.
Note: The art rejection has been omitted as some of the limitations are not clear and examiner is unable give interpretation. The 112b issues have been discussed with applicant representative Raphael Valencia. He indicates, applicant need time to review the claims and specification to reproduce the claims.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MD I UDDIN whose telephone number is (571)270-3559. The examiner can normally be reached M-F, 8:00 am to 5:00 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sherief Badawi can be reached at 571-272-9782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MD I UDDIN/Primary Examiner, Art Unit 2169
Prosecution Insights