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 .
Applicant’s amendment and response, filed 5/18/2026, have been entered and carefully considered, but are not completely persuasive.
Claims 1-4, 24, 35, 40-41, 43, 45, 51-54 are pending and under consideration. All other claims have been canceled.
The substitute specification, filed 5/18/2026, has been entered.
This application is a National Stage application under 35 USC 371, claiming priority to PCT CN2019/111146, filed Oct 15, 2019, which claims priority to CN 201811197975.2, filed Oct 15, 2018. The certified copy of the priority document has been provided by the IB.
No certified translation of the priority document appears to be of record. The effective filing date for the claims therefor is 10/15/2019. The examiner has reviewed all PCT related papers of record.
The objection to claims 7 and 24 is moot in view of the amendments made.
The rejection under 35 USC 112(d) of claims 7 and 24 is withdrawn in view of amendments made.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation (BRI) using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
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 1-4, 24, 35, 40-41, 43, 45, 51-54 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental steps, mathematic concepts, organizing human activity, or a natural law without significantly more.
Applicant is directed to MPEP 2106 for the most current and complete guidelines in the analysis of patent- eligible subject matter. The current MPEP is the primary source for the USPTO’s patent eligibility guidance.
Several claims have been heavily amended. Only the amended claims are re-analyzed here.
With respect to step (1): YES, the claims are drawn to statutory categories: Independent claims 1 and 35 are drawn to processes, and independent claim 45 is drawn to a system for carrying out the method of claim 35.
With respect to step (2A) (1): YES, the claims recite an abstract idea, law of nature and/or natural phenomenon. The claims explicitly recite elements that, individually and in combination, constitute one or more judicial exceptions (JE).
Mathematic concepts, Mental Processes or Elements in Addition (EIA) in the claim(s) include:
1. (Currently amended) A method for labeling a protection scope of claims of a gene sequence, wherein the method is applied to a retrieval engine comprising at least one processor and a memory, the method comprising the following steps of:
(Preamble, setting forth a method, a goal of the method, and an EIA, the use of a general-purpose computer.)
recognizing, by the retrieval engine, a gene sequence from claims of a current patent application to be analyzed;
((Mental process of data observation and recognition, MPEP 2106.04(a) section III; Specification [0104] identifying text string, [0105] recognizing identifier, [0106] using optical character recognition.)
extracting, by the retrieval engine, descriptive texts of the gene sequence from the claims based on a preset keyword, wherein the descriptive texts comprise a length identifier that defines a length of a partial subsequence in the gene sequence; and
(Mental process of observing a description of a length identifier, and using a present keyword, extracting the length of some part of the recognized element from the previous step. MPEP 2106.04(a) section III; Specification [0108] natural language processing technique using pre-trained ML and specifically labeled training data).
determining, by the retrieval engine, a percentage corresponding to the gene sequence according to the length identifier in the extracted descriptive texts,
(Mathematic concept of calculating a percentage value. MPEP 2106.04(a) section 1; Specification [0113] calculating percentage, adding, subtracting, dividing.)
taking the percentage as similarity information of the gene sequence, and
(Mental process of observing the percentage value, and identifying it as similarity information MPEP 2106.04(a)(2) III)
labeling a lower limit value of the protection scope of the claims of the gene sequence according to the similarity information, and
(Mental process of data annotation, using the similarity information MPEP 2106.04(a)(2)III)
storing the lower limit value in the memory, wherein the lower limit value indicates that any gene sequence having a similarity to the gene sequence equal to or greater than the percentage falls within the protection scope,
(EIA- routine output / data storage of a calculated value)
wherein recognizing the gene sequence from the claims of the current patent application to be analyzed comprises one of:
(i) recognizing a letter sequence consisted of specified letters from the claims of the current patent application to be analyzed, and taking the letter sequence as the gene sequence when a length of the letter sequence reaches a specified length threshold value; or
(ii) recognizing a sequence identifier from the claims of the current patent application to be analyzed by text matching, and reading a gene sequence corresponding to the sequence identifier from a sequence table of the current patent application to be analyzed,
(Mental processes, of observation, analysis and judgement. MPEP 2106.04(a)(2) III)
wherein extracting descriptive texts of the gene sequence from the claims based on the preset keyword comprises:
recognizing from the claims a position where the gene sequence is located by using a trained natural language model, and looking up a length identifier that defines a length of a partial subsequence in the gene sequence from context of the recognized position; and
taking the length identifier as the preset keyword,
extracting a sentence containing the length identifier and the gene sequence, and
taking the extracting sentence as the descriptive texts of the gene sequence and storing the descriptive texts in the memory.
(Mental processes, of observation, analysis and judgement. As well as an EIA, routine storage of extracted data. MPEP 2106.04(a)(2) III)
2. (Mental process and mathematic concepts of data recognition, length value comparisons, matching text strings, recognizing text elements, and “reading” or obtaining corresponding information from another portion of the document.)
3. (Mental process of data recognition, and data extraction, obtaining data, selecting a sentence in a document)
4. (Mental processes and mathematic concepts of data recognition and selection, comparing percentage values, recognizing positional information related to some other aspect of the string, measuring a length, calculating a percentage value.)
24. (Currently amended) The method according to claim 1, further comprising, before the recognizing step:
grabbing a text gene sequence from a patent application of a patent library, and
comparing the gene sequence to be retrieved with the grabbed text gene sequence, to determine a target gene sequence similar to the gene sequence to be retrieved; and
determining patent applications containing the target gene sequence as the current patent application to be analyzed; and,
further comprising, after the labeling step:
displaying a retrieval result of a patent application containing the target gene sequence.
(EIA- data gathering of a text string from a database, Mental Processes of comparison of text strings, to make a judgement as to “similarity”, identification of records in a database comprising a target, and EIA of a routine display step)
35. (Currently amended) A method for labeling infringement risk information of a gene sequence, wherein the method is applied to a retrieval engine comprising at least one processor and a memory, the method comprising:
(Preamble, setting forth a method, a goal of the method, and an EIA, the use of a general-purpose computer.)
acquiring, by the retrieval engine, a gene sequence, and
(EIA- data gathering of a gene sequence: a text string; specification [0027, 0162])
querying patent applications containing a target gene sequence similar to the gene sequence;
(Mental process of observation of the gene sequence, and comparison to other gene sequences in a set of targets. Specification [0128, 0161] text comparison/ matching)
extracting, by the retrieval engine, descriptive texts containing the target gene sequence from the claims of the patent applications,
wherein the descriptive texts comprise a length identifier that defines a length of a partial subsequence in the gene sequence;
(Mental process of observing a description of a length identifier, and using a present keyword, extracting the length of some part of the recognized element from the previous step. MPEP 2106.04(a) section III; Specification [0108, 0167] natural language processing technique using pre-trained ML and specifically labeled training data).
determining, by the retrieval engine, a percentage corresponding to the gene sequence according to the length identifier in the extracted descriptive texts, and
(Mathematic concept of calculating a percentage value. MPEP 2106.04(a) section 1; Specification [0113] calculating percentage, adding, subtracting, dividing.)
determining a scope of the claims of the target gene sequence based on the percentage;
(Mental process of observation of the percentage and making a judgement. MPEP 2106.04(a) section III; Specification [0027, 0108-0115])
determining, by the retrieval engine, a similarity between the gene sequence to be retrieved and the target gene sequence, and
(Mathematic concept of calculating a measure of similarity between two strings of data. MPEP 2106.04(a) section I; specification [0108-0115])
comparing the similarity with the scope of claims of the target gene sequence; and
(Mental process of comparison of data, and making a judgement. MPEP 2106.04(a) section III. Specification [0108-0115])
labeling, by the retrieval engine, infringement risk information of the patent applications with respect to the gene sequence to be retrieved based on a comparison result and
(Mental process of data annotation, based on the judgement of the previous step. MPEP 2106.04(a) section III. Specification [0173-0175])
storing the infringement risk information in the memory,
(EIA- routine output / data storage of a calculated value)
wherein extracting descriptive texts containing the target gene sequence from the claims of the patent applications comprises:
determining a sequence identifier of the target gene sequence in the claims from a sequence table of the patent applications by text matching, and
recognizing from the claims a position where the sequence identifier is located by using a trained natural language model;
looking up a length identifier that defines a length of a partial subsequence in the target gene sequence from the context of the recognized position; and
extracting a sentence containing the length identifier and the sequence identifier, and
taking the extracted sentence as the descriptive texts containing the target gene sequence and
storing the descriptive texts in the memory,
(Mental Processes of observation, data recognition, data extraction, annotation of the extracted data, and an EIA of data storage. MPEP 2106.04(a)(2) III.)
wherein determining the scope of the claims of the target gene sequence comprises one of:
(i) recognizing a percentage of a similarity variable range to which the target gene sequence corresponds from the descriptive texts, and
taking the percentage of the similarity variable range as a lower limit value of the scope of the claims of the target gene sequence; or
(ii) recognizing regional information for defining a position of a gene subsequence or a core function sequence in the target gene sequence from the descriptive texts, and
determining a length of the gene subsequence or the core function sequence according to the regional information; and
calculating a percentage of the length of the gene subsequence or the core function sequence in a total length of the target gene sequence, and taking the calculated percentage as a lower limit value of the scope of claims of the target gene sequence.
(Mental Processes of observation, data recognition, data extraction, annotation of the extracted data, and a mathematic concept of calculating percentages. MPEP 2106.04(a)(2) III.)
40. (Currently amended) The method according to claim 35, wherein the method further comprises:
after querying the patent applications matching the gene sequence,
converting the patent applications obtained by query into a similarity map according to the similarity between the target gene sequence in the patent applications and the gene sequence;
wherein in the similarity map, a distance between the patent application and the gene sequence is inversely proportional to the similarity.
(Mathematic concept of data transformation, using a similarity or distance calculation)
41. (EIA of receipt of data, and mental processes and mathematic concepts of data recognition, data annotation, observation of aspects of data, calculating percentage values.)
43. (Currently amended) The method according to claim 35, wherein the method further comprises one of:
after querying the patent applications matching the gene sequence,
constructing the patent applications obtained by query as a gene sequence development progress map according to information of filing date; and
after querying the patent applications matching the gene sequence,
recognizing a core function sequence from the gene sequence to be retrieved, and
filtering target patent applications containing the core function sequence from the patent applications obtained by query; and
constructing the target patent applications as a core sequence development progress map according to information of filing date.
(Mental process of creating a progress “map” utilizing recognized filing date information, and other recognized aspects of the gene sequence data, and mental processes of removal of data.
45. (Currently amended) A system for labeling infringement risk information of a gene sequence,
(Preamble setting forth a computer system, and an intended use of the system.)
comprising a retrieval engine having at least one processor and at least one computer readable non-transitory medium comprising instructions which, when executed by the processor cause the retrieval engine to, perform the following actions of:
(EIA- elements of a general-purpose computer)
acquiring a gene sequence, and
(EIA- data gathering of a gene sequence: a text string; specification [0027, 0162])
querying patent applications containing a target gene sequence similar to the gene sequence;
(Mental process of observation of the gene sequence, and comparison to other gene sequences in a set of targets. Specification [0128, 0161] text comparison/ matching)
extracting descriptive texts containing the target gene sequence from the claims of the patent application,
wherein the descriptive texts comprise a length identifier that defines a length of a partial subsequence in the gene sequence;
(Mental process of observing a description of a length identifier, and using a present keyword, extracting the length of some part of the recognized element from the previous step. MPEP 2106.04(a) section III; Specification [0108, 0167] natural language processing technique using pre-trained ML and specifically labeled training data).
determining a percentage corresponding to the gene sequence according to the length identifier in the extracted descriptive texts, and
(Mathematic concept of calculating a percentage value. MPEP 2106.04(a) section 1; Specification [0113] calculating percentage, adding, subtracting, dividing.)
determining a scope of claims of the target gene sequence based on the percentage;
(Mental process of observation of the percentage and making a judgement. MPEP 2106.04(a) section III; Specification [0027, 0108-0115])
determining a similarity between the gene sequence and the target gene sequence, and
(Mathematic concept of calculating a measure of similarity between two strings of data. MPEP 2106.04(a) section I; specification [0108-0115])
comparing the similarity with the scope of the claims of the target gene sequence; and
(Mental process of comparison of data, and making a judgement. MPEP 2106.04(a) section III. Specification [0108-0115])
labeling infringement risk information of the patent applications with respect to the gene sequence, based on a comparison result and
(Mental process of data annotation, based on the judgement of the previous step. MPEP 2106.04(a) section III. Specification [0173-0175])
storing the infringement risk information in the at least one computer readable non-transitory medium,
(EIA- routine output / data storage of a calculated value)
wherein extracting descriptive texts containing the target gene sequence from the claims of the patent applications comprises:
determining a sequence identifier of the target gene sequence in the claims from a sequence table of the patent applications by text matching, and
recognizing from the claims a position where the sequence identifier is located by using a trained natural language model;
looking up a length identifier that defines a length of a partial subsequence in the target gene sequence from the context of the recognized position; and
extracting a sentence containing the length identifier and the sequence identifier, and
taking the extracted sentence as the descriptive texts containing the target gene sequence and
storing the descriptive texts in the at least one computer readable non-transitory medium,
(Mental Processes of observation, data recognition, data extraction, annotation of the extracted data, and an EIA of data storage. MPEP 2106.04(a)(2) III.)
wherein determining the scope of the claims of the target gene sequence comprises:
(i) recognizing a percentage of a similarity variable range to which the target gene sequence corresponds from the descriptive texts, and
taking the percentage of the similarity variable range as a lower limit value of the scope of the claims of the target gene sequence, or
(ii) recognizing regional information for defining a position of a gene subsequence or a core function sequence in the target gene sequence from the descriptive texts, and
determining a length of the gene subsequence or the core function sequence according to the regional information; and
calculating a percentage of the length of the gene subsequence or the core function sequence in a total length of the gene sequence, and
taking the calculated percentage as a lower limit value of the scope of claims of the target gene sequence.
(Mental Processes of observation, data recognition, data extraction, annotation of the extracted data, and a mathematic concept of calculating percentages. MPEP 2106.04(a)(2) III.)
51. (Currently amended) The system according to claim 45, wherein the instructions which, when executed by the processor, further perform the following actions of:
when acquiring the gene sequence, receiving a specified similarity range input by a user;
correspondingly, a similarity between the target gene sequence contained in the patent applications obtained by query and the gene sequence is within the specified similarity range.
(EIA- data gathering step: receipt of data)
52. (Currently amended) The system according to claim 45, wherein the instructions which, when executed by the processor, perform the following actions of:
after querying the patent applications matching the gene sequence,
converting the patent applications obtained by query into a similarity map according to the similarity between the target gene sequence in the patent applications and the gene sequence;
wherein in the similarity map, a distance between the patent application and the gene sequence is inversely proportional to the similarity.
(Mathematic concept of data transformation, using a similarity or distance calculation)
53. (EIA of receipt of data, and mental processes and mathematic concepts of data recognition, data annotation, observation of aspects of data, calculating percentage values.)
54. (Currently amended) The system according to claim 52, wherein the instructions which, when executed by the processor, perform one of the following actions of:
after querying the patent applications matching the gene sequence to be retrieved,
constructing the patent applications obtained by query as a gene sequence development progress map according to information of filing date; and
after querying the patent applications matching the gene sequence to be retrieved,
recognizing a core function sequence from the gene sequence to be retrieved, and
filtering target patent applications containing the core function sequence from the patent applications obtained by query; and
constructing the target patent applications as a core sequence development progress map according to information of filing date.
(Mental process of creating a progress “map” utilizing recognized filing date information, and other recognized aspects of the gene sequence data, and mental processes of removal of data.)
BRI analysis:
These claims recite a judicial exception of organizing human behavior. MPEP 2106.04(a). The behavior is following rules or instructions for the examination of patent applications. Claims drawn to methods or systems for “labeling a protection scope of claims of a gene sequence” in a patent application, encompass the government-mandated processes and procedures for patent examination. Those rules exist in the MPEP (see the Introduction to the MPEP “Constitutional Basis”, 35 USC 1, and MPEP 701). In examination of a patent application with claims that recite a gene sequence, the examiner observes the pending claims, recognizes the presence of a polynucleotide, gene sequence, or SEQ ID NO, and extracts text information about that sequence from the language of the claims or the sequencing listing (which includes the length parameter). Recognizing the length parameter as the claimed “full length” of the sequence, gene or SEQ ID NO: from the sequence listing uses the preset keyword of “length” in the sequence listing, and is automatically stored in that sequence listing data file. The provision of the length as a parameter of similarity is used in subsequent searches of the “sequence to be analyzed” against public sequence databases, patent application databases, patent databases, as in claim 24. The examiner performs sequence similarity searching between the “gene sequence to be analyzed” and one or more sequences from a database comprising sequences present in patent applications and patents, using length as one parameter in the calculation of “similarity” between two DNA sequences. The search provides an output of a plurality of alignments between the “sequence to be analyzed” and the sequences of the databases, each of which provides a percentage value for sequence identity or similarity, the length of the match, and the source (the application or patent) of the sequence. The Examiner considers the aspects of each match and compares them to textual information in the claims of the application of the “sequence to be analyzed” and the claims of the application or patent providing the match. Should the scope of each claim overlap, the examiner makes a determination as to whether one sequence would anticipate or make obvious the other. This final determination considers all of the collected information. After identifying an application that has claims which recite sequences which fall within the scope of the claims of the application with the “sequence to be analyzed” the retrieval result is obtained, saved, and displayed to applicant as a part of the Office Action. The office action explains how the displayed retrieval result falls within the scope of the pending claims, based on the measures of similarity including length, and other associated information. MPEP: 701, 704, 706-708, (examination), MPEP 904.01, (sequence search procedures), MPEP 2103, (examination), MPEP 2111 (BRI), MPEP 2300 (Interference), and MPEP 2412-2435 (biotechnology and sequence rule information). Once a claim in a pending application has been determined to be patentable, and is allowed, that application leaves the jurisdiction of Examination and the examiner.
Claims drawn to methods or systems for “labeling infringement risk information of a gene sequence” in a patent application, encompass the government-mandated processes and procedures for patent litigation involving issued patent claims having a presumption of validity, and are an attempt to predict an outcome of a possible future litigation.
With respect to step 2A (2): NO, the claims do not integrate the JE into a practical application (MPEP 2106.04(d)):
“Examiners evaluate integration into a practical application by: (1) identifying whether there are any additional elements recited in the claim beyond the judicial exception(s); and (2) evaluating those additional elements individually and in combination to determine whether they integrate the exception into a practical application, using one or more of the considerations introduced in subsection I supra, and discussed in more detail in MPEP §§ 2106.04(d)(1), 2106.04(d)(2), 2106.05(a) through (c) and 2106.05(e) through (h).”
Claim(s) 1, 24, 35, 41, 45, 51, 53 recite the additional non-abstract element(s) of data gathering, or a description of the data gathered.
Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data necessary to carry out the JE. MPEP 2106.05(g).
The data gathering does not impose any meaningful limitation on the JE, or how the JE is performed. MPEP 2106.05(g).
The data gathering steps constitute a general link to a technological environment: the data gathered is gene sequence data. (MPEP 2106.05(h), citing Mayo, Bilski, electric Power Group, Genetic Techs Ltd v Merial LLC.)
The additional limitation (data gathering) must have more than a nominal or insignificant relationship to the identified judicial exception to provide integration into a practical application. (MPEP 2106.05(g) citing Mayo, PerkinElmer, Inc. v. Interna Ltd, Intellectual Ventures LLC v. Erie Indem. Co., Electric Power Group LLC v. Alstom S.A.).
Claim(s) 1, 24, 35, 45 recite the additional non-abstract element (EIA) of a general-purpose computer system or parts thereof.
The claims do not provide any details of how specific structures of the computer elements are used to implement the JE. MPEP 2106.05(a), contrasting decisions identifying how the computer implements an abstract idea, such as in McRo to decisions which found no specific interaction with the computer, such as in Affinity Labs of Tex v. DirecTV, LLC.
The computer elements of the claims do not provide improvements to the functioning of the computer itself. MPEP 2106.05(a) I, contrasting decisions indicating an improvement to the computer, such as DDR Holdings, LLC v. Hotels.com LP, with decisions that did not identify an improvement to the computer, such as FairWarning IP, LLC v. Iatrix Sys.
The computer elements of the claims do not provide improvements to any other technology or technical field. MPEP 2106.05(a) II: contrasting decisions indicating an improvement to the technology, such as Diamond v. Diehr, Trading Techs. Int’l v. CQG Inc, or Intellectual Ventures I v. Symantec Corp, with decisions that did not identify an improvement to the technology, such as Alice Corp, Versata Dev. Group, Inc. v. SAP AM. Inc, or TLI Communications.
The computer elements of the claims do not utilize a particular machine. MPEP 2106.05(b): contrasting decisions wherein a particular machine was identified, such as MacKay Radio & Tel. Co. v. Radio Corp. of America, Eibel Process Co. v. Minn. & Ont. Paper Co., with decisions where a general-purpose computer does not qualify as a particular machine, such as Ultramercial, Inc. v. Hulu, LLC, TLI communications, or Eon Corp. IP holdings LLC v. AT&T Mobility LLC.
Hence, these are mere instructions to apply the JE using a computer, and therefore the claim does not recite integrate that JE into a practical application.
Dependent claim(s) 2-4, 40-41, 43, 52-54 recite(s) an abstract limitation to the JE reciting additional mathematic concepts, or mental processes. Additional abstract limitations cannot provide a practical application of the JE as they are a part of that JE.
In combination, the limitations of data gathering, for the purpose of carrying out the JE, using a general-purpose computer merely provide extra-solution activity, and fail to integrate the JE into a practical application.
With respect to step 2B: NO, the claims do not recite a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05).
“… an "inventive concept" is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself. Alice Corp…”
With respect to claim(s) 1, 24, 35, 41, 45, 51, 53: The limitation(s) identified above as non-abstract elements (EIA) related to data gathering do not rise to the level of significantly more than the judicial exception.
The data obtained is gene sequence information, gene identifier information, length identifier information or percentage information.
Karsch-Mizrachi (2017) The international nucleotide sequence database collaboration. Nucleic Acids Research, vol 46, D48-D51. discloses a plurality of databases comprising gene sequence information, including identifiers, length et al.
Andree (2008) A comparative study of patent sequence databases. World Patent Information, vol 30 p300-308. discloses database sources for patent publications, for gene sequences and gene sequence information. Andee notes that GENESEQ, CAS Registry, PCTGEN, GenBank, EMBLbank, EBI Fasta all contain patent related sequence disclosures including identifiers and related information.
Lee (2007) Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. Nucleic Acids Research vol 35, D47-D50. discloses Patome, a database designed for sequence annotation and analysis for sequences in patents and patent applications.
Li (2013) The Annotation-enriched non-redundant patent sequence databases. Database, vol 2013, bat005, 6 pages. Li discloses obtaining gene sequence information, identifier information, and other aspects of biosequence information related to patent applications and issued patents.
These elements meet the BRI of the identified data gathering limitations. As such, the prior art recognizes that this data gathering element is routine, well understood and conventional in the art. MPEP 2106.05(d): “If, however, the additional element (or combination of elements) is no more than well-understood, routine, conventional activities previously known to the industry, which is recited at a high level of generality, then this consideration does not favor eligibility.”
Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data necessary to carry out the JE. MPEP 2106.05(g).
The data gathering does not impose any meaningful limitation on the JE, or how the JE is performed. MPEP 2106.05(g).
The additional limitation (data gathering) must have more than a nominal or insignificant relationship to the identified judicial exception to provide an inventive concept. (MPEP 2106.05(g) citing Mayo, PerkinElmer, Inc. v. Interna Ltd, Intellectual Ventures LLC v. Erie Indem. Co., Electric Power Group LLC v. Alstom S.A.)
The data gathering steps constitute a general link to a technological environment: biosequence information. (MPEP 2106.05(h), citing Mayo, Bilski, electric Power Group, Genetic Techs Ltd v Merial LLC.)
Therefore, simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception are insufficient to provide significantly more (as discussed in Alice Corp.,).
With respect to claim(s) 1, 24, 35, 45: the limitations identified above as non-abstract elements (EIA) related to general-purpose computer systems do not rise to the level of significantly more than the judicial exception.
Each of Karsch-Mizrahi, Andee, Li and Lee disclose computer systems or computing elements which meet the BRI of the claimed computer system or computer system elements, comprising input, output/ display, a processor, and memory.
As such, the prior art recognizes that these computing elements are routine, well understood and conventional in the art.
The specification, at [189-192, 203-205] discloses the use of routine general-purpose computers for carrying out the invention, and/or the use of commercially available computer system elements.
The claims do not provide any details of how specific structures of the computer elements are used to implement the JE. MPEP 2106.05(a), contrasting decisions identifying how the computer implements an abstract idea, such as in McRo to decisions which found no specific interaction with the computer, such as in Affinity Labs of Tex v. DirecTV, LLC.
The computer elements of the claims do not provide improvements to the functioning of the computer itself. MPEP 2106.05(a) I, contrasting decisions indicating an improvement to the computer, such as DDR Holdings, LLC v. Hotels.com LP, with decisions that did not identify an improvement to the computer, such as FairWarning IP, LLC v. Iatrix Sys.
The computer elements of the claims do not provide improvements to any other technology or technical field. MPEP 2106.05(a) II: contrasting decisions indicating an improvement to the technology, such as Diamond v. Diehr, Trading Techs. Int’l v. CQG Inc, or Intellectual Ventures I v. Symantec Corp, with decisions that did not identify an improvement to the technology, such as Alice Corp, Versata Dev. Group, Inc. v. SAP AM. Inc, or TLI Communications.
The computer elements of the claims do not utilize a particular machine. MPEP 2106.05(b): contrasting decisions wherein a particular machine was identified, such as MacKay Radio & Tel. Co. v. Radio Corp. of America, Eibel Process Co. v. Minn. & Ont. Paper Co., with decisions where a general-purpose computer does not qualify as a particular machine, such as Ultramercial, Inc. v. Hulu, LLC, TLI communications, or Eon Corp. IP holdings LLC v. AT&T Mobility LLC.
Hence, these are mere instructions to apply the JE using a computer, and therefore the claim does not provide significantly more.
Dependent claim(s) 2-4, 40-41, 43, 52-54 each recite a limitation requiring additional mathematic concepts or mental processes. Additional abstract limitations cannot provide significantly more than the JE as they are a part of that JE (MPEP 2106.05).
In combination, the data gathering steps providing the information required to be acted upon by the JE, performed in a generic computer or generic computing environment fail to rise to the level of significantly more than that JE. The data gathering steps provide the data for the JE, which is carried out by the general-purpose computers. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Applicant’s Arguments:
Applicant’s arguments have been carefully considered but are not completely persuasive.
Applicant argues the categorization or identification of abstract ideas, and/or a natural law in the claims. The Examiner has specifically identified each limitation in the claim, and what category of judicial exception is encompassed. The abstract ideas identified in the independent claims are the same as those identified as mathematic correlations, mathematic calculations, and mathematical relationships or as mental processes, concepts performed in the human mind including observations, evaluations, judgements and opinions, in MPEP 2106.04.
With respect to Applicant’s arguments that the claims provide an improvement to computer information processing functions, these arguments are not persuasive. The addition of a general-purpose computer, comprising routine memory and processing capabilities, is not sufficient to support an improvement to the “information processing functions.” The general-purpose computing elements do not have any interactions with the data that exceed normal data processing activities.
MPEP 2106.05(a): “To show that the involvement of a computer assists in improving the technology, the claims must recite the details regarding how a computer aids the method, the extent to which the computer aids the method, or the significance of a computer to the performance of the method. Merely adding generic computer components to perform the method is not sufficient. Thus, the claim must include more than mere instructions to perform the method on a generic component or machinery to qualify as an improvement to an existing technology.”
The listed improvement of “using a natural language model to recognize, from unstructured claim text, the position of the gene sequence and a length identifier; extracting the percentage or regional information from the legal language into computer processable numerical values; and calculating a lower limit value of the protection scope based on those values” refers to elements of the claims which make up the judicial exception.
MPEP 2106.05(a): “However, it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. For example, in Trading Technologies Int’l v. IBG, 921 F.3d 1084, 1093-94, 2019 USPQ2d 138290 (Fed. Cir. 2019), the court determined that the claimed user interface simply provided a trader with more information to facilitate market trades, which improved the business process of market trading but did not improve computers or technology.”
MPEP 2106.05(a): “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. See the discussion of Diamond v. Diehr, 450 U.S. 175, 187 and 191-92, 209 USPQ 1, 10 (1981)) in subsection II, below. In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception.”
The elements in addition to the JE are the use of general-purpose computer for obtaining, processing and storing data, and elements of data gathering. The general-purpose computer does not meet the requirements for a particular machine, as in MPEP 2106.05(b):
“It is important to note that a general-purpose computer that applies a judicial exception, such as an abstract idea, by use of conventional computer functions does not qualify as a particular machine. Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709, 716-17, 112 USPQ2d 1750, 1755-56 (Fed. Cir. 2014). See also TLI Communications LLC v. AV Automotive LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (mere recitation of concrete or tangible components is not an inventive concept); Eon Corp. IP Holdings LLC v. AT&T Mobility LLC, 785 F.3d 616, 623, 114 USPQ2d 1711, 1715 (Fed. Cir. 2015) … Merely adding a generic computer, generic computer components, or a programmed computer to perform generic computer functions does not automatically overcome an eligibility rejection. Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, 223-24, 110 USPQ2d 1976, 1983-84 (2014). See In re Alappat, 33 F.3d 1526, 1545, 31 USPQ2d 1545, 1558 (Fed. Cir. 1994); In re Bilski, 545 F.3d 943, 88 USPQ2d 1385 (Fed. Cir. 2008).”
The additional element of data gathering represents extra-solution activity (MPEP 2106.05(g)). The data gathering of biological sequence information is akin to MPEP 2106.05(g)(3) wherein the limitation “selects a particular data source or type of data to be manipulated”
“Below are examples of activities that the courts have found to be insignificant extra-solution activity:
• Mere Data Gathering:
i. Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989); …
iii. Presenting offers to potential customers and gathering statistics generated based on the testing about how potential customers responded to the offers; the statistics are then used to calculate an optimized price, OIP Technologies, 788 F.3d at 1363, 115 USPQ2d at 1092-93; …
vi. Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis).
• Selecting a particular data source or type of data to be manipulated:
i. Limiting a database index to XML tags, Intellectual Ventures I LLC v. Erie Indem. Co., 850 F.3d at 1328-29, 121 USPQ2d at 1937; …
iii. Selecting information, based on types of information and availability of information in a power-grid environment, for collection, analysis and display, Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1354-55, 119 USPQ2d 1739, 1742 (Fed. Cir. 2016);…”
Further, the claims do not set forth the type of language model, how the language model was trained, or how the language model acts on the unstructured text to perform those alleged improvements.
MPEP 2106.05(a): “An important consideration in determining whether a claim improves technology is the extent to which the claim covers a particular solution to a problem or a particular way to achieve a desired outcome, as opposed to merely claiming the idea of a solution or outcome. McRO, 837 F.3d at 1314-15, 120 USPQ2d at 1102-03; DDR Holdings, 773 F.3d at 1259, 113 USPQ2d at 1107.”
With respect to the arguments setting forth “categories” of risk, and Applicant’s argument that “The comparison yields either "similarity > lower limit value" or "similarity < lower limit value," and based on that result, the corresponding risk label and color are output. This is a complete computational process: input (unstructured text) -> processing (recognition, extraction, calculation, comparison) -- output (risk label and color)”, Applicant’s arguments are directed to limitations not present in the claims. The calculation of the risk in the rejected claims does not identify or classify the risk into the listed categories. The calculation of the risk in the rejected claims does not lead to the assignment of a display color. The claims do not clearly provide the alleged improved output of “a tangible, visual computer data object (e.g., a red "infringement" label)”. There are no specific limitations directed to the display or the presentation of the characterization beyond providing a few lines of text or a numerical result. As such these arguments are not persuasive.
With respect to the arguments that the operations cannot be carried out by the human mind, including an amount of data to be processed, these arguments are not persuasive. The claims do not require processing of any particular amount of data. The Query sequence, and the Target sequence are compared, one at a time, for the listed information. Even if the claims were to recite processing large numbers of sequences from a target sequence database, that comparison is still one that is made one at a time, Query to Target. The comparison of two gene sequence text strings, for length and/or similarity includes mental steps of observing and matching, as well as data recognition. This comparison does not require any process for which the human mind is not equipped.
MPEP 2106.04(a)(2) Section III A: “Claims do not recite a mental process when they do not contain limitations that can practically be performed in the human mind, for instance when the human mind is not equipped to perform the claim limitations. See SRI Int’l, Inc. v. Cisco Systems, Inc., 930 F.3d 1295, 1304 (Fed. Cir. 2019) (declining to identify the claimed collection and analysis of network data as abstract because "the human mind is not equipped to detect suspicious activity by using network monitors and analyzing network packets as recited by the claims"); CyberSource, 654 F.3d at 1376, 99 USPQ2d at 1699 (distinguishing Research Corp. Techs. v. Microsoft Corp., 627 F.3d 859, 97 USPQ2d 1274 (Fed. Cir. 2010) …”
“In contrast, claims do recite a mental process when they contain limitations that can practically be performed in the human mind, including for example, observations, evaluations, judgments, and opinions. Examples of claims that recite mental processes include:
• a claim to "collecting information, analyzing it, and displaying certain results of the collection and analysis," where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016);
• claims to "comparing BRCA sequences and determining the existence of alterations," where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014);
• a claim to collecting and comparing known information (claim 1), which are steps that can be practically performed in the human mind, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011); and …”
The amount of data, in and of itself is not a limitation which takes a process out of the realm of the human mind. It is the process performed on that data which is the mental step, and mental steps identified in the claims do not have to be fastest, most efficient, or require specialized computing elements. Data collection, extraction, comparison, alignment, and annotation can all be performed in the human mind, albeit very slowly, using pen and pencil, and slightly faster using the general-purpose computer as a tool or in a computing environment. Computations on large amounts of data performed mentally, or with paper and pencil, would take considerable time and effort, that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations).
The MPEP sets forth that “if the examiner concludes the disclosed invention does not improve technology, the burden shifts to applicant to provide persuasive arguments supported by any necessary evidence to demonstrate that one of ordinary skill in the art would understand that the disclosed invention improves technology. Any such evidence submitted under 37 CFR 1.132 must establish what the specification would convey to one of ordinary skill in the art and cannot be used to supplement the specification.” Applicant’s arguments cannot take the place of evidence.
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 1-4, 24, 35, 40-41, 43, 45, 51-54 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.
The claims have been heavily amended, partly in response to this rejection, however indefiniteness remains or was introduced by amendment.
All rejections of terms or phrases apply equally to all claims, wherever those terms or phrases appear.
The amendments to the independent claims, to append “wherein” limitations after the positive active method steps, are confusing. The claim structure would be better served if the “recognizing” step contained all the positive active method steps required to achieve the recognition, the “extracting” step contained all the positive active method steps required to achieve extraction, and the “determination” step set forth all the necessary and sufficient limitations required to achieve the “labeling a protection scope” or “labeling an infringement risk” as set forth in the specification and arguments. Further, each limitation should be separated clearly using indentations and an ending semicolon, without overuse of “and” between clauses. MPEP 608.
A possible example of such a structure could be:
“1. A computer-implemented method for labeling a protection scope of a gene sequence claimed in a current patent application, wherein the method is applied to a retrieval engine comprising at least one processor and a memory, the method comprising the following steps of:
recognizing, by the retrieval engine, a gene sequence from claims of a current patent application to be analyzed;
wherein recognizing the gene sequence from the claims of the current patent application to be analyzed comprises one of:
(i) recognizing a letter sequence consisted of specified letters from the claims of the current patent application to be analyzed, and
taking the letter sequence as the gene sequence when a length of the letter sequence reaches a specified length threshold value; or
(ii) recognizing a sequence identifier from the claims of the current patent application to be analyzed by text matching, and
reading a gene sequence corresponding to the sequence identifier from a sequence table of the current patent application to be analyzed;
retrieving, by the retrieval engine, the selected gene sequence data record;
extracting, by the retrieval engine, descriptive texts of the gene sequence from the claims of the current patent application based on a preset keyword, including a length identifier that defines a length of a subsequence in the gene sequence;
wherein extracting descriptive texts of the gene sequence from the claims based on the preset keyword comprises:
recognizing from the claims a position where the gene sequence is located by using a trained natural language model;
looking up a length identifier that defines a length of a subsequence in the gene sequence from context of the recognized position;
taking the length identifier as the preset keyword;
extracting a sentence containing the length identifier and the gene sequence; and
taking the extracted sentence as the descriptive texts of the gene sequence;
storing the descriptive texts in the selected gene sequence data record, in the retrieval engine memory;
determining, by the retrieval engine, a percentage corresponding to the length of the subsequence of the gene sequence according to the length identifier in the extracted descriptive texts;
taking the percentage as similarity information of the gene sequence;
labeling a lower limit value of the protection scope of the claims of the gene sequence according to the similarity information;
wherein the lower limit value indicates that any target gene sequence having a similarity to the gene sequence equal to or greater than the percentage falls within the protection scope of the claim of the patent application; and
storing the lower limit value in the gene sequence data record in the retrieval engine memory.”
The metes and bounds of claim 1 remain unclear. It is unclear what sequence is being protected- the Query sequence in the application, or the Target sequence in the database of patent applications. It is unclear which is being assessed. It is unclear if this is being applied to a whole database of claims of patent applications, in preparation to analyze a Query sequence in a different method, or whether this is being performed on a single Query from a user, extracting information about the single Query sequence, including length, and annotating the data file associated with the single Query sequence. These interpretations are not equivalent.
The term “partial subsequence in the gene sequence” in claim 1 is a relative term which renders the claim indefinite. The term “partial subsequence” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is entirely unclear what constitutes a partial subsequence of a gene. A subsequence of a gene would include any sequence less than full length. The recitation of partial prior to subsequence is redundant and confusing, the examiner suggests deleting “partial”.
The metes and bounds of claim 1, with respect to “similarity” remain unclear. Claim 1 now recites: “determining, by the retrieval engine, a percentage corresponding to the gene sequence according to the length identifier in the extracted descriptive texts, taking the percentage as similarity information of the gene sequence, and labeling a lower limit value of the protection scope of the claims of the gene sequence according to the similarity information.” The claim fails to particularly point out and distinctly claim how the DNA similarity is determined merely by comparing length information.
In DNA technology, similarity is not defined merely by two polynucleotide sequences (of any sequence) having the same length. In the comparisons of two text strings, each representing a DNA sequence of a gene, multiple aspects are considered. 1) Nucleotide sequence identity is the comparison of two polynucleotide sequence data files A and B, identifying the number of exact nucleotide matches between A and B, divided by the length of the aligned region, and is normally provided as a percentage value. (Polynucleotide sequence data file A is 15 % identical to polynucleotide sequence data file B.) The value only represents consecutive exact matches, excluding conservative substitutions, mutations, or indels. 2) Nucleotide sequence similarity is the comparison of two polynucleotide sequence data files A and B, where the process of matching or comparing the data string of A to B includes identifying exact matches, and best matches between the two strings which identify conservative substitutions, mutations/ variations, and can add or account for gaps/ indels, over the length of the alignment, and is normally provided as a percentage value. (Polynucleotide sequence data file A is 76% similar to polynucleotide sequence data file B.) 3) Nucleotide sequence homology addresses identifying sequences which evolved from a common ancestor gene. (Polynucleotide sequence data files A and B share significant homology to ancestor gene C.)
While length is a parameter of all these comparisons, the determination of “similarity” between two DNA sequences does not depend on length of the sequences alone. (Zhu, 2020, EigenBlog: Sequence Identity & similarity & homology, Github.) Claim 1 does not set forth a comparison step of the “gene sequence to be analyzed” to any other polynucleotide sequence, thus it is unclear to what the Query gene sequence is similar. This is not a limitation that obtains the “gene sequence to be analyzed” as polynucleotide sequence data file A, and compares it to one or more polynucleotide sequence data files B-D, to see how the length of A compares to the length of B, C and/or D. This is not a limitation that obtains the “gene sequence to be analyzed” and identifies the related gene of the genome, such that the length of the “gene sequence to be analyzed” may represent how much of the related gene of the genome is represented by the “gene sequence to be analyzed.” (polynucleotide sequence data file having length X is 58% of the length of Gene Z.) Merely stating that any sequence which is the same length, or less than the Query is “similar” does not make scientific sense. If length is merely a parameter used to filter out sequences of differing lengths, this limitation cannot be read into the claims.
Claim 1 fails to particularly point out and distinctly claim how the lower limit value is assigned, “according to the similarity information” as required. It is unclear if this merely copies the percentage value related to length and assigns it, with no change, as the “lower limit” or whether some other process is employed to make the assignment.
Claim 4 fails to particularly point out and distinctly claim the required elements for carrying out the desired actions. It is entirely unclear how claim 4 “recognizes” any information particularly with respect to functions, sequences, regional information, or similarity information. This information is not provided in claim 1, and not necessarily provided in the claims of the patent application. Patent application claims to gene sequence information are not required to identify subsequences, regions of significance, core function sequences, or even length information. This limitation is not the analysis of “the gene sequence to be analyzed” by comparing it to a data record of the gene of the genome, which may be annotated with regions linked to particular functions or other parameters. This limitation is not the use of a language model to analyze the “gene sequence” for the presence of characteristics such as promoter, enhancer, open reading frame, protein binding region et al. This limitation is not the use of the “gene sequence” to search a database to identify possible functions represented by the gene sequence as a results of sequence identity or similarity. It is entirely unclear how any of these elements are recognized based on the data at hand in claim 1.
Claim 24 fails to particularly point out and distinctly claim how sequence similarity is to be determined between the “gene sequence to be analyzed” and the “text gene sequence from a patent application” as now required, “to determine similarity”. The similarity is used to identify “the patent application to be analyzed” no matter the level of similarity identified. If Patent Application A has a text gene sequence 5% similar to “the gene sequence to be analyzed” is that sufficient? No consequences, or thresholds are applied to the similarity for the selection of the patent application. This is further unclear as the limitation recites “determining patent applications containing the target” which implies the sequences are to be identical, as “containing” implies the application text files contains the same string as the target.
Claim 35 fails to particularly point out and distinctly claim the elements required for “labeling infringement risk information”. The metes and bounds of the term “infringement risk” with respect to claims and gene sequence information is entirely unclear. It is unclear what the risk is intended to encompass, and entirely unclear how it is to be measured. Claim 35 is rejected for the reasons set forth for claim 1, as to how infringement risk is determined, given the various indefiniteness issues with the length identifier, identifying matching or similarity values, comparing length values, the basis of the determination of similarity, the “scope of protection” and how any of these values is acted upon by the claim to obtain a calculation of a risk of infringement. The examiner attempted to determine a plain meaning of “risk of infringement.” Risk of infringement is not calculated via a single mathematical formula. Instead, it is a forward-looking probability assessment (known as Freedom to Operate, or FTO). FTO is calculated by multiplying the 1) likelihood of encroachment by the 2) potential financial and operational impact. (Patsnap.com, “FTO Risk and Patent Infringement basics, 2026, 13 pages.) The claim fails to provide the data necessary to make this calculation. When calculating the risk of patent infringement for a calculated gene sequence, the process evaluates how closely the “sequence to be analyzed” matches the valid, enforceable claims of existing biotechnology patents. Aspects of sequence identity, similarity and functional equivalence are required for the determination, along with the analysis of the language of the claims of the patents, which is characterized overall as a complex legal process. The claim fails to provide the data required to identify “valid, enforceable claims” in biotech patents, and it fails to provide any data related to judicial actions or decisions regarding infringement. The claim fails to provide how any determination of protection scope was manipulated or used to predict any risk of infringement. This claim attempts to predict what the outcome would be of a judicial process, without setting forth or particularly claiming how that prediction is specifically made.
Claim 40 fails to particularly point out and distinctly claim how any conversion of information is to be carried out, and what the converted data is intended to contain, or how it is to be displayed. No particular features relevant to a “map” are set forth. No objects are disposed on a plane such that a distance between two objects has any relevance to the claimed invention. The claim fails to set forth any particular type of data conversion, the data required, the determination of similarity, or the particular distances to be converted or applied to any “map”. A patent application itself is not a map, nor is it clear, in any way, how to convert an entire patent application in to a map, based only on similarity information.
Claim 41 fails to particularly point out and distinctly claim how any further steps are to be applied to the “map” of claim 40, as the data required does not appear to be readily available from any prior claim. Claim 41 fails to particularly point out and distinctly claim the required elements for recognizing aspects of the gene sequence, with respect to functions, positions, sequences, regional information, or similarity information. This information is not provided in claim 35, and not necessarily provided in the claims of the patent application. Patent application claims to gene sequence information are not required to identify subsequences, positions, regions or significance, core function sequences, or even length information. It is entirely unclear how any of these elements are recognized based on the data at hand in claim 35 or claim 40 from which claim 41 depends.
Claim 43 fails to particularly point out and distinctly claim how any “gene sequence development map” is to be “constructed” “according to information of filing date” as set forth. No filing date information is obtained or retrieved in any previous claim. It is entirely unclear how to use any filing date information to construct or determine a course of development, as it is entirely unclear WHAT is being developed. The metes and bounds of a “gene sequence development map” are entirely unclear as to what information is required, how it is organized and how it is displayed.
In claim 43 the “after querying the patent application matching the gene sequence to be retrieved” is unclear. A patent application is not a map, and one does not query an application. One queries a database comprising information. It is entirely unclear how the phrase “to be retrieved” is to modify this limitation.
Claim 43 fails to particularly point out and distinctly claim the required elements for recognizing aspects of the gene sequence, with respect to functions, positions, sequences, regional information, or similarity information. This information is not provided in claim 35, and not necessarily provided in the claims of the patent application. Patent application claims to gene sequence information are not required to identify subsequences, positions, regions or significance, core function sequences, or even length information. It is entirely unclear how any of these elements are recognized based on the data at hand in claim 35 or claim 40 from which claim 41 depends.
System claims 45, 51-54 are indefinite in the same places for the same reasons as in the previously rejected method claims.
MPEP 2173: “It is of utmost importance that patents issue with definite claims that clearly and precisely inform persons skilled in the art of the boundaries of protected subject matter.”
Applicant’s arguments:
Applicant’s arguments have been carefully considered but are not fully persuasive. While some limitations have obviated rejections previously made, indefiniteness remains or was introduced by amendment.
MPEP 2171: “"…The second requirement is an objective one because it is not dependent on the views of the inventor or any particular individual, but is evaluated in the context of whether the claim is definite — i.e., whether the scope of the claim is clear to a hypothetical person possessing the ordinary level of skill in the pertinent art. Although an essential purpose of the examination process is to determine whether or not the claims define an invention that is both novel and nonobvious over the prior art, another essential purpose of patent examination is to determine whether or not the claims are precise, clear, correct, and unambiguous.”
MPEP 2173: “During prosecution the Office construes claims by giving them their broadest reasonable interpretation consistent with the specification in an effort to establish a clear record of what the applicant intends to claim. Such claim construction during prosecution may effectively result in a lower threshold for ambiguity than a court's determination. Packard, 751 F.3d at 1323-24, 110 USPQ2d at 1796-97 (Plager, J., concurring). However, applicant has the ability to amend the claims during prosecution to ensure that the meaning of the language is clear and definite prior to issuance or provide a persuasive explanation (with evidence as necessary) that a person of ordinary skill in the art would not consider the claim language unclear. In re Buszard, 504 F.3d 1364, 1366, 84 USPQ2d 1749, 1750 (Fed. Cir. 2007) (claims are given their broadest reasonable interpretation during prosecution "to facilitate sharpening and clarifying the claims at the application stage"); see also In re Yamamoto, 740 F.2d 1569, 1571, 222 USPQ 934, 936 (Fed. Cir. 1984); In re Zletz, 893 F.2d 319, 322, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989); Ex parte McAward, Appeal 2015-006416 (PTAB Aug. 25, 2017) (precedential).”
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2, 3 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
The limitations of claim 2 have been amended into claim 1, thus claim 2 is duplicative and fails to further limit claim 1.
The limitations of claim 3 have been amended into claim 1, thus claim 3 is duplicative and fails to further limit claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-4, 24, 35, 40-41, 43, 45, 51-54 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 function of the written description requirement is to ensure that the inventor had possession of the specific subject matter later claimed as of the filing date of the application relied on... In re Herschler, 591 F.2d 693, 700-01, 200 USPQ 711, 717 (CCPA 1979), further reiterated in In re Kaslow, 707 F.2d 1366, 217 USPQ 1089 (Fed. Cir. 1983); see also MPEP §§ 2163 - 2163.04.
Original, amended, or new claims are each given their broadest reasonable interpretation in light of, and consistent with the written description of the invention.
Claims may lack written description when the claims define the invention in functional language specifying a desired result but the specification does not sufficiently describe how the function is performed or how the result is to be achieved. The algorithm or steps or procedures taken to perform the function must be described with sufficient detail so that one of ordinary skill in the art would understand how the inventor intended the function to be performed to achieve the desired results. See MPEP §§ 2163.02 and 2181, subsection IV. As set forth in MPEP 2161, 2181 and 2185, “the claims must be supported by adequate written description of the step-by-step directions, algorithms, or structures to carry out the claimed steps.”
It is not enough for the patentee simply to state or later argue that persons of ordinary skill in the art would know what structures to use to accomplish the claimed function. The court in Biomedino, LLC v. Waters Technologies Corp., 490 F.3d 946, 953[, 83 USPQ2d 1118, 1123] (Fed. Cir. 2007), put the point this way: "The inquiry is whether one of skill in the art would understand the specification itself to disclose a structure, not simply whether that person would be capable of implementing that structure."
The description needed to satisfy the requirements of 35 U.S.C. 112 "varies with the nature and scope of the invention at issue, and with the scientific and technologic knowledge already in existence." Capon v. Eshhar, 418 F.3d at 1357, 76 USPQ2d at 1084. For inventions in emerging and unpredictable technologies, or for inventions characterized by factors not reasonably predictable which are known to one of ordinary skill in the art, more evidence is required to show possession.
Considering claims 1-4, 24, 35, 40-41, 43, 45, 51-54, the claimed technology of labeling scope of protection and infringement risk information of a gene sequence is considered in the art to be unpredictable.
The level of the skill and knowledge of one skilled in the art of bioinformatics is high. Bioinformatics combines biological and technical knowledge with skills related to computers and sophisticated data analysis. In particular, the complex nature of calculating or identifying infringement risk information for gene sequences illustrates the unpredictable nature of the technology, and underscores the requirement for a higher level of disclosure required.
In order to practice the claimed invention one of skill in the art must label a gene sequence being analyzed with scope of protection or infringement risk information, by obtaining that sequence, determining parameters related to the sequence, perform a matching process with a database of sequence information from claims of patent applications, and using the similarity information and the length information somehow identify a risk of infringement, and label the sequence accordingly. The actual calculations, algorithms, or steps for specifically performing the steps related to identifying, calculating, or determining a level of risk, based solely on similarity information and length are not clearly provided by the disclosure. While the specification provides some algorithms or flowcharts related to one or more processes or calculations, there is not a clear basis linking specific algorithmic processes to specific steps within the entire scope of the claim, and an issue exists as to whether the disclosure is adequate to perform the entire claimed function(s).
The specification provides a high level, generic description of the invention in the summary at p1-3. Generic description of possible data, possible interpretations, possible applied algorithms and possible outcomes are set forth in Detailed description, beginning at p5. Figures 1-5, 9 provide generic flow charts using the same language as the claims. The description of the invention beginning at page 5 sets forth a variety of steps, models, and techniques not clearly required by the independent claims, including OCR (optical character recognition), natural language models, trained natural language models using a NLP technique (natural language processing), the identification of ranges for parameters such as length or positions, semantic analysis of claim text, specific similarity search parameters (“KMP, Shift-And, Shift-Or, BM, Horspool, BNDM, BOM and etc.” p11, see also Fig 10), particular information in the retrieval result, and the determination of “protection scope.”
The specification provides details on the user interface, both for entering data, and viewing results, which are not set forth in the independent claims. Beginning at page 13, various mapping aspects are disclosed, which appear to require a graphical user interface that is not described or claimed. (Figs 7, 8). The user interface has interactive capabilities, and can connect the user to various other data records based on the results. Maps connecting applications based on parameters related to sequence similarity, timelines, ranges of similarity, “development progress”, and functional information are all generically described, without setting forth how each is to be performed and without the step-by-step process or algorithms required.
The disclosure related to labeling infringement risk of a gene sequence begins at page 17 and the generic flowchart of Fig 11. The specification does not provide a definition of infringement, nor how to calculate a risk of infringement using the data obtained in the steps of the method. The disclosure beginning at p17 sets forth the initial sequence, a set of target sequences in a database of patent application sequences, and the step of determining a similarity between the initial sequence, and those in the database. The disclosure notes that the sequences in the database of patent applications may contain irrelevant sequences not in the claims, and disposal of such sequences is recommended. Sequences having a high level of similarity to the initial sequence are retained. The disclosure, at p18 sets forth the specific use of trained natural language models, using a natural language processing technique, to analyze claim language related to scope of protection. Various prospective training data is generically described and labeled at pages 18-19. Semantic analysis of the claims by the NLP, along with similarity information and length information are collected for each application having a claimed sequence with sufficient similarity to the initial sequence. The data is used to calculate a protection scope, somehow employing all the information collected. How this scope is particularly calculated for the breadth of the claims is not disclosed. Once the scope of protection is determined, the disclosure attempts to provide infringement risk information, based on that scope of protection. (p20). The graphical user interface provides hyperlinked information of identified patent applications.
The only steps specifically related to infringement risk information, as set forth by the disclosure, are based on the similarity information, and the scope of the claims in question (021).
“[0177] On the other hand, the retrieval engine may compare the similarity and the scope of claims in the background, and if the similarity falls within the scope of claims, it indicates that the current gene sequence to be retrieved is at risk of infringement.”
The disclosure provides three categories of infringement risk: high, possible and no risk. However, how any data collected is to be sorted or classified into these categories is not provided.
“[0177]… In practical application, the infringement risk information can be represented by a combination of text and background color. For example, when the gene sequence to be retrieved is within the protection scope of the target gene sequence, the word "infringement" may be labeled, and the background color of the word "infringement" can be red. For another example, when the gene sequence to be retrieved is outside the protection scope of the target gene sequence, but a difference between the similarity and the lower limit value of the scope of claims is small, the words "possible infringement" may be labeled, and the background color of the words may be yellow. For another example, when the gene sequence to be retrieved is outside the protection scope of the target gene sequence, but a difference between the similarity and the lower limit value of the scope of claims is large, the words "no infringement risk" may be labeled, and the background color of the words may be green. Of course, in practical application, the infringement risk information may also be labeled by other means, which is not limited thereto herein.”
This appears to require both a stratification or classification of the scope of protection and similarity information, and a particularly programmed GUI to display the elements. These are not set forth in the claims.
The specification notes that similarity information and scope of protection are not the only parameters required to label infringement risk information at p25.
“However, in scenarios such as infringement retrieval analysis, it is not sufficient to provide only a retrieval result of similarity of the gene sequences. Assuming that the user conducts an infringement retrieval analysis on a gene sequence, the patent application retrieved based on the similarity may have only a target gene sequence with a similarity of 90%, but have no completely consistent gene sequence. However, it can not be concluded that the gene sequence can be used freely at this time. The reason is that the target gene sequence contained in the retrieved patent application usually has a protection scope, this protection scope may cover, for example, a gene sequence having a similarity of 80% or more to the target gene sequence involved in the patent application. Thus, since the similarity between the gene sequence to be retrieved and the target gene sequence is 90%, which actually falls within the protection scope of the patent application, and thus there is still a possibility of infringement. In view of this, in the present disclosure, after the patent application is obtained by performing retrieval based on the similarity, descriptive texts containing the target gene sequence may be further extracted from the claims of the patent application, and a protection scope of the target gene sequence may be determined according to the descriptive texts. Then, the similarity corresponding to the patent application along with the protection scope can be displayed in the retrieval result, so that the user can compare the size relationship between the similarity and protection scope, so as to judge whether the gene sequence to be retrieved has the possibility of infringement.”
The actual risk of infringement is to be a step of judgement by a user, and is not a result of the computer-implemented method.
The plain meaning of “infringement” in patent law is the
“unauthorized use of a patented invention, as defined under 35 U.S.C. § 271. This includes making, using, selling, offering to sell, or importing a patented invention within the United States during the term of the patent. Critically, infringement is determined by whether the accused product or process falls within the scope of at least one claim of the patent, not by general similarity or intent. Each claim sets specific boundaries. A valid infringement analysis requires showing that every element of a claim is met, either exactly or by legal equivalence. Once you understand patent infringement, it’s key to grasp how claims define and prove it. Claims are essential in determining infringement.” Lumenci (Lumenci.com, Understanding the Basics of Patent Infringement, downloaded 7/2026).
Elements of patent ownership, the details of the act of infringement, and the comparison of the accused product or process to the claims of the patent are required. Claim construction is a judicial process is determined, typically in a Markman hearing before a judge.
“The court’s interpretation often determines whether infringement exists, especially in software, electronics, or life sciences cases where language ambiguity is common.”
If the case proceeds to the infringement trial, the courts analyze the evidence provided to make a determination of whether a product or process infringes on a valid claim of a US Patent, under the controlling federal laws. The application fails to provide any such information, or step-by-step instructions to carry out labeling infringement risk information as set forth by the plain meaning of the terms.
The method appears to be more analogous to the idea of determining a “freedom to operate” for an invention (FTO), or a “clearance opinion” from a legal professional.
“FTO refers to the legal clearance to make, use, or sell a product without infringing on someone else’s existing patent rights. Unlike a patentability search, which checks whether your idea is new, an FTO search focuses on whether your product might run into legal obstacles from already granted patents. Even if your technology is developed independently, it can still fall within the scope of another company’s active claims. FTO analysis helps you spot these risks in advance, so you’re not blindsided later.” Lumenci (Lumenci.com, Conducting a Freedom to Operate Patent Analysis, downloaded 7/2026).
However, FTO is not a single, simple calculation. Detailed information about the product or process must be obtained, identification of technical features that may intersect with existing patents, thorough searching of the patent landscape must be performed, and careful analysis of the claims of identified patents are all required. The “clearance opinion” takes the results of the FTO or clearance search, considers the scope of the claims, and provides a legal opinion as to whether a specific product or process infringes one or more claims of a valid US patent. The legal opinion often considers the validity and enforceability of the patent claims in question. (Wikipedia, Patent Infringement, downloaded 7/2026). The specification fails to disclose all the required steps, algorithms, and specific processes for the scope of the pending claims.
Alderucci et al. (Alderucci, D. et al. (2019) applying artificial intelligence to the patent system, Technology and Innovation, vol 20 p415-425.) illustrates the complex issues raised in the analysis of patent claim text, scope of protection and infringement risk prediction. Alderucci notes difficulties in semantic analysis of claim language, depending on the field of the patent, and the nature of claim construction, as well as difficulties in training language models to act on the various elements of patent claims.
“Developing these patent-specific AI capabilities will require significant research to overcome current limitations in the state of the art.” P416
“Many of the interesting NLP tasks in the legal domain require a deep understanding of the meaning of text. One broad category of NLP task for the legal domain is AI-assisted legal decision-making. In the patent realm, one type of legal decision-making is determining whether a patent claim satisfies a requirement for patentability, such as the definiteness requirement. This task requires understanding more than the gist or surface-level meaning of the words of the claim—an intimate and nuanced appreciation for each word in the claim may be necessary.” P418
“Complex processing of domain-specific texts, such as patents, suggests that we move beyond the standard NLP techniques and develop techniques that are tailored to patents. This implies that we should not have high expectations from tools that do not have domain-specific features. It can be quite useful to train a general-purpose tool, such as a part-of speech tagger on patent text. However, this still does not yield a tool that is adapted to process patent-specific concepts, such as term definitions, steps of a process, alternative embodiments, and means-plus function elements.” P418
“A legal decision involves a collection of relevant facts and the application of those facts to a particular law or rule. In the patent realm, the relevant facts often include the state of technology in a particular field and the meaning of words describing that technology. This information can be hidden somewhere among hundreds of patents and other documents. For example, to determine whether a patent claim satisfies the definiteness requirement, the decision maker might want information such as what the key terms in the claim are, whether those terms are defined in the patent, whether they are industry standard terms, and whether the terms have a single accepted definition. Inferences can be drawn based on these pieces of information, such as that a particular term in a claim might not have a reasonably certain meaning.
Another example of legal decision-making is patent infringement analysis. This requires that a claim be interpreted and compared with a particular product. A product infringes a claim if every feature described in the claim is also present in the accused product. One could begin this analysis with a claim and a description of a product. However, it would not be enough to simplistically compare the words of the claim to the words of the product. Different words, such as “car” and “automobile,” are often used to describe equivalent concepts. More importantly for patents is that certain words have a type-subtype relationship but are not synonyms. For example, if the text of a patent claim is “a writing instrument with an eraser,” then that claim would be infringed by a product that is “a pencil with an eraser” or “a pen with an eraser.” In other words, a “pencil” and a “pen” are both types of “writing instruments.” AI software must understand synonyms, type-subtype, and other word relationships in order to perform the patent infringement analysis.”
“As difficult as it is for a person to evaluate claim definiteness, it is even harder for software to do so. Evaluating the definiteness of a claim requires two cognitive tasks that software does not do very well: determining the precise meaning of an arbitrary sequence of words and determining what those words mean to a particular type of person, specifically the hypothetical “person of ordinary skill in the art.” The first cognitive task is difficult enough because it requires that the software be capable of decoding vast amounts of human knowledge from text. The second task adds to this difficulty by referencing the understanding of a particular type of audience. At first blush, it would seem that AI has no place in the definiteness analysis. After all, if it is difficult for humans to conduct this cognitive task, then surely software would be incapable of doing so. However, AI can identify, search for, and provide the human decision maker with information that is useful to the required legal analysis.” P420
The specification as filed fails to provide algorithms, structures or step by step directions for determining scope of protection for a gene sequence to be analyzed; it fails to provide the algorithms, structures, or directions as how specifically to process the sequence to be analyzed, how to compare it to relevant sequences, how to specifically perform relevant sematic analysis of claim language; it fails in providing the training data necessary; it fails in providing details as to how the language model is trained, and how it acts upon the data to generate an output, and fails to provide the details necessary to analyze the results, such that an scope of protection, or infringement risk information can be identified.
The skilled practitioner would first turn to the instant specification to identify the specific algorithms or steps required by the specialized functions recited by the claims. However, the instant disclosure does not provide a written description of those specialized functions, and fails to link the particular algorithms or processes disclosed by the specification to specific functional limitations of the claims. As such, the skilled practitioner would turn to the prior art for guidance as to any known correlations between the disclosed structures or algorithms, and the specialized functions of the claims, however, the prior art shows that no known algorithms clearly are able to determine a scope of protection or a risk of infringement. As such, the claims lack adequate written description.
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) 1-3, 24, 35, 40, 45, 52 is/are rejected under 35 U.S.C. 102a1 as being anticipated by Bergmann (2008).
Bergmann, I. et al. (2008) Evaluating the risk of patent infringement by means of semantic patent analysis: the case of DNA chips. R & D Management vol 38 no 5, p550-564.
Bergmann is directed to “a method for detecting the risks of patent infringement by evaluating similarities between patent documents on the basis of semantic patent analysis. This approach enables the user to visualize similarities in the contents on a semantic patent map by means of multi-dimensional scaling… This paper will open out to the field of biotechnology, where patents can easily comprise several hundreds of pages. The method presented here conveys an interdisciplinary approach and combines computer-aided natural language processing with domain-specific expertise of biochemical processes. This is illustrated by an authentic case of infringement involving two manufacturers of DNA chips. Our experiment will show how the infringement case is visualized on a patent map based on semantic patent analysis.”
With respect to claim 1 and a method of labeling a protection scope, claim 24 including searching databases for similar applications or patents, and claim 35, including infringement information; as well as systems for carrying out these methods, all of Bergmann’s processes are computer-implemented, using computers having processors and memory.
Bergmann provides an overview of why scope of protection, and infringement risk is important to businesses and industry, at p550-551.
With respect to claims 1-3: (the limitations of claims 2 and 3 were amended into claim 1)
Bergmann set forth patent application claims to DNA chips, wherein DNA sequences are attached to a solid surface (p551-552 and section 2.1.1). Data regarding the DNA sequences was recognized and extracted from a set of patent applications to Applicant A (Affymetrix), as set forth in Fig 2. This could include SEQ ID NO, or probe number, or text nucleotide sequence. Claims comprising sequence information were subjected to text identification and extraction, or natural language processing to recognize and extract information about those sequences.
“Stage 2: Domain-specific speech filters have been developed for standardization and minimization of the highly differentiated idiom of biotechnology. Thus, SAO structures are modified to take synonyms (synonymizing filter) and concept hierarchies (generalizing filter) into account. This
also facilitates comparison and the detection of similarities in phrases with the same meaning. For
example, these speech filters refer to the semantic relationship of terms such as protein, polypeptide,
DNA, RNA, cDNA, mRNA, oligonucleotide, polynucleotide, and nucleic acid.” P555
“Stage 3: For the analysis of the biotechnological patents, a new comparative algorithm was developed. Based on existing similarity indicators, the similarity is measured by way of the number of identical SAO structures.”
Length of a nucleotide sequence is a parameter, or “Object” in the SAO structure (see Table 2). Comparison of SAO structures using Eq 1 can provide a percentage value related to similarity. The extracted keywords, semantic information and similarity percentage determined by a trained language model are stored by the patent information analysis software tool. As such, claims 1-3 are anticipated.
With respect to claim 24, Bergmann grabs gene sequence information from a patent application from a patent application library comprising patents to Applicant B (Synteni or OGT), and comparing the processed similarity information of A to the processed similarity information of B, using their SAO similarity structures, which includes length and similarity. P555-556.
With respect to claims 35 and 45, Bergmann takes the similarity matrix, which compares SAO of the gene information of A to the SAO of the gene information of B, generates visualization of the similarity matrices in an n-dimensional viewing space (Fig 6) to identify and label infringement risk information. P557-558. “The MDS produces a patent map in which patents are represented as data points and their similarity relationships are represented by distances.” Analysis of the mapping provides information regarding how likely one claim is to “interfere” with another, based on the distances, concepts, similarity information, and additional information. Clusters of patents, with common keyword information (descriptive texts), sequence parameter information as well as calculations of “stress values” provide interference risk information.
With respect to claims 40 and 52, Bergmann turns the data into similarity maps, as set forth in Fig 2 and Fig 6.
Claim Rejections - 35 USC § 103
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 4, 41, 43, 51, 53 and 54 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bergmann (2008) as applied to claims 1-3, 24, 35, 40, 45, and 52 above, in view of Berthels (2011).
Bergmann, I. et al. (2008) Evaluating the risk of patent infringement by means of semantic patent analysis: the case of DNA chips. R & D Management vol 38 no 5, p550-564.
Berthels, N. et al. (2011) Impact of gene patents on diagnostic testing. European Journal of Human Genetics, vol 19, p1114-1121.
As set forth above, Bergmann teaches the limitations of claims 1-3, 24, 35, 40, 45 and 52.
Bergmann provides an overview of why scope of protection, and infringement risk is important to businesses and industry, at p550-551.
With respect to claims 1-3: (the limitations of claims 2 and 3 were amended into claim 1)
Bergmann set forth patent application claims to DNA chips, wherein DNA sequences are attached to a solid surface (p551-552 and section 2.1.1). Data regarding the DNA sequences was recognized and extracted from a set of patent applications to Applicant A (Affymetrix), as set forth in Fig 2. This could include SEQ ID NO, or probe number, or text nucleotide sequence. Claims comprising sequence information were subjected to text identification and extraction, or natural language processing to recognize and extract information about those sequences.
“Stage 2: Domain-specific speech filters have been developed for standardization and minimization of the highly differentiated idiom of biotechnology. Thus, SAO structures are modified to take synonyms (synonymizing filter) and concept hierarchies (generalizing filter) into account. This
also facilitates comparison and the detection of similarities in phrases with the same meaning. For
example, these speech filters refer to the semantic relationship of terms such as protein, polypeptide,
DNA, RNA, cDNA, mRNA, oligonucleotide, polynucleotide, and nucleic acid.” P555
“Stage 3: For the analysis of the biotechnological patents, a new comparative algorithm was developed. Based on existing similarity indicators, the similarity is measured by way of the number of identical SAO structures.”
Length of a nucleotide sequence is a parameter, or “Object” in the SAO structure (see Table 2). Comparison of SAO structures using Eq 1 can provide a percentage value related to similarity. The extracted keywords, semantic information and similarity percentage determined by a trained language model are stored by the patent information analysis software tool. As such, claims 1-3 are anticipated.
With respect to claim 24, Bergmann grabs gene sequence information from a patent application from a patent application library comprising patents to Applicant B (Synteni or OGT), and comparing the processed similarity information of A to the processed similarity information of B, using their SAO similarity structures, which includes length and similarity. P555-556.
With respect to claims 35 and 45, Bergmann takes the similarity matrix, which compares SAO of the gene information of A to the SAO of the gene information of B, generates visualization of the similarity matrices in an n-dimensional viewing space (Fig 6) to identify and label infringement risk information. P557-558. “The MDS produces a patent map in which patents are represented as data points and their similarity relationships are represented by distances.” Analysis of the mapping provides information regarding how likely one claim is to “interfere” with another, based on the distances, concepts, similarity information, and additional information. Clusters of patents, with common keyword information (descriptive texts), sequence parameter information as well as calculations of “stress values” provide interference risk information.
With respect to claims 40 and 52, Bergmann turns the data into similarity maps, as set forth in Fig 2 and Fig 6.
Bergmann does not describe in detail how the SAO similarity matrices and map may be affected by ranges of similarity in the objects (such as sequence length, or function), which then affect the scope of protection or infringement risk information. Bergmann provides the SAO similarity map to provide infringement information based on distance information, and similarity information, but does not provide a color-based display of the infringement information.
In the same field of patent claims analysis, gene sequence information, and language processing, Berthels applies a patent categorization method to rank the impact of patents on genes important for testing for Spinocerebellar Ataxias (SCAs).
“Within the autosomal, dominant SCAs, about 30 monogenic subtypes are currently distinguished through genetic mapping, with the causative gene being identified for 16 subtypes
(Supplementary Table 1). The most accurate way to diagnose this genetic disease is molecular genetic testing, using a gene panel that typically includes individual assays for the five most prevalent SCA
subtypes (SCAl, SCA2, SCA3, SCA6, SCA7) and aiming to detect the pathogenic CAG-repeat expansion in one of these genes.” P1114.
Berthels obtains patents related to SCA genes, and checks the legal status of the patents with claims encompassing or reciting those genes, as set forth at p 1115 and Fig 1.
“A patent categorization method has been developed to weigh the impact of patents on genetic diagnostic services for SCA (Figure 1). A patent is considered to be hampering access to a genetic diagnostic test if the relevant patent (step 1) is valid in the country of interest (step 2), claims an essential part of the genetic test (step 3) that cannot be circumvented (step 4), is actively enforced and is not licensed at a reasonable cost (step 5).” P1115.
Respective SCA genes were identified, based on keywords, gene name, text comparison, identifier information, etc. A set of 47 patent documents was selected as the patent / application pool.
“The duration and the territorial scope of patents are two essential elements often overlooked by non-patent practitioners. The relevance of a patent can therefore be largely misjudged. Patents can be withdrawn or lapse during or after prosecution, for example, through non-payment of maintenance fees. Checking whether a patent is in force in the country of interest is therefore a prerequisite to any
freedom-to-operate analysis or patent landscaping effort assessing current patent obstacles.” P1115
Berthels analyzed the descriptive texts of the claims, to evaluate a scope of protection for the pending or granted claims, based on context.
“Claims were analyzed and interpreted in light of the patent specification. We evaluated the reasonable scope of the pending/granted claims based on the context (eg, the claim itself, other claims, the description, drawings, file wrapper). In Europe, Art. 69 of the European Patent Convention (EPC) and its Protocol form the basis for such interpretation, striving for a balance
between a fair protection for the patentee and a reasonable degree of certainty for third parties. In the United States, basis for claim interpretation can be found in the US Utility Patent Act §112, asking for a 'clear written description' and the 'best mode for carrying out the invention'.” P1115.
“The third step in patent categorization involves a meticulous analysis of the claim scope in order to determine the relevance for genetic testing. The most subjective part of any patent analysis is probably the interpretation of the claims in light of the description of the invention, as neither a strict, literal reading of the claims, nor a loose interpretation of the claims as mere guidelines, is appropriate. Rather, a fair protection for the patentee has to be balanced against a reasonable
degree of certainty for third parties (Protocol on the Interpretation of Art. 69 EPC). All pending and granted claims were considered valid as it is not the purpose of this study to judge on the validity of the claims in terms of patentability requirements.” P1115-1116.
Various ways to claim SCA gene sequence data are shown in Table 1. The gene sequence itself, methods of use of the gene sequence, cDNA fragments, detecting allelic variants of the gene, transgenic animals including or knocking out the gene, detecting certain repeat-expansions in the genes, genotyping/ haplotyping genes are all included.
“The scope of a claim to a DNA sequence is prone to various interpretations by different national courts. The implementation of the Biotechnology Directive (98/44/EC) resulted in national laws specifying the scope of patents related to biotechnological inventions. However, the absence of relevant case law in most countries leaves the interpretation of these provisions unclear. Moreover, important differences may occur in claim interpretation between United States courts and European national courts.” P1117
“Finding out whether a DNA claim is relevant for a particular genetic testing method cannot be generalized but requires an in-depth analysis on a case-by-case basis.19 Within the SCA patents identified in this study, nucleotide sequences are claimed in 66% of the 47 patent documents. The entire, human SCA genes are claimed in 45% of the patent documents.” P1117
Berthels expands on issues regarding extraction of DNA sequence information, semantic information and a scope of protection at page 1117:
“In case the invention comprises the identification of a human gene and the occurrence of predisposing mutations therein, the entire gene is likely to be claimed, and the sequence is often
specified. Alternatively, a claim towards a short gene sequence, if open ended, can be interpreted to cover a polynucleotide of any length comprising the claimed sequence, including the entire gene.
Claim 10 of US 5.834.183 claims a nucleic acid fragment, defined by the protein it encodes, which could encompass the entire SCAl gene. Moreover, due to the degenerative character of the genetic code, all sequences that encode the specified SCA! protein are protected by this claim.
Genetic testing based on PCR amplification of the CAG repeat region is unlikely to infringe this claim because the claimed fragment is neither used nor produced. Firstly, the claimed fragment is unlikely to be used as a PCR template. Secondly, the claimed fragment is more than 580 bp in size and it is unlikely that a PCR amplicon of that size is generated. However, it should be noted that claim interpretation is subject to high variability across various jurisdictions. In the United States, a broader interpretation in the light of the US's strong commercial focus is typically expected. In addition, other claims in this patent may probably infringe PCR methods.” P1117
Berthels provides core sequence function information (the presence or expansion of a specific repeat motif) and similarity ranges (all sequences encoding the SCA protein) as a part of the scope of protection or infringement risk. Berthels also identifies “hidden” claims as set forth at p 1119.
“A patent family entitled 'A gene related to migraine in man' and assigned to Rijksuniversiteit Leiden (NL), is, contrary to what the title suggests, drawn to three different diseases related to the CACNAlA gene, including SCA6. Gene sequences and detection methods are claimed, but whether the claims cover SCA6 diagnostic testing is unclear at first sight.”
All the information recognized and extracted by Berthels is utilized to determine a scope of protection or infringement risk information for SCA genes.
“The data obtained in the previous steps - finding relevant patents (step 1), checking patent validity (step 2), determining scope of claims (step 3) and checking availability of a license (step 4) - have been ultimately combined to systematically rank the patents into five categories according to their actual impact on access to genetic diagnostic testing. Metaphorically speaking, we tend to believe that the impact of patents in the area of diagnostic testing increases from 'no hampering effect', to 'stumbling rock', 'hurdle', 'roadblock' or 'patent thicket' (Figure 1, Supplementary Information). The patent landscaping method was similarly applied to the patent applications identified in this study.” P1119
Berthels, in Table 2, provides the following: sequences of SCA1 and 2 are at a high risk of infringing certain US patents, as shown in RED. Red indicates blocking patents and a high risk of infringement. Patents highlighted in YELLOW provide a moderate or low risk of infringement, and GREEN indicates no infringement.
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Applying the KSR standard of obviousness to Bergmann and Berthels, the Examiner concludes that the combination of the NLP processing program to extract gene information from claims of patents and patent applications, to label scope of protection or infringement risk as disclosed by Bergmann with the added gene sequence information and consideration of similarity provided by Berthels, including the use of similarity, function and color-coded display represents the use of a known technique to improve similar methods. The nature of the problem to be solved may lead inventors to look at references relating to possible solutions to that problem. Gene sequence information is complex in patent application claims, requiring multiple techniques for keyword identification and extraction, text identification, consideration of synonyms and gene naming systems, gene sequence parameter information. While Bergmann considered the length of the sequence as one parameter in the SAO map, one of skill in the art would have been motivated to add sequence similarity calculations, presence of functional or critical domains, or core function information to improve the MDS mapping, to identify the best scope of protection information, or the most accurate assessment of risk of infringement. Berthels illustrates these concepts with the specific genes for a specific disease, including the presence of short probes or primers in claims, sequence similarity as illustrated by known disease-associated mutations, sequence structures such as a domain repeat, and gene functions. Berthels applies these extracted SAO elements to an analysis of the scope of protection / infringement risk for the genes associated with SCA. One of skill would have had a reasonable expectation of success at applying these objects to the SAO of Bergmann, as Bergmann utilizes an n-dimensional mapping space based on the number of objects. Providing a color coded display marking the conclusions regarding infringement would have also been well within the skill of one of the art, as illustrated by Berthels. As such, the claimed invention would have been prima facie obvious for one of skill in the art at the time of filing, absent evidence to the contrary.
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.
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/MARY K ZEMAN/ Primary Examiner, Art Unit 1686
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