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 .
Claim Status
Claims 1-20 are currently pending and are herein under examination.
Claims 1-20 are rejected.
Claims 6, 13 and 20 are objected.
Priority
The instant application claims domestic benefit as a 371 filing of international stage application PCT/US2021/016208 filed 02/02/2021, which claims domestic benefit to U.S. Provisional Application No. 62/969,915 filed 02/04/2020. The claims to domestic benefit are acknowledged for claims 1-20. As such, the effective filing date for claims 1-20 is 02/04/2020.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description:
216-2 and 218-2 in Figure 2E.
302-1, 302-2, 304-1, 304-2, 306-1, 306-2 and 302-N in Figure 3A.
354-1, 354-2, 354-n in Figure 3B.
530 in Figure 5.
250 in Figure 7.
802-b, 804-b, 806-b, 808-b and 810-b in Figure 8.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference sign(s) mentioned in the description:
300, 302-i, 304-i, and 306-i in para. [42].
354-i in para. [44].
744 in para. [81].
802, 804, 806 and 808 in para. [87].
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(4) because reference character “704” designates both the system memory and video adaptor in Figure 7. Reference character “744” designates both the video adapter in para. [81] and the remote computer in para. [82].
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 6, 13 and 20 are objected to because of the following informalities:
Claims 6, 13 and 20 (last line) recite “among to the” which should be “among the”.
Appropriate correction is required.
Claim Interpretation
35 USC 112(f)
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation 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. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitations are described below:
Claims 1, 8 and 15 recite an analysis instrument configured to analyze a collection of samples.
Claim 15 recites a hardware interface configured to communicate with an analysis instrument, wherein communicating with the analysis instrument comprises receiving results of an analysis of the collection of samples.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. These structures are recited below:
The structure for the analysis instrument is being interpreted as any of the following or equivalents thereof: a high-throughput capillary electrophoresis or a device capable of measuring fluorescence, phosphorescence, or voltage. See specification paras. [27][53][60].
The structure for the hardware interface is being interpreted as any of the structures listed in specification paras. [83][84][89] and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
35 USC 112(b)
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 1-7, 10-11 and 13-20 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.
Claim 1, line 2, recites the phrase “the processors” which renders the claim indefinite. It is unclear which processors are being referenced because line 2 recites “one or more processors”. To overcome this rejection, clarify which processors are being referenced.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). Claim 1 line 2 recites a broad recitation of “one or more processors” and line 2 also recites “the processors” which is a narrower limitation of the broad recitation. The claim is indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Furthermore, claims 2-7 are also rejected because they depend on claim 1, which is rejected, and because they do not resolve the issue of indefiniteness.
Claim 3 (line 2), claim 10 (line 2) and claim 17 (line 2) recite the phrase “the conversion” which lacks antecedent basis. To overcome this rejection, change the phrase to “a conversion”.
Claim 4 (lines 5-6), claim 11 (lines 5-6), and claim 18 (line 5-6) recite the phrases “the time-series measurement of the test sample” and “the time-series measurement of the control sample” which render the claims indefinite. It is unclear which time-series measurement is being referenced for the test and control sample because claim 1 (lines 8-9), claim 8 (lines 7-8) and claim 15 (lines 7-9) appear to recite time-series measurements for both the test and control samples (i.e. each sample may have more than one measurement). To overcome this rejection, clarify which measurement is being referenced or clarify that both the test and control sample each have only one time-series measurement.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). Claim 4 (lines 5-6), claim 11 (lines 5-6), and claim 18 (lines 5-6) recite a broad recitation of “one or more first peaks” and “one or more second peaks”. Claim 4 (line 8), claim 11 (line 8) and claim 18 (line 8) then recite “the first peaks and the second peaks”, which is a narrower limitation of the broad recitation. The claim is considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 4 (line 8), claim 11 (line 8), and claim 18 (line 8) recite the phrase “the first peaks and the second peaks” which renders the claims indefinite. It is unclear which first peaks and which second peaks are being referenced because claim 4 (lines 5-6), claim 11 (lines 5-6), and claim 18 (lines 5-6) recite “one or more first peaks” and “one or more second peaks”. To overcome this rejection, clarify which peaks are being referenced.
Claim 4 (lines 10-12), claim 11 (lines 10-12), and claim 18 (lines 10-12) recite the following phrase that renders the claims indefinite: “a first time-series measurement of the control sample from a second-time series measurement of the test sample”. It is unclear whether “first” and “second” are merely a naming scheme, or if they refer to a chronological order of measurements in the time-series (e.g. the second time-series measurement being after a first time-series measurement in the test sample). To overcome this rejection, clarify how the phrase should be interpreted.
Claim 6 (lines 3-4), claim 13 (lines 3-4), and claim 20 (lines 3-4) recite the phrase “the time-series measurement of the control sample and the time-series measurement of the test sample” which renders the claims indefinite. It is unclear which time-series measurement is being referenced for the test and control sample because claim 1 (lines 8-9), claim 8 (lines 7-8) and claim 15 (lines 7-9) appear to recite time-series measurements for both the test and control samples (i.e. each sample may have more than one measurement). To overcome this rejection, clarify which measurement is being referenced or clarify that both the test and control sample each have only one time-series measurement.
Claim 6 (line 6), claim 13 (line 6), and claim 20 (line 6) recite the phrase “the control sample” which renders the claims indefinite. It is unclear which control sample is being referenced because claims 6, 13 and 20 recite “the control sample from among a plurality of control samples”. If referring to the selected control sample, Applicant can change the phrase to “the selected control sample”.
Claim 6 (lines 5-7), claim 13 (lines 5-7), and claim 20 (lines 5-7) recite the following limitation that renders the claims indefinite: “the control sample selected as a match with the test sample based on identifying that the control sample has the smallest computed distance from the test sample from among to the plurality of control samples.” It’s unclear whether this limitation is a product by process and thus is not required by the claim, or if this limitation is a required step as indicated by “selected … based on identifying”. For examination purposes, this limitation is being interpreted as a product by process. To overcome this rejection, clarify how the phrase should be interpreted.
Claim 7 recites the phrase “further storing instructions for identifying … and submitting” which renders the claim indefinite. It is unclear if this phrase means that the computer-readable medium has further instructions stored that the processor is configured to execute, or if the processor actively stores instructions in some yet unspecified location. For examination purposes, this phrase is being interpreted to mean that the medium contains further instructions that the processors is configured to perform. To overcome this rejection, clarify how the phrase should be interpreted.
Claim 14 recites the phrase “further storing instructions for identifying … and submitting” which renders the claim indefinite. It’s unclear whether the phrase indicates that other (as of yet unspecified) instructions are also stored (in a yet unspecified location), or if the phrase means something like “the method of claim 8, further comprising: storing”. To overcome this rejection, clarify the interpretation of this phrase.
Furthermore, claims 16-20 are also recited because they depend on claim 15, which is rejected, and because they do not resolve the issue of indefiniteness.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1:
Step 1 asks whether the claims recite statutory subject matter. In the instant application, claims 1-7 recite a CRM, claims 8-14 recite a method, and claims 15-20 recite a system. As such, these claims recite statutory subject matter (Step 1: YES).
Step 2A, Prong 1:
Claims that recite statutory subject matter are analyzed under Step 2A, Prong 1 to determine if they recite any concepts that equate to an abstract idea, law of nature or natural phenomena. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claims 1 and 8 recite “align the time-series measurements of the collection of samples; programmatically identify a sample of interest by comparing the aligned time-series measurements of the test sample and the control sample; and generate an output comprising an identifier for the identified sample of interest.”
Claims 4, 11 and 18 recite “aligning the time-series measurements comprises: identifying one or more first peaks in the time-series measurement of the test sample, identifying one or more second peaks in the time-series measurement of the control sample, and allowing the first peaks and the second peaks to float relative to each other within a predefined tolerance window; and programmatically identifying the sample of interest comprises subtracting or dividing a first time-series measurement of the control sample from a second time-series measurement of the test sample.”
Claims 5 and 12 recite “the samples comprise at least one of a protein, DNA, RNA, polysaccharide, lipid, polymer, or small molecules; the sample of interest includes at least one of a protein, DNA, RNA, polysaccharide, lipid, polymer, or small molecules not present in the control sample;”
Claims 6, 13 and 20 recite “wherein programmatically identifying the sample of interest comprises: computing a distance between the time-series measurement of the control sample and the time-series measurement of the test sample, and selecting the control sample from among a plurality of control samples, the control sample selected as a match with the test sample based on identifying that the control sample has the smallest computed distance from the test sample from among to the plurality of control samples.”
Claims 7 and 14 recite “wherein the output comprises a table of spectral peaks … identifying a database of experimental results.”
Claim 15 recites “align the time-series measurements of the collection of samples, and to programmatically identify a sample of interest by comparing the aligned time-series measurements of the test sample and the control sample;”
Claim 19 recites “the sample of interest includes at least one of a protein, DNA, RNA, polysaccharide, lipid, polymer, or small molecules not present in the control sample;”
Limitations reciting a mental process.
Claims 1, 4, 6, 8, 11, 13, 15, 18 and 20 contain limitations recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind. The paragraphs below discuss the broadest reasonable interpretation (BRI) of the limitations in these claims that recite a mental process.
Regarding claims 1 and 8, aligning time-series measurements includes drawing data on pen and paper such as spectral peaks. Identifying a sample of interest by comparing aligned measurements includes making mental determinations. Generating an output of an identifier includes displaying information on pen and paper.
Regarding claim 15, aligning time-series measurements includes drawing data on pen and paper such as spectral peaks. Identifying a sample of interest by comparing aligned measurements includes making mental determinations. Regarding claims 4, 11 and 18, identifying peaks includes analyzing data and making mental determinations. Allowing peaks to flow relative to one another is another mental determination. Subtracting or dividing measurements includes performing math on pen and paper. Regarding claims 6, 13 and 20, computing a distance includes calculation Euclidean distance on pen and paper. Selecting a control sample includes making a mental determination. Regarding claims 7 and 14, a human can search for a database.
Limitations reciting a mathematical concept.
Claims 4, 6, 11, 13, 18 and 20 recite limitations that equate to a mathematical concept because they are similar to the concepts of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. Regarding claims 4, 11 and 18, subtracting and dividing recite math. Regarding claims 6, 13 and 20, computing distance includes calculating Euclidean distance.
Limitations included in the recited judicial exception.
Regarding claims 5, 7, 12 and 14, these limitations are included in the judicial exception in claims 1 and 8 of identifying a sample of interest and generating an output because they further limit the sample of interest and output. Regarding claim 19, this limitation is included in the judicial exception in claim 15 of identifying a sample of interest because it further limits the sample of interest.
As such, claims 1-20 recite an abstract idea (Step 2A, Prong 1: YES).
Additional Elements:
Once limitations have been identified that recite a judicial exception, the claims are evaluated for additional elements. The additional elements are then analyzed under Step 2A, Prong 2 then Step 2B. The instant claims recite the following additional elements:
Claim 1 recites “A non-transitory computer-readable medium storing instructions that, when executed by one or more processors, cause the processors to: interface with an analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample; receive results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples;”
Claims 2-7 recites “The medium of claim 1”
Claims 2 and 9 recite “wherein the time-series measurements comprise one or more of spectral absorbance measurements, phosphorescence measurements, fluorescence measurements, or voltage measurements.”
Claims 3 and 10 recite “wherein the time-series measurements comprise one or more of energy, force, torque, light, or position measurements, or the conversion of an energy, force, torque, light, or position measurement to an electrical signal.”
Claims 4 and 11 recite “the control sample does not include a component of interest and the test sample does include a component of interest;”
Claims 5 and 12 recite “and the analysis comprises an electrophoresis analysis.”
Claims 7 and 14 recite “further storing instructions for … and automatically submitting the output to the database.”
Claim 8 recites “interfacing with an analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample; receiving results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples;”
Claim 15 recites “a hardware interface configured to communicate with an analysis instrument, the analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample; wherein communicating with the analysis instrument comprises receiving results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples; a hardware processor configured to …; and a non-transitory computer-readable medium configured to store an output comprising an identifier for the identified sample of interest.”
Claim 16 recites “The apparatus of claim 15, wherein the time-series measurements comprise one or more of spectral absorbance measurements, phosphorescence measurements, fluorescence measurements, or voltage measurements.”
Claim 17 recites “The apparatus of claim 15, wherein the time-series measurements comprise one or more of energy, force, torque, light, or position measurements, or the conversion of an energy, force, torque, light, or position measurement to an electrical signal.”
Claim 18 recites “The apparatus of claim 15, the control sample does not include a component of interest and the test sample does include a component of interest.”
Claim 19 recites “The apparatus of claim 15, the samples comprise at least one of a protein, DNA, RNA, polysaccharide, lipid, polymer, or small molecules; and the analysis comprises an electrophoresis analysis.”
Claim 20 recites “The apparatus of claim 15”
These above recited additional elements are analyzed below under both Step 2A, Prong 2 and Step 2B:
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” and/or to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)) and to insignificant, extra-solution activity (MPEP 2106.05(g)). The paragraphs below discuss the additional elements recited above in the instant claims.
Regarding claims 1-7 of the processor executing instructions on a CRM and claims 15-20 of an apparatus comprising a hardware interface (which may be ethernet para. [89]), a processor, and a CRM. There are no limitations that these components require anything other than a generic computer and/or generic computing system. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding claims 1, 8 and 15 of using a hardware interface or a processor to interface/communicate with an analysis system and receive results and claims 7 and 14-15 of storing instructions and output, these limitations equate to invoking a computer as a tool to perform an existing process such as receiving, storing, or transmitting data. See MPEP 2106.05(f)(2). These limitations also equate to insignificant extra-solution activity of data gathering and outputting because they gather data to perform the judicial exception in claims 1, 8 and 15 and output the result of the judicial exception.
Regarding claims 2-5, 9-12 and 16-19, these limitations equate to data gathering because they further limit the type of data gathered in claims 1, 8 and 15 (i.e. time-series measurements, analysis, control sample, test sample, and the collection of samples) used to perform the judicial exception.
As such, claims 1-20 are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The paragraphs below discuss the additional elements recited above in the instant claims.
Regarding claims 1-7 of the processor executing instructions on a CRM and claims 15-20 of an apparatus comprising a hardware interface (which may be ethernet para. [89]), a processor, and a CRM. There are no limitations that these components require anything other than a generic computer and/or generic computing system. Therefore, these limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
Regarding claims 1, 8 and 15 of using a processor or hardware interface (i.e. ethernet) to interface/communicate with an analysis system and receive results and claims 7 and 14 of submitting an output to a database. These limitations equate to receiving/transmitting data over a network, which the courts have established as WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014). Furthermore, the limitations in claims 2-5, 9-12 and 16-19 that further limit the time-series measurements, analysis, control sample, test sample, and the collection of samples also equate to receiving/transmitting data over a network because they merely limit the type of data being transferred/received.
Regarding claims 1, 7 and 14-15 of storing instructions and output, these limitations equate to storing information in memory, which the courts have established as a WURC function of a generic computer in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
Regarding the additional elements in claims 1, 8 and 15 when viewed in combination, these limitations equate to WURC limitations as taught by Mark et al. et al. (Spectroscopy 34, no. 5 (2019): 28-45) and Trzcinski et al. (“Trzcinski”; Applied Spectroscopy 70, no. 5 (2016): 905-915). Mark discloses a commercially available smartphone-based Raman spectrometer from Cloudminds that uploads data to a cloud via cellular, Wi-Fi or Bluetooth (pg. 11, last para.). Trzcinski discloses collecting data from portable spectrometers using smartphones by means of Bluetooth, Wi-Fi and ultra-wide band (abstract). Figure 1 shows both the spectrometer and smartphone using a wireless interface. Thus, Mark and Trzcinski demonstrate that a cellular computing device (containing a processor, memory, and a hardware interface) is WURC when in combination with an analysis instrument such as a spectrometer.
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they equate to WURC functions/components of a generic computer in combination with an analysis instrument as taught above by Mark and Trzcinski. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 1-20 are not patent eligible.
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.
Claims 1, 8 and 15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tautenhahn et al. (“Tautenhahn”; US 2017/0338089 A1).
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
Claims 1, 8 and 15:
(claim 1) A non-transitory computer-readable medium storing instructions that, when executed by one or more processors, cause the processors to:
(claim 8) A method comprising:
(claim 15) An apparatus comprising:
Tautenhahn analyzes mass spectrometry data (Figure 1). Figure 8 shows a computer system 800 containing processors 804 and memory 806 for controlling a mass spectrometry platform 100 [50].
(claims 1 and 8) interface with an analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample; receive results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples;
(claim 15) a hardware interface configured to communicate with an analysis instrument, the analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample, wherein communicating with the analysis instrument comprises receiving results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples;
Computer system 800 communicates with the mass spectrometry platform’s 100 controller 108 through a bus 802 (hardware interface) [50]. The spectrometer 100 analyzes a plurality of samples and provides the results to the computer system 800 [24] (Figure 2). The plurality of samples includes an initial dataset with known “normal” samples (control sample) and additional datasets with unknown samples (test sample) [24] [27]. The datasets contain retention times, intensity, and m/z values (time series-measurements) [26] [29].
(claims 1 and 8) align the time-series measurements of the collection of samples;
(claim 15) a hardware processor configured to align the time-series measurements of the collection of samples,
Figure 4 shows that a new dataset comprising a test dataset can be aligned to an existing dataset such as a known dataset [32]. This alignment identifies features of interest within the test dataset [32].
(claims 1 and 8) programmatically identify a sample of interest by comparing the aligned time-series measurements of the test sample and the control sample; and
(claim 15) a hardware processor configured to programmatically identify a sample of interest by comparing the aligned time-series measurements of the test sample and the control sample;
Figure 5 shows test samples can be grouped and identified by comparing their features to a set of grouping criteria derived from the initial datasets [36]. After alignment, compounds can be classified (abstract).
(claims 1 and 8) generate an output comprising an identifier for the identified sample of interest.
(claim 15) a non-transitory computer-readable medium configured to store an output comprising an identifier for the identified sample of interest.
Figure 7 displays compounds identified in a test sample by comparison to reference samples. Data can be stored on non-transitory computer-readable media [48][58].
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claims 1-3, 5, 8-10, 12, 15-17 and 19 are rejected under 35 USC 103 as being unpatentable over Jaeger (US 2007/0112534 A1) in view of Desimas et al. (“Desimas”; WO 2017/197408 A1).
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
Claims 1, 8 and 15:
(claim 1) A non-transitory computer-readable medium storing instructions that, when executed by one or more processors, cause the processors to:
(claim 8) A method comprising:
(claim 15) An apparatus comprising:
Jaeger calibrates peak patterns acquired from separation techniques such as electrophoresis and chromatography (abstract) [15] (Figure 1). The method can be executed by a processing unit of a data processing system using software stored in memory [29] (claim 19 and 32).
(claims 1 and 8) interface with an analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample; receive results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples;
(claim 15) a hardware interface configured to communicate with an analysis instrument, the analysis instrument configured to analyze a collection of samples, the samples comprising a test sample and a control sample, wherein communicating with the analysis instrument comprises receiving results of an analysis of the collection of samples, the analysis comprising time-series measurements for the collection of samples;
Jaegar acquires peak patterns from a sample of interest (test sample) and a calibration sample (control sample) by using a separation flow path which may be electrophoresis or chromatography [4] [12] [15] [16]. Figure 1 shows the separation flow path which analyses a plurality of different sample compounds including the sample of interest and calibration sample [15] [40]. Acquired peak pattern are analyzed (claim 1). The processing unit performs analysis [29].
However, Jaegar does not teach interfacing with or receiving data from the measurement device using a processor or a hardware interface.
Desimas automates analysis of electrophoresis data (abstract). Desimas teaches a processing station, comprising a processor and memory, that interfaces/communicates with an electrophoresis apparatus (pg. 8, last para.). The processing station receives data collected by the electrophoresis apparatus to perform automated peak detection (pg. 9, para. 2-3).
It would have been prima facie obvious to have interfaced the data processing system of Jaeger (claim 19) to the separation flow path of Jaegar (claims 20, 22 and 24) in order to receive data, as taught by Desimas. The motivation for doing so is to have an integrated system capable of performing automated analysis, as taught by Desimas (pg. 8, last para. – pg. 9, para. 3). Desimas also teaches that their system improves analysis of analytes using an electrophoresis apparatus. There would have been a reasonable expectation of success to interface the data processing system to the electrophoresis device of Jaeger (Figure 1) [15] because Desimas teaches interfacing a computer with an electrophoresis device (pg. 8, last para. – pg. 9, para. 3).
(claims 1 and 8) align the time-series measurements of the collection of samples;
(claim 15) a hardware processor configured to align the time-series measurements of the collection of samples,
Jaeger aligns sample peak patterns against calibration peak patterns (abstract) (Figured 4A-4C) [48]. Processing unit performs data analysis [29].
(claims 1 and 8) programmatically identify a sample of interest by comparing the aligned time-series measurements of the test sample and the control sample; and
(claim 15) a hardware processor configured to programmatically identify a sample of interest by comparing the aligned time-series measurements of the test sample and the control sample;
Jaeger teaches that alignment allows for identification of compounds in an unknown sample by comparison to samples with known compounds [2]. Figures 4A-4C show labels for samples of interest (S1-S4) being compared to calibration samples (L1 and L2). Processing unit performs data analysis [29].
(claims 1 and 8) generate an output comprising an identifier for the identified sample of interest.
(claim 15) a non-transitory computer-readable medium configured to store an output comprising an identifier for the identified sample of interest.
Jaegar shows in Figures 4A-4C graphs of aligned peaks of the samples of interest and calibration samples. Certain peaks represent compounds of interest and each sample of interest has an identifier (S1-S1 in Figure 4) [4] [8]. Jaegar discloses storing data of the analysis in a data carrier [29].
Claims 2-3, 9-10 and 16-17:
Jaeger teaches “peak patterns are acquired by detecting fluorescence intensity as a function of time” [16]. The peak patterns are defined in part based on position [4-8].
Claims 5, 12 and 19:
Jaeger teaches that the electrophoresis samples are used for DNA and protein analysis [2] [41]. The sample of interest may contain various species of interest that are not contained in the calibration samples [8].
Claims 4, 11 and 18 are rejected under 35 USC 103 as being unpatentable over Jaeger (US 2007/0112534 A1) in view of Desimas et al. (“Desimas”; WO 2017/197408 A1), as applied above to claims 1, 8 and 15, and in further view of Korifi et al. (“Korifi”; Journal of separation science 37, no. 22 (2014): 3276-3291) and Wang et al. (“Wang”; US 8,304,719 B2).
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
The limitations of claims 1, 8 and 15 have been taught in the rejection above by Jaeger and Desimas.
Claims 4, 11 and 18:
the control sample does not include a component of interest and the test sample does include a component of interest;
Jaeger teaches “The calibration peak patterns each comprise a first reference peak and one or more second reference peaks. In addition to peaks related to species of interest, the sample peak pattern also comprises the first reference peak and at least one of the second reference peaks” [8]. The peaks related to species of interest represent compounds [2] that are not necessarily in the calibration samples.
aligning the time-series measurements comprises: identifying one or more first peaks in the time-series measurement of the test sample, identifying one or more second peaks in the time-series measurement of the control sample, and
Jaeger aligns a plurality of peaks from each of the samples of interest and the calibration sample (claim 1) (Figures 4A-4C).
allowing the first peaks and the second peaks to float relative to each other within a predefined tolerance window; and
Jaeger recites “From FIG. 6B, it can be seen that both the first ladder peaks LP1 and the last ladder peaks LPn are perfectly aligned, whereas the peak positions of the other ladder peaks LP2 to LP(n−1) may still vary” [62].
However, Jaeger and Desimas do not teach that the variation is within a predefined tolerance window.
Korifi discloses a comparative study on alignment methods for chromatographic data (title). Discussing peak matching algorithms, Korifi recites “For each reference peak, the algorithm is looking for the sample peak, which most closely matches it in a user-defined window width” (pg. 8, sec. 3.5).
It would have been prima facie obvious to have aligned the peak patterns of the sample of interest and the calibration sample of Jaegar by using the peak matching algorithm of Korifi that uses a user-defined window. The motivation for doing so is taught by Korifi who states that alignment is necessary (abstract) and peak matching using window sizes has the advantage of being easy to understand (pg. 14, Table 5, row “Peak matching”). There would have been a reasonable expectation of success because Jaeger uses chromatography data [15] and so does the peak alignment method of Korifi (abstract) (Table 5).
programmatically identifying the sample of interest comprises subtracting or dividing a first time-series measurement of the control sample from a second time-series measurement of the test sample.
Jaeger identifies peaks corresponding to compounds of interest [2][4][12]. However, Jaeger, Desimas, and Korifi do not subtract a measurement of a control sample from a measurement of a test sample.
Wang discloses background subtraction for identifying components of interest in complex samples (abstract). Upon detection of an ion in a defined section of a control sample, the ion is background subtracted in the corresponding section of a test sample (col. 9, line 61 – col. 10, line 14).
It would have been prima facie obvious to have performed background subtraction as taught by Wang in Jaeger by subtracting a calibration sample measurement from a sample of interest measurement. Wang teaches motivation when reciting “precisely and thoroughly background-subtracted data would allow for the detection of components of interest in complex samples” (col. 3, lines 48-51). There would have been a reasonable expectation of success because Wang and Jaeger are directed to analyzing chromatographic data as well as electrophoresis data (Wang at claim 19) (Jaeger at claim 9).
Claims 6, 13 and 20 are rejected under 35 USC 103 for being unpatentable over Jaeger (US 2007/0112534 A1) in view of Desimas et al. (“Desimas”; WO 2017/197408 A1), as applied above to claims 1, 8 and 15, and in further view of Norton (WO 2003/095978 A2).
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
The limitations of claims 1, 8 and 15 have been taught in the rejection above by Jaeger and Desimas.
Claims 6, 13 and 20:
computing a distance between the time-series measurement of the control sample and the time-series measurement of the test sample, and
Jaeger teaches peak patterns of the sample of interest and the calibration sample (abstract).
However, Jaeger and Desimas do not compute distances between data of control and test samples.
Norton discloses a dynamic time warping (DTW) method for time-aligning chromatography-mass spectrometry data sets (claim 1) [60]. Norton teaches “the DTW method considers a set of possible time point mappings and identifies the mapping that minimizes an accumulated distance function between the reference and test data sets” [28]. After minimizing the distance, the data sets are aligned (claim 1 step b).
selecting the control sample from among a plurality of control samples, the control sample selected as a match with the test sample based on identifying that the control sample has the smallest computed distance from the test sample from among to the plurality of control samples.
Jaeger teaches various calibration samples labeled as L1 and L2 in Figures 4-7. However, Jaegar and Desimas do select a control sample based on identifying the control sample as having a smallest computed distance from a test sample.
Norton analyzes various mass chromatograms for each of test and references datasets and detects an optimal path that minimizes the accumulated distance function between the test and reference data sets [30]. Once the optimal route is detected the reference and test data can be aligned [33].
It would have been prima facie obvious to have used the DTW method of Norton in Jaeger by using a calibration sample that minimizes a distance between corresponding peaks in the sample of interest and the calibration sample. Norton teaches motivation by reciting that DTW resolves the issue of nonlinear variability of chromatographic retention times [4-5]. There would have been a reasonable expectation of success because Norton and Jaeger use chromatogram data.
Claims 7 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Tautenhahn et al. (“Tautenhahn”; US 2017/0338089 A1) in view of MaSC (“Data Submission”; published online 2015).
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
The limitations of claims 1 and 8 have been taught by Tautenhahn in section Claim Rejections - 35 USC § 102.
Claims 7 and 14:
wherein the output comprises a table of spectral peaks,
Tautenhahn generates spectral peaks from spectrometry data (abstract) [25], which can be stored in a file [26] [41]. However, Tautenhahn does not teach that the file is a table.
MaSC discloses a mass spectral database where a user can submit an ASCII text file containing x,y values where x corresponds to mass and y corresponds to the intensity at that mass (pg. 1, sec. Mass Spectral Data Extraction). The file can be in JCAMP-DX format, which is also a table (pg. 2, para. 1) (pg. 2, sec. General Notes on JCAMP-DX files).
It would have been prima facie obvious to have modified the file containing spectral peaks of Tautenhahn to be an ASCII text file or in JCAMP-DX format because MaSC states that these formats are advantageous because they can be imported and exported by a number of software programs (pg. 2, para. 1). There would have been a reasonable expectation of success because Tautenhahn uses mass spectrometry data and MaSC teaches a format for mass spectrometry data.
and further storing instructions for identifying a database of experimental results and automatically submitting the output to the database.
Tautenhahn teaches loading reference features from the database (identify a database of experimental results) (Figure 4, ref. chara. 406). Analyzed initial and additional datasets can be automatically uploaded and stored to the database [27] [48] (claim 1). Instructions for embodiments are stored on memory and executed by a processor [50].
Conclusion
No claims are allowed.
Notable, but not relied upon, prior art includes: Noda (US 2014/0129169 A1), Sadygov (US 2008/0046447 A1), Labreche (US 10,539,541 B2), Karabiber (Journal of bioinformatics and computational biology 11, no. 05 (2013): 1350011), and Vu et al. (Metabolites 3, no. 2 (2013): 259-276).
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685