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 .
Note about Prior art
The prior art does not teach or make obvious the SiteCRS compression in Fig. 6 [625]. As best as examiner can tell, Claim 8 seeks to claim a compression like siteCRS, see below.
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A problem with this siteCRS compression 625 is that the element 625 is never described or mentioned in the specification. This is true for elements 635 and 645 also – they are not described in the specification. Therefore, there is no art to teach this type of compression, but this type of compression is not clearly claimed and it may not be described in the specification.
The prior art of record does not teach or make obvious claim 13’s elements, “a step (410) of determining, by a computing system, a distribution of chemical reaction classes within the encoded dataset,
a step (300) of augmenting the dataset, wherein the augmenting comprises either (A) a step (121) of extracting, by a computing device, of a bond table for reagents and products from a computer memory, said encoding being performed as a function of said bond table or (B) a step of removing, from the first encoding resulting from the first step (110) of encoding, of at least one atom identifier from at least one reagent and/or product, each said atom being removed as a result of the step (115) of determination in the event said atom and the associated bonds are located in a product and/or reagent that remains unchanged from reagent the reaction stage to the product stage of the chemical reaction, for at least one chemical reaction class as a function of the determined distribution…”
With respect to claim 14, the prior art doesn’t teach or make obvious “a step (510) of operating, by a computing system, a recursive neural network architecture configured to use, as input, the dataset of chemical reaction graphs to classify the chemical reaction bond evolution as a function of the input and…”
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 1-3 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because applicant claims software per se. Software alone is not a statutory category.
Claims 1-8 and 10-18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea. The claims recite the mental concept of encoding chemical formulas, determining something about the formulas and encoding the determination without significantly more – Applicant’s “encoding” is a form of notation for machine readable chemical formulas/reaction graphs. This type of notation can be done be done mentally or with pen and paper. This judicial exception is not integrated into a practical application because the abstract idea is merely linked to the field of chemistry. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the computing device and display of results on a computer interface are generic computers and insignificant extra-solution activity, respectively.
Claim 9 is directed to a particular machine that carries out the reaction in a physical device – and produces the product from the reagents. This amounts to significantly more than the abstract idea.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claim 13 is 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. Applicant claims determining a “distribution of chemical reaction classes within the encoded dataset” but never describes how to make that determination. Further, the kind of distribution is never described in the application.
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.
Claims 8 and 10-18 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 8 recites “each said atom being removed as a result of the step (115) of determination in the event said atom and the associated bonds are located in a product and/or reagent that remains unchanged from reagent the reaction stage to the product stage of the chemical reaction.” The event is not previously introduced. The phrase “the step…of determination in the event said atom and the associated bonds” doesn’t make sense. The associated bonds were not previously introduced. The reaction stage was not previously introduced. The product stage was not previously introduced.
Claim 10 recites the limitation “encoded chemical reaction… obtained by the method (100) according to claim 4”. There is insufficient antecedent basis for this limitation in the claim. There are several encodings between the claims that claim 10 depends on – a first encoding and second encoding in claim 4.
Claim 11 recites the limitation “the encoding”. There is insufficient antecedent basis for this limitation in the claim. There are several encodings between the claims that claim 11 depends on: a first encoding and second encoding in claim 4; and an “encoded chemical reaction” in claim 10. claim 11 recites “at least one string of at least one character…” Strings are made up of at least two characters. This claiming makes it unclear whether applicant intends to shift a string or a character. And the element doesn’t make sense because Applicant’s “change of bond” associations are always at least two characters with two neutral tags in the specification, e.g. “{-=}” Spec. 143.
Claim 12 recites the limitation "the format". There is insufficient antecedent basis for this limitation in the claim. This claim would not be fixed by calling it a format of figure 9.
Claim 13 recites “said encoding”. There is insufficient antecedent basis for this limitation. Applicant claims “each said atom being removed as a result of the step (115) of determination in the event…” This clause doesn’t make sense.
Claim 14 recites “the compressed encoding”, this lack antecedent basis. The “chemical reaction bond evolution” lacks antecedent basis. The “input” lacks antecedent basis.
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.
Claim 12 is 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. Claim 12 depends on claims separately dependent claims 9 and 11 at the same time. Dependent claims “shall contain a reference to a claim previously set forth…” 35 U.S.C. 112(d). 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.
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.
Claims 1-7, 10 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Condensed Graph of Reaction: considering a chemical reaction as one single pseudo molecule by Hoonakker et al, Atom-to-atom mapping: a benchmarking study of popular mapping algorithms and consensus strategies by Lin et al and US20120303563A1 to Russak.
Claims 9 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Condensed Graph of Reaction: considering a chemical reaction as one single pseudo molecule by Hoonakker et al, Atom-to-atom mapping: a benchmarking study of popular mapping algorithms and consensus strategies by Lin et al, US20120303563A1 to Russak and A robotic platform for flow synthesis of organic compounds informed by AI planning by Coley et al.
Hoonakker teaches claims 1 and 4. Chemical reaction encoding software for one-step, multi-step and equilibrium reactions, characterised in that it executes instructions corresponding to the following steps: (Hoonakker sec. 2 “A Condensed Graph of Reaction [8] represents a superposition of reactants and products graphs. A CGR is a complete connected and non oriented graph in which each node represents an atom and each edge a bond…. An editor of CGR has been added to our software environment specialised in chemical data mining: ISIDA (In SIlico Design and Analysis)…”)
a step (105) of receiving, upon a computer interface, a chemical reaction graph comprising at least one chemical reaction reagent and at least one chemical reaction product, (Hoonakker fig. 1 below)
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a first step (110) of encoding, by a computing device, said chemical reaction graph describing the structure of at least one said reagent and said product, (Hoonakker fig. 1b below)
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a step (115) of determination, by a computing device, of changing bonds within the encoding representative of the chemical structures of said at least one reaction reagent and said product, (Hoonakker p. 2 Sec. 2 “CGR uses both conventional bonds (single, double, aromatic, etc.) which are not transformed in the course of reaction, and dynamical bonds corresponding to those created, broken or modified during the reaction (cf. figure 1).” Hoonakker p. 3 sec. 2 “Then the connection table of reactants and products are examined to find the reactivity flag and write the dynamical bond in the CGR. Figure 1.(b) shows the CGR corresponding to the reaction above. Let us emphasize that the bond types assigned between the carbon 6 and the brome 13 denotes a broken single bond and the bond type between carbons 6 and 12 denotes the creation of a single bond.” The bonds are determined, e.g. “dynamical bonds” and “broken single bond”.)
a second step (120) of encoding, by a computing device, in a single string of characters, for at least one changing bond determined, at least one character representative of an atom subject to the change of bond, at least one character representative of the type of changing bond determined and at least one character representative of an atom resulting from the change of bond, in which a changing bond is encoded (Hoonakker fig. 2 below shows the string of characters with letter representing atoms in the reagent and the second character, e.g. “-“, representing the bond type.)
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a step (125) of providing, (Hoonakker fig. 2 shows the provided strings.)
Hoonakker doesn’t teach the two-character reagent-bond product-bond notation.
However, Lin teaches a set of two characters representative of the changing bond determined, the first character being representative of the reagent bond and the second character being representative of the product bond. (Lin fig. 3 “(a) and then transformed to a CGR (b) where the dynamic bond “2>1” means the reduction of a double bond between two carbon atoms 8 and 9 to a single bond, and “0>1” means the formation of a single bond between two carbon atoms 8 and 17.” The 2 and the 1 are the reagent bond and product bond after reaction, respectively. Hoonakker’s 2>1 and 0>1 is the same as Applicant’s “=-“ and “!-” in Spec. 146.)
Hoonakker, Lin and the claims are all directed to chemical notation. It would have been obvious to a person having ordinary skill in the art, at the time of filing, to select which ever mapping strategy (encoding/notation style) “according to the minimal CD following the principle ‘lower the CD – less transformations are in the reaction – better the mapping’.” Lin pg. 7. There are many known encoding strategies in the prior art and they are selected to minimize Chemical Distance (CD), according to Lin.
Hoonakker doesn’t have a computer display.
However, Russak teaches displaying messages to a user upon a computer interface. (Russak para 97-98 “The display may be used to convey messages to a user of the portable device 1000.
[0098] For example, upon successful classification of the new assay, the result of the classification of the new assay may be conveyed to the user of the portable device 1000, say by turning on one of the LED lights (say a green light), or through a message presented on the small LCD screen (say a `Positive Assay` message).”)
Russak, Hoonakker and the claims are all directed to chemical reaction graphs. It would have been obvious to a person having ordinary skill in the art, at the time of filing, to display the reaction graphs in order to “to convey the classification's result to a user.” Russak para 256.
Hoonakker teaches claim 2. Software according to claim 1, in which the second (120) step of encoding is configured to embed the two characters representative of the changing bonds determined in between two neutral tag characters representative of the presence of an encoding of said changing bonds. (Lin fig. 3 “where the dynamic bond “2>1” means the reduction of a double bond between two carbon atoms 8 and 9 to a single bond, and “0>1” means the formation of a single bond between two carbon atoms 8 and 17.” The quotation marks are neutral characters.
Hoonakker teaches claims 3 and 5. Software according to claim 1, in which multistep reactions, represented by a succession of change of bonds between two atoms, are encoded by a succession of single characters, (Hoonakker fig. 2 below shows strings with dynamic bonds, like claimed, above. Hoonakker p. 3 sec. 2 “Moreover, some flags are added to describe the bonds that change, as described in the ”CTFile format” document [10] from Elsevier MDL…”)
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Hoonakker fig. 2.
Hoonakker doesn’t teach successive states encoded in the string representing an order of changes of the bonds.
However, Lin teaches each single character being representative of the successive state of a bond between said two atoms, the order of the characters being representative of the order of changes of bonds between said two atoms. (Lin fig. 3 “where the dynamic bond “2>1” means the reduction of a double bond between two carbon atoms 8 and 9 to a single bond, and “0>1” means the formation of a single bond between two carbon atoms 8 and 17.” The > represents presence of an encoding of a changing bond.)
Hoonakker teaches claim 6. Method (100) according to claim 4, in which the first step (110) of encoding is configured to encode the chemical reaction graph into a line notation, the method further comprising, prior to the second step (120) of encoding, a step (130) of augmenting the line notation encoding. (Hoonakker fig. 2 and p. 3 “Some example of fragments in their linear notation are shown in figure 2. The first example (Cl/−S-C*C*C*C) represent the shortest path between the two marked atoms (length = 6).” Hoonakker p. 4 “This kind of fragmentation produces a large number of descriptors some of which are dependent, eg. Cl/−S and Cl/−S-C on figure 2. Consequently the correlated descriptors are eliminated,…”)
Hoonakker teaches claim 7. Method (100) according to claim 4, in which the second step (120) of encoding comprises a step (121) of extracting, by a computing device, of a bond table for reagents and products from a computer memory, said encoding being performed as a function of said bond table. (Lin intro p. 2 “the reactions are provided via canonical SMILES…”)
Hoonakker teaches claim 9. Method (100) according to claim 4,
Hoonakker doesn’t teach synthesizing the products.
However, Coley teaches which comprises a step (135) of obtaining the products of the encoded chemical reaction by performing said chemical reaction in a physical device. (Coley fig. 1 below and abstract on 1 “Synthetic routes are proposed through generalization of millions of published chemical reactions and validated in silico to maximize their likelihood of success. Additional implementation details are determined by expert chemists and recorded in reusable recipe files, which are executed by a modular continuous-flow platform that is automatically reconfigured by a robotic arm to set up the required unit operations and carry out the reaction.”)
Coley, Hoonakker and the claims all do in-silico design of reactions. It would have been obvious to a person having ordinary skill in the art, at the time of filing, to use Coley because “The ability to synthesize organic compounds on demand has the potential to transform molecular discovery tasks.” Coley left column page 1.
Hoonakker and Lin teach claim 10. Encoded chemical reaction comprising a string of characters (205, 210), characterised in that it is obtained by the method (100) according to claim 4. (Hoonakker fig. 2 string notation combined with Lin’s bond change notation.)
Hoonakker and Lin teach claim 11. Chemical reaction dataset augmentation method (300), characterised in that it comprises:
a step (305) of receiving, upon a computer interface, a string of characters according to the encoding of claim 10, (Hoonaker Fig. 2 below and bond change notation in Lin Fig. 3.)
a step (310) of reordering, by a computing system, the string of characters in order to shift at least one character representative of an atom and at least one string of at least one character representative of a change of bond associated to the corresponding atom and (Hoonaker fig. 2 shows shifting the atoms and change of bonds, see below. The change of bonds are the dynamic bons shown below and in sec. Hoonakker sec. 2 p. 3 “Then the connection table of reactants and products are examined to find the reactivity flag and write the dynamical bond in the CGR.”)
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Hoonakker fig. 2.
a step (320) of outputting(Hoonakker fig. 2 above.)
Hoonakker doesn’t have a computer display.
However, Russak teaches displaying messages to a user upon a computer interface. (Russak para 97-98 “The display may be used to convey messages to a user of the portable device 1000.
[0098] For example, upon successful classification of the new assay, the result of the classification of the new assay may be conveyed to the user of the portable device 1000, say by turning on one of the LED lights (say a green light), or through a message presented on the small LCD screen (say a `Positive Assay` message).”)
Hoonaker teaches claim 12. Augmentation method (300) according to claim 11, which further comprises a step (315) of associating, by a computing system, at least two string of characters according to the format of claim 9, each said string of characters being representative of the same chemical reaction graph. (There is no format in claim 9, Examiner interprets this claim to mean at least two line notations like in Hoonakker fig. 2.)
Conclusion
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/AUSTIN HICKS/ Primary Examiner, Art Unit 2142