Methods and systems for analyzing complex biological systems
First Claim
1. A system for creating a coherent data set for modeling biological systems, comprising:
- a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing data comprising metabolite data in said computer tracking system, wherein said data comprising metabolite data are linked to said unique identifier;
c) means for converting said linked data to a numeric format; and
d) means for converting said numeric format data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system.
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Accused Products
Abstract
The present invention provides methods and systems for organizing complex and disparate data. More specifically, the present invention provides methods and systems for organizing complex and disparate data into coherent data sets. Coherent data sets resulting from the methods and systems of the present invention serve as models for biological systems. Methods and systems for integrating data and creating coherent data sets are useful for numerous biological applications, such as, for example, determining gene function, identifying and validating drug and pesticide targets, identifying and validating drug and pesticide candidate compounds, profiling drug and pesticide compounds, producing a compilation of health or wellness profiles, determining compound site(s) of action, identifying unknown samples, and numerous other applications in the agricultural, pharmaceutical, forensic, and biotechnology industries.
83 Citations
296 Claims
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1. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing data comprising metabolite data in said computer tracking system, wherein said data comprising metabolite data are linked to said unique identifier;
c) means for converting said linked data to a numeric format; and
d) means for converting said numeric format data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 114, 118)
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18. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing data comprising metabolite data in said computer tracking system, wherein said data comprising metabolite data are linked to said unique identifier;
c) means for converting said linked data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution;
e) means for converting said Gaussian distribution data to a common unit system; and
f) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36)
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37. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing data comprising metabolite data in said computer tracking system, wherein said data comprising metabolite data are linked to said unique identifier;
c) means for converting said linked data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution; and
e) means for converting said Gaussian distribution data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54)
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55. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing data comprising metabolite data in said computer tracking system, wherein said data comprising metabolite data are linked to said unique identifier;
c) means for converting said linked data to a numeric format;
d) means for converting said numeric format data to a common unit system; and
e) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72)
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73. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and other data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format; and
d) means for converting said numeric format data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90)
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91. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and other data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution;
e) means for converting said Gaussian distribution data to a common unit system; and
f) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110)
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111. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and other data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format;
d) means for converting said numeric format data to a common unit system; and
e) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (112, 113, 115, 116, 117, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129)
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130. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and other data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution; and
e) means for converting said Gaussian distribution data to a common unit system wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (131, 132, 133, 134, 135, 136, 137, 138, 139, 143, 144, 145, 146, 147, 148)
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- 140. The system according to claim 140, wherein the biological sample is selected from the group consisting of human primate, non-human primate, canine, feline, equine, bovine, porcine, rabbit, rodent, liver tissue, liver spheroids, primary hepatocytes, liver cell lines, and HepG2 cells.
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149. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and at least two other types of data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format; and
d) means for converting said numeric format data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166)
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167. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and at least two other types of data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution;
e) means for converting said Gaussian distribution data to a common unit system; and
f) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186)
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187. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and at least two other types of data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format;
d) means for converting said numeric format data to a common unit system; and
e) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205)
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206. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a computer tracking system;
b) means for storing in said computer tracking system disparate data, wherein said disparate data comprise metabolite data and at least two other types of data, and said disparate data are linked to said unique identifier;
c) means for converting said linked disparate data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution; and
e) means for converting said Gaussian distribution data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224)
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225. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a laboratory information management system (LIMS);
b) means for storing data comprising RNA data, phenotype data, and metabolite data in said LIMS, wherein said data are linked to said unique identifier;
c) means for converting said linked data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution;
e) means for converting said Gaussian distribution data to a common unit system, wherein said common unit system is deviation from a baseline; and
f) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243)
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244. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a laboratory information management system (LIMS);
b) means for storing data comprising RNA data, phenotype data, and metabolite data in said LIMS, wherein said data are linked to said unique identifier;
c) means for converting said linked data to a numeric format; and
d) means for converting said numeric format data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260)
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261. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a laboratory information management system (LIMS);
b) means for storing data comprising RNA data, phenotype data, and metabolite data in said LIMS, wherein said data are linked to said unique identifier;
c) means for converting said linked data to a numeric format;
d) means for transforming said numeric format data into a Gaussian distribution; and
e) means for converting said Gaussian distribution data to a common unit system, wherein said common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278)
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279. A system for creating a coherent data set for modeling biological systems, comprising:
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a) means for entering a unique identifier of at least one biological sample into a laboratory information management system (LIMS);
b) means for storing data comprising RNA data, phenotype data, and metabolite data in said LIMS, wherein said data are linked to said unique identifier;
c) means for converting said linked data to a numeric format;
d) means for converting said numeric format data to a common unit system; and
e) means for reducing the dimensionality of said common unit system data, wherein said dimensionally reduced common unit system data are a coherent data set which serves as a model for a biological system. - View Dependent Claims (280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296)
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Specification