Drug discovery methods
First Claim
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1. A method for identifying a drug discovery target which comprises:
- (a) providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts;
(b) generating one or more subsets of genomics information from the database wherein at least one of the one or more subsets is a disease-related pathway; and
(c) identifying the biological interactions and actor concepts in the disease-related pathway whereby each of the actor concepts involved in each such reaction is a drug discovery target.
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Abstract
Methods for identifying disease-related pathways that can be used to identify drug discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes.
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Citations
62 Claims
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1. A method for identifying a drug discovery target which comprises:
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(a) providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts;
(b) generating one or more subsets of genomics information from the database wherein at least one of the one or more subsets is a disease-related pathway; and
(c) identifying the biological interactions and actor concepts in the disease-related pathway whereby each of the actor concepts involved in each such reaction is a drug discovery target. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 60)
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33. A method for evaluating user-supplied genomics data using a structured database that permits the computation of complex relationships among genes and/or gene products contained in the database, comprising:
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(a) defining a profile model based on one or more profile definition criterion;
(b) building a collection of profiles according to the profile model;
(c) identifying one or more profiles that overlap at least a portion of the user-supplied genomics data and determining, for each such overlapped profile, whether the overlap is statistically significant; and
(d) analyzing one or more statistically significant profiles together with the user-supplied genomics data including inspecting database-asserted biological interactions embodied in the one or more statistically significant profiles. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53)
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54. A method for identifying a new use for a known therapy comprising the steps of providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts;
- generating subsets of genomics information from the database wherein the subsets include disease-related pathways comprising a known therapy target;
selecting at least one of such disease-related pathways wherein the known therapy target is also comprised within a second disease-related pathway; and
identifying a treatment of the second disease as a new use for the known therapy.
- generating subsets of genomics information from the database wherein the subsets include disease-related pathways comprising a known therapy target;
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55. A method for prioritizing candidate development compounds for further development that comprises the steps of providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts;
- generating one or more subsets of genomics information from the database; and
querying the one or more subsets to identify all pathways associated with the target of each candidate development compound and assigning higher priority to development compounds on the basis of whether or not they are likely to result in an undesirable effect based on their involvement in other biological pathways.
- generating one or more subsets of genomics information from the database; and
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56. A method for identifying disease-related pathways wherein the disease is a side effect of drug therapy that comprises the steps of providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts;
- identifying a disease-related pathway affected by a drug or drug discovery target;
generating one or more subsets of genomics information from the database relating to the disease-related pathway; and
querying the one or more subsets to identify alternative pathways that are also affected by the drug or the drug discovery target and that result in the undesirable phenotype.
- identifying a disease-related pathway affected by a drug or drug discovery target;
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57. A method for identifying or validating a genotypic marker for a disease state that comprises providing a means for accessing genomics information in a database wherein said means permits computational analysis of biological relationships among the stored concepts;
- generating one or more subsets of genomics information from the database; and
querying the one or more subsets to identify a genotypic marker that is associated with the disease state.
- generating one or more subsets of genomics information from the database; and
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58. A method for identifying a drug discovery target which comprises querying one or more subsets of genomics information generated from a database to identify a disease-related pathway, the biological interactions and actor concepts in the disease-related pathway, whereby at least one of the actor concepts involved in each such reaction is a drug discovery target and wherein the one or more subsets reside on a computer system comprising a means for accessing genomics information in the database and a means for computational analysis of biological relationships among the concepts contained within the subsets.
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59. A method of conducting business that comprises receiving compensation from a customer in return for identifying to the customer a drug discovery target discovered by querying a computer system to identify a disease-related pathway and identifying the biological interactions and actor concepts in the disease-related pathway whereby each of the actor concepts involved in each such reaction is a drug discovery target and wherein the computer system comprises a means for accessing genomics information in a database, generating subsets of genomics information from the database, and a means for computational analysis of biological relationships among the concepts represented in the subsets.
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61. A method of drug discovery that comprises:
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(a) identifying a drug discovery target discovered by querying a computer system to identify a disease-related pathway and identifying the biological interactions and actor concepts in the disease-related pathway whereby one or more of the actor concepts involved in each such reaction is a drug discovery target and wherein the computer system comprises a means for computing subsets of genomics information specific to one or more target diseases using a database of genomics information, and a means for computational analysis of biological relationships among the concepts included within the subsets; and
(b) screening compounds against a drug discovery target to identify drug candidates. - View Dependent Claims (62)
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Specification