Visualization and manipulation of biomolecular relationships using graph operators
First Claim
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1. A computer-implemented method for performing an operation upon one or more graphs, wherein each graph represents a set of relationships between a set of biological molecules, wherein each graph comprises vertices representing the biological molecules and edges representing the relationships between the biological molecules, the method comprising performing one or more operations on the one or more graphs to produce one or more product graphs.
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Abstract
A system for analyzing and graphically visualizing biomolecular data, such as genomic data, is provided.
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Citations
63 Claims
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1. A computer-implemented method for performing an operation upon one or more graphs, wherein each graph represents a set of relationships between a set of biological molecules, wherein each graph comprises vertices representing the biological molecules and edges representing the relationships between the biological molecules, the method comprising
performing one or more operations on the one or more graphs to produce one or more product graphs.
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50. A computer-implemented method for performing an operation upon a graph, the graph representing relationships between biological molecules and having vertices representing the molecules and edges representing the relationships, the method comprising
identifying a subset of zero or more of the edges, identifying a subset of zero or more of the vertices, and performing a unary operation upon the identified subset of edges and vertices to produce a product graph.
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52. A computer-implemented method for representing relationships between biological molecules using one or more graphs each having vertices and edges, the method comprising
representing a set of biological molecules, wherein each molecule is represented by a vertex of the graph, and representing a set of relationships between the biological molecules, wherein each relationship is represented by an edge of the graph, wherein the edge connects two vertices, wherein the graph is produced by performing one or more operations on one or more input graphs to produce the one or more graphs.
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53. A computer program product for performing an operation upon one or more graphs, wherein each graph represents a set of relationships between a set of biological molecules, wherein each graph comprises vertices representing the biological molecules and edges representing the relationships between the biological molecules, the computer program product comprising a computer data medium on which is carried
a means for performing one or more operations on the one or more graphs to produce one or more product graphs.
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54. A computer program product for performing an operation upon a graph, the graph representing relationships between biological molecules and having vertices representing the molecules and edges representing the relationships, the computer program product comprising a computer data medium on which is carried
a means for identifying a subset of zero or more of the edges, a means for identifying a subset of zero or more of the vertices, and a means for performing a unary operation upon the identified subset of edges and vertices to produce a product graph.
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55. A computer program product for representing relationships between biological molecules using a graph having vertices and edges, the computer program product comprising a computer data medium on which is carried
a means for representing a set of biological molecules, wherein each molecule is represented by a vertex of the graph, and a means for representing a set of relationships between the biological molecules, wherein each relationship is represented by an edge of the graph, wherein the edge connects two vertices.
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56. A computer-implemented method for representing relationships between biological molecules using a graph having vertices and edges, the method comprising
representing a set of biological molecules, wherein each molecule is represented by a vertex of the graph, and representing a set of relationships between the biological molecules, wherein each relationship is represented by an edge of the graph, wherein the edge connects two vertices.
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57. A representation of relationships between biological molecules comprising one or more graphs each having vertices and edges, each graph comprising
a set of biological molecules, wherein each molecule is represented by a vertex of the graph, and a set of relationships between the biological molecules, wherein each relationship is represented by an edge of the graph, wherein the edge connects two vertices, wherein the graph is produced by performing one or more operations on one or more input graphs to produce the one or more graphs.
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60. A data structure comprising a representation of relationships between biological molecules, the representation comprising a graph having vertices and edges, the graph comprising
a set of biological molecules, wherein each molecule is represented by a vertex of the graph, and a set of relationships between the biological molecules, wherein each relationship is represented by an edge of the graph, wherein the edge connects two vertices.
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61. A computer-implemented method for performing an operation upon one or more graphs, wherein each graph represents a set of relationships between a set of biological molecules, wherein each graph comprises vertices representing the biological molecules and edges representing the relationships between the biological molecules, wherein the biological molecules, the relationships between the biological molecules, or both, are derived from different sources, the method comprising
performing one or more operations on the one or more graphs to produce one or more product graphs.
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62. A computer-implemented method for performing an operation upon one or more graphs, wherein each graph represents a set of relationships between a set of biological molecules, wherein each graph comprises vertices representing the biological molecules and edges representing the relationships between the biological molecules,
wherein at least two of the vertices represent different types of biological molecules, at least two edges represent different types of relationships between the biological molecules represented by the vertices connected by the edges, at least one edge represents a plurality of different types of relationships between the biological molecules represented by the vertices connected by the edge, at least one vertex represents a plurality of different types of biological molecules, or a combination thereof, the method comprising performing one or more operations on the one or more graphs to produce one or more product graphs.
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63. A computer-implemented method for performing an operation upon one or more graphs, wherein each graph represents a set of relationships between a set of biological molecules, wherein each graph comprises vertices representing the biological molecules and edges representing the relationships between the biological molecules, wherein the biological molecules, the relationships between the biological molecules, or both, are derived from heterogeneous molecular biological data, the method comprising
performing one or more operations on the one or more graphs to produce one or more product graphs.
Specification