Biological data structure having multi-lateral, multi-scalar, and multi-dimensional relationships between molecular features and other data

Abstract

A computer system maintains a biological data structure having molecular feature data. The system receives data elements indicating biological molecular features and knowledge elements that represent biological concepts. The system individually associates unique identifiers with the elements. For individual elements, the system maintains an internal element set of the other unique identifiers for the other elements that are directly associated with that one individual element. For the individual elements, the system maintains an external element set of the other unique identifiers for the other elements that have that one individual element in their own internal element sets. Although not required, the computer system may process a query indicating a search scope and a molecular feature for an individual biological entity, and responsively process the molecular feature and the elements based on the search scope to induce a knowledge sub-graph for the individual biological entity.

What is claimed is: 
     
         1 . A method of operating a computer system to maintain a biological data structure having molecular feature data, the method comprising:
 receiving data elements indicating biological molecular features and receiving knowledge elements that represent biological concepts;   individually associating unique identifiers with the elements;   for individual ones of the elements, maintaining an internal element set of the other unique identifiers for the other elements that are directly associated with that one individual element; and   for the individual ones of the elements, maintaining an external element set of the other unique identifiers for the other elements that have that one individual element in their own internal element sets.   
     
     
         2 . The method of  claim 1  wherein:
 the data elements indicating the biological molecular features indicate at least one of: genes, gene variants, gene expression data, and gene states; and further comprising 
 receiving additional data elements indicating at least one of: drugs, drug states, diseases, and disease states. 
 
     
     
         3 . The method of  claim 1  wherein the biological concepts comprise at least one of: disease signatures, disease classifications, drug signatures, drug classifications, signaling pathways, and nucleic acid repairs. 
     
     
         4 . The method of  claim 1  further comprising:
 receiving data attributes indicating values; 
 individually associating attribute identifiers with the attributes; 
 for individual ones of the attributes, maintaining an element set of the unique identifiers for the elements that are directly associated with that one individual attribute; and 
 for the individual ones of the elements, maintaining an attribute set of the attribute identifiers for the attributes that are directly associated with that one individual element. 
 
     
     
         5 . The method of  claim 1  wherein the data attributes comprise at least one of: age, geographic location, ethnicity, and gender. 
     
     
         6 . The method of  claim 1  further comprising:
 receiving data functions representing data processing instructions; 
 individually associating function identifiers with the functions; 
 for individual ones of the functions, maintaining an element set of the unique identifiers for the elements that are directly associated with that one individual function; 
 for the individual ones of the elements, maintaining a function set of the function identifiers for the functions that are directly associated with that one individual element. 
 
     
     
         7 . The method of  claim 1  wherein the data functions comprise at least one of: event handlers, message triggers, and counters. 
     
     
         8 . The method of  claim 1  further comprising:
 receiving a data query indicating the molecular feature data for an individual biological entity and a search scope indicator; 
 processing the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; 
 if the search scope indicator comprises an internal and external scope, then generating a knowledge sub-graph for the individual biological entity based on both the internal element sets and the external element sets of the identified data elements having the corresponding biological molecular features; 
 if the search scope indicator comprises an internal scope, then generating the knowledge sub-graph for the individual biological entity based on the internal element sets but not the external element sets of the identified data elements having the corresponding biological molecular features; and 
 if the search scope indicator comprises an external scope, then generating the knowledge sub-graph for the individual biological entity based on the external element sets but not the internal element sets of the identified data elements having the corresponding biological molecular features. 
 
     
     
         9 . The method of  claim 1  further comprising:
 receiving a data query indicating the molecular feature data for an individual biological entity and a search scope indicator; 
 processing the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; 
 if the search scope indicator comprises a second order scope, then generating a knowledge sub-graph for the individual biological entity based on the first order element sets of the identified data elements having the corresponding biological molecular features and also based on the second order element sets of the other data elements indicated in the first order element sets of the identified data elements having the corresponding biological molecular features. 
 
     
     
         10 . The method of  claim 1  further comprising:
 receiving a data query indicating the molecular feature data for an individual biological entity and a search scope indicator that indicates a number of orders and an external/internal search indicator for each of the orders; 
 processing the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; 
 generating a knowledge sub-graph for the individual biological entity based the number of orders, the external/internal search indicator for each of the orders, and the data elements having corresponding biological molecular features. 
 
     
     
         11 . A computer apparatus to operate a computer system to maintain a biological data structure, the computer apparatus comprising:
 at least one non-transitory computer-readable media having computer-useable instructions embodied thereon;   the computer-useable instructions configured to direct the computer system, when executed by the computer system, to receive data elements indicating biological molecular features and receive knowledge elements that represent biological concepts, to individually associate unique identifiers with the elements, to maintain, for individual ones of the elements, an internal element set of the other unique identifiers for the other elements that are directly associated with that one individual element, and to maintain, for the individual ones of the elements, an external element set of the other unique identifiers for the other elements that have that one individual element in their own internal element sets.   
     
     
         12 . The computer apparatus of  claim 11  wherein the data elements indicating the biological molecular features indicate at least one of: genes, gene variants, gene expression data, and gene states, and wherein the computer-useable instructions are configured to direct the computer system to receive additional data elements indicating at least one of: drugs, drug states, diseases, and disease states. 
     
     
         13 . The computer apparatus of  claim 11  wherein the biological concepts comprise at least one of:
 disease signatures, disease classifications, drug signatures, drug classifications, signaling pathways, and nucleic acid repairs. 
 
     
     
         14 . The computer apparatus of  claim 11  wherein the computer-useable instructions are configured to direct the computer system to:
 receive data attributes indicating values; 
 individually associate attribute identifiers with the attributes; 
 for individual ones of the attributes, maintain an element set of the unique identifiers for the elements that are directly associated with that one individual attribute; and 
 for the individual ones of the elements, maintain an attribute set of the attribute identifiers for the attributes that are directly associated with that one individual element. 
 
     
     
         15 . The computer apparatus of  claim 11  wherein the data attributes comprise at least one of: age, geographic location, ethnicity, and gender. 
     
     
         16 . The computer apparatus of  claim 11  wherein the computer-useable instructions configured to direct the computer system to:
 receive data functions representing data processing instructions; 
 individually associate function identifiers with the functions; 
 for individual ones of the functions, maintain an element set of the unique identifiers for the elements that are directly associated with that one individual function; 
 for the individual ones of the elements, maintain a function set of the function identifiers for the functions that are directly associated with that one individual element. 
 
     
     
         17 . The computer apparatus of  claim 11  wherein the data functions comprise at least one of:
 event handlers, message triggers, and counters. 
 
     
     
         18 . The computer apparatus of  claim 11  wherein the computer-useable instructions are configured to direct the computer system to:
 receive a data query indicating the molecular feature data for an individual biological entity and a search scope indicator; 
 process the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; 
 if the search scope indicator comprises an internal and external scope, then generate a knowledge sub-graph for the individual biological entity based on both the internal element sets and the external element sets of the identified data elements having the corresponding biological molecular features; 
 if the search scope indicator comprises an external scope, then generating the knowledge sub-graph for the individual biological entity based on the external element sets but not the internal element sets of the identified data elements having the corresponding biological molecular features; and 
 if the search scope indicator comprises an internal scope, then generating the knowledge sub-graph for the individual biological entity based on the internal element sets but not the external element sets of the identified data elements having the corresponding biological molecular features. 
 
     
     
         19 . The computer apparatus of  claim 11  wherein the computer-useable instructions configured to direct the computer system to:
 receive a data query indicating the molecular feature data for an individual biological entity and a search scope indicator; 
 process the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; 
 if the search scope indicator comprises a second order scope, then generate a knowledge sub-graph for the individual biological entity based on the first order element sets of the identified data elements having the corresponding biological molecular features and also based on the second order element sets of the other data elements indicated in the first order element sets of the identified data elements having the corresponding biological molecular features. 
 
     
     
         20 . The computer apparatus of  claim 11  wherein the computer-useable instructions configured to direct the computer system to:
 receive a data query indicating the molecular feature data for an individual biological entity and a search scope indicator that indicates a number of orders and an external/internal search indicator for each of the orders; 
 process the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; 
 generate a knowledge sub-graph for the individual biological entity based the number of orders, the external/internal search indicator for each of the orders, and the data elements having the corresponding biological molecular features.