Compiling Co-associating Bioattributes Using Expanded Bioattribute Profiles

Abstract

A bioinformatics method, software, database and system for compiling attribute combinations that co-associate with a query attribute (i.e., an attribute of interest) are presented in which expanded attribute profiles associated with a group of query-attribute-positive individuals and expanded attribute profiles associated with a group of query-attribute-negative individuals are accessed, and combinations of attributes having a higher frequency of occurrence in the set of expanded attribute profiles associated with the group of query-attribute-positive individuals are identified and stored to generate a compilation of attribute combinations that co-associate with the query attribute.

1 . A bioinformatics method for generating a compilation containing combinations of attributes that co-associate with a query attribute, comprising:
 a) accessing, within a computer memory, at least one numerical primary attribute associated with individuals from a database containing attribute profiles of individuals;   b) creating at least one expanded attribute associated with the individuals by applying a rule to the at least one numerical primary attribute, wherein the at least one expanded attribute includes at least one of a genetic, epigenetic, pangenetic, physical, behavioral, situational, or historical attribute, and wherein the expanded attribute has a lower resolution than the at least one numerical primary attribute;   c) receiving a query attribute which identifies a group of query-positive-positive individuals and a group of query-attribute-negative individuals;   d) creating a set of query-attribute-positive attribute profiles containing the at least one expanded attribute from the set of query-attribute-positive individuals and a set of query-attribute-negative attribute profiles containing the at least one expanded attribute from the set of query-attribute-negative profiles;   e) determining a set of candidate attributes by selecting attributes from the set of query-attribute-positive profiles that do not occur in a portion of the set of query-attribute-negative profiles, wherein the candidate attributes contain at least one expanded attribute profile;   f) computing the frequencies of occurrence of combinations of the candidate attributes in the set of query-attribute-positive profiles and in the set of query-attribute-negative profiles; and   g) storing, within the computer memory, one or more candidate attribute combinations having higher frequencies of occurrence in the set of query-attribute-positive profiles than in the set of query-attribute-negative profiles to generate a compilation of attribute combinations that co-occur with the query attribute.   
     
     
         2 . The bioinformatics method of  claim 1 , wherein the rule applied to create the expanded attribute is the assignment of the numerical primary attribute into a set of discrete bins. 
     
     
         3 . The bioinformatics method of  claim 1 , wherein the rule includes a determination of the histogram of the assigned numerical primary attribute into the set of discrete bins. 
     
     
         4 . The bioinformatics method of  claim 1 , wherein the rule applied to create the expanded attribute is the conversion of a continuous valued attribute into a discrete valued attribute. 
     
     
         5 . The bioinformatics method of  claim 1 , wherein the rule applied to create the expanded attribute is a heuristic rule. 
     
     
         6 . The bioinformatics method of  claim 1 , wherein the rule applied to create the expanded attribute contains a thresholding operation. 
     
     
         7 . The bioinformatics method of  claim 1 , further comprising storing the frequencies of occurrence of the attribute combinations in the compilation. 
     
     
         8 . The bioinformatics method of  claim 1 , further comprising:
 h) storing statistical results, generated based on the frequencies of occurrence, which indicate the strength of association of each of the attribute combinations in the compilation with the query attribute.   
     
     
         9 . The bioinformatics method of  claim 1 , wherein the identity of one or more of the individuals is masked or anonymized. 
     
     
         10 . The bioinformatics method of  claim 1 , wherein at least a portion of the compilation is transmitted as output to at least one destination selected from the group consisting of a user, computer readable memory, a computer readable medium, a computer processor, a computer network, a printout device, a visual display, a digital electronic receiver, and a wireless receiver. 
     
     
         11 . A program storage device readable by a machine and containing a set of instructions which, when read by the machine, causes execution of a bioinformatics method for generating a compilation containing combinations of attributes that co-associate with a query attribute, comprising:
 a) accessing, within a computer memory, at least one numerical primary attribute associated with individuals from a database containing attribute profiles of individuals;   b) creating at least one expanded attribute associated with the individuals by applying a rule to the at least one numerical primary attribute, wherein the at least one expanded attribute includes at least one of a genetic, epigenetic, pangenetic, physical, behavioral, situational, or historical attribute, and wherein the expanded attribute has a lower resolution than the at least one numerical primary attribute;   c) receiving a query attribute which identifies a group of query-positive-positive individuals and a group of query-attribute-negative individuals;   d) creating a set of query-attribute-positive attribute profiles containing the at least one expanded attribute from the set of query-attribute-positive individuals and a set of query-attribute-negative attribute profiles containing the at least one expanded attribute from the set of query-attribute-negative profiles;   e) determining a set of candidate attributes by selecting attributes from the set of query-attribute-positive profiles that do not occur in a portion of the set of query-attribute-negative profiles, wherein the candidate attributes contain at least one expanded attribute profile;   f) computing the frequencies of occurrence of combinations of the candidate attributes in the set of query-attribute-positive profiles and in the set of query-attribute-negative profiles; and   g) storing, within the computer memory, one or more candidate attribute combinations having higher frequencies of occurrence in the set of query-attribute-positive profiles than in the set of query-attribute-negative profiles to generate a compilation of attribute combinations that co-occur with the query attribute.   
     
     
         12 . The bioinformatics method of  claim 11 , wherein the rule applied to create the expanded attribute is the assignment of the numerical primary attribute into a set of discrete bins. 
     
     
         13 . The bioinformatics method of  claim 11 , wherein the rule includes a determination of the histogram of the assigned numerical primary attribute into the set of discrete bins. 
     
     
         14 . The bioinformatics method of  claim 11 , wherein the rule applied to create the expanded attribute is the conversion of a continuous valued attribute into a discrete valued attribute. 
     
     
         15 . The bioinformatics method of  claim 11 , wherein the rule applied to create the expanded attribute is a heuristic rule. 
     
     
         16 . The bioinformatics method of  claim 11 , wherein the rule applied to create the expanded attribute contains a thresholding operation. 
     
     
         17 . The bioinformatics method of  claim 11 , further comprising storing the frequencies of occurrence of the attribute combinations in the compilation. 
     
     
         18 . The bioinformatics method of  claim 11 , further comprising:
 h) storing statistical results, generated based on the frequencies of occurrence, which indicate the strength of association of each of the attribute combinations in the compilation with the query attribute.   
     
     
         19 . The bioinformatics method of  claim 11 , wherein the identity of one or more of the individuals is masked or anonymized. 
     
     
         20 . The bioinformatics method of  claim 11 , wherein at least a portion of the compilation is transmitted as output to at least one destination selected from the group consisting of a user, computer readable memory, a computer readable medium, a computer processor, a computer network, a printout device, a visual display, a digital electronic receiver, and a wireless receiver. 
     
     
         21 . A bioinformatics database system for generating a compilation containing attribute combinations that co-associate with a query attribute comprising:
 a) a first data structure containing attribute profiles for individuals, wherein the attribute profiles contain at least one numerical primary attribute associated with the individuals, and wherein the primary attribute;   b) a processor for:
 i. accessing the first data structure; 
 ii. expanding the at least one numerical primary attribute wherein the expanding is accomplished through the application of a rule to the at least one numerical primary attribute to result in an expanded attribute which includes at least one of a genetic, epigenetic, pangenetic, physical, behavioral, situational, or historical attribute, and wherein the expanded attribute has a lower resolution than the at least one numerical primary attribute; 
 iii. receiving a query attribute which identifies a group of query-positive-positive individuals and a group of query-attribute-negative individuals; 
 iv. creating a set of query-attribute-positive attribute profiles containing the at least one expanded attribute from the set of query-attribute-positive individuals and a set of query-attribute-negative attribute profiles containing the at least one expanded attribute from the set of query-attribute-negative profiles; 
 v. determining a set of candidate attributes by selecting attributes from the set of query-attribute-positive profiles that do not occur in a portion of the set of query-attribute-negative profiles, wherein the candidate attributes contain at least one expanded attribute profile; 
 vi. computing the frequencies of occurrence of combinations of the candidate attributes in the set of query-attribute-positive profiles and in the set of query-attribute-negative profiles; and 
 vii. storing, within the first data structure, one or more candidate attribute combinations having higher frequencies of occurrence in the set of query-attribute-positive profiles than in the set of query-attribute-negative profiles to generate a compilation of attribute combinations that co-occur with the query attribute. 
   
     
     
         22 . The bioinformatics database system of  claim 21 , wherein the processor is also for:
 viii. storing statistical results, generated based on the frequencies of occurrence, which indicate the strength of association of each of the attribute combinations with the query attribute.