Method and system for providing a polymorphism database

Abstract

Systems and methods for organizing information relating to study of polymorphisms. A database model is provided which interrelates information about one or more of, e.g, subjects from whom samples are extracted, primers used in extracting the DNA from the subjects, about the samples themselves, about experiments done on samples, about particular oligonucleotide probe arrays used to perform experiments, about analysis procedures performed on the samples, and about analysis results. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of subjects, samples, experiments, chips, etc.

What is claimed is:  
     
         1 . A computer-readable storage medium having stored thereon: 
 an item table listing a plurality of item records identifying items;    an item attribute table listing a plurality of item attribute records identifying attributes of said items; and    wherein there is a many-to-many relationship between item records and item attribute records.    
     
     
         2 . The computer-readable storage medium of  claim 1  wherein an item attribute item map table implements said many-to-many relationship between item records and item attribute records, said item attribute item map table listing a plurality of map records identifying both a particular item attribute and a particular item.  
     
     
         3 . The computer-readable storage medium of  claim 1  having further stored thereon: 
 an item derivation table listing a plurality of item derivation records identifying transformations between ones of said items used in biological analysis.  
 
     
     
         4 . The computer-readable storage medium of  claim 3  having further stored thereon: 
 a protocol table listing a plurality of protocol records specifying parameters of said transformation.  
 
     
     
         5 . The computer-readable storage medium wherein said items are used in a biological analysis.  
     
     
         6 . The computer-readable storage medium of  claim 1  wherein said biological analysis comprises a polymorphism analysis.  
     
     
         7 . A computer-readable storage medium having stored thereon: 
 an atom result table listing a plurality of atom result records, specifying relative wild-type and mutant sequence concentrations in targets; and    a subject sequence position table listing a plurality of subject sequence position records, specifying combinations of subjects from whom said targets are derived and sequence positions, each said atom result record being associated with one or more atom result records.    
     
     
         8 . The computer-readable storage medium of  claim 7  wherein said atom result records further specify upper and lower bounds for said concentrations.  
     
     
         9 . The computer-readable storage medium of  claim 7  having further stored thereon: 
 a subject table listing subject records specifying said subjects.  
 
     
     
         10 . A computer-readable storage medium having stored thereon: 
 a polymorphism table listing polymorphism sequence records specifying sequences known to contain polymorphisms; and    a patent application table listing patent application records specifying one or more polymorphisms specified by said polymorphism sequence records.    
     
     
         11 . The computer-readable storage medium of  claim 10  wherein said polymorphism sequence records specify for each one of said polymorphisms a polymorphism position, a reference allele, and a base allele.  
     
     
         12 . The computer-readable storage medium of  claim 11  wherein said polymorphism sequence records further specify for each one of said polymorphisms a measured heterozygocity.  
     
     
         13 . A computer-implemented method comprising: 
 creating n item table listing a plurality of item records identifying items used in biological analysis; and    creating an item attribute table listing a plurality of item attribute records identifying attributes of said items; and    wherein there is a many-to-many relationship between item records and item attribute records.    
     
     
         14 . The computer-implemented method of  claim 13  further comprising the step of: 
 creating an item attribute item map table implements said many-to-many relationship between item records and item attribute records, said item attribute item map table listing a plurality of map records identifying both a particular item attribute and a particular item.  
 
     
     
         15 . The computer-implemented method of  claim 13  comprising: an item derivation table listing a plurality of item derivation records identifying transformations between ones of said items used in biological analysis.  
     
     
         16 . The computer-implemented method of  claim 15  further comprising: 
 creating a protocol table listing a plurality of protocol records specifying parameters of said transformation.  
 
     
     
         17 . The computer-implemented method of  claim 13  wherein said biological analysis comprises a polymorphism analysis.  
     
     
         18 . A computer-implemented method comprising: 
 creating an atom result table listing a plurality of atom result records, specifying relative wild-type and mutant sequence concentrations in targets; and creating a subject sequence position table listing a plurality of subject sequence position records, specifying combinations of subjects from whom said targets are derived and sequence positions, each said atom result record being associated with one or more atom result records.    
     
     
         19 . The computer-implemented method of  claim 18  wherein said atom result records further specify upper and lower bounds for said concentrations.  
     
     
         20 . The computer-implemented method of  claim 18  further comprising: 
 creating a subject table listing subject records specifying said subjects.  
 
     
     
         21 . A computer-implemented method comprising: 
 creating a polymorphism table listing polymorphism sequence records specifying sequences known to contain polymorphisms; and    creating a patent application table listing patent application records specifying one or more polymorphisms specified by said polymorphism sequence records.    
     
     
         22 . The computer-implemented method of  claim 21  wherein said polymorphism sequence records specify for each one of said polymorphisms a polymorphism position, a reference allele, and a base allele.  
     
     
         23 . The computer-implemented method of  claim 22  wherein said polymorphism sequence records further specify for at least one of said polymorphisms a measured heterozygocity.