Data structures representing polysaccharides and databases and methods related thereto

Abstract

A data structure, tangibly embodied in a computer-readable medium, representing a polymer of chemical units is disclosed. The data structure includes an identifier including a plurality of fields for storing values corresponding to properties of the polymer. The polymer may, for example, be a polysaccharide and the chemical units may be saccharides. Also disclosed is a computer-implemented method for determining whether properties of a query sequence of chemical units match properties of a polymer of chemical units. The query sequence is represented by a first data structure, and the polymer is represented by a second data structure, each are tangibly embodied in a computer-readable medium, including an identifier including a plurality of bit fields for storing values corresponding to properties of the query sequence and polymer, respectively. The invention also involves a notational system referred to as Property Encoded Nomenclature.

1 . A data structure, tangibly embodied in a computer-readable medium, representing a polysaccharide, the data structure comprising:
 an identifier including one or more fields, each field for storing a value corresponding to one or more properties of the polysaccharide,   wherein at least one field stores a non-character-based value.   
   
   
       2 . The data structure of  claim 1 , wherein each of the fields stores a binary value. 
   
   
       3 . The data structure of  claim 1 , wherein the identifier is representable as a single-digit hexadecimal number. 
   
   
       4 . The data structure of  claim 1 , wherein the identifier is representable as a decimal value. 
   
   
       5 . The data structure of  claim 4 , wherein the decimal value may be reduced to a plurality of prime divisors, wherein each prime divisor represents a monosaccharide or disaccharide of the polysaccharide. 
   
   
       6 . The data structure of  claim 1 , wherein the one or more properties comprise one or more chemical unit properties, each chemical unit property being a property of one of the monosaccharides or disaccharides of the polysaccharide. 
   
   
       7 . The data structure of  claim 6 , wherein the one or more properties comprise one or more charges, each charge being a charge of one of the monosaccharides or disaccharides of the polysaccharide. 
   
   
       8 . The data structure of  claim 6 , wherein the one or more properties comprise one or more chemical unit identities, each chemical unit identity being an identity of a monosaccharide or disaccharide of the polysaccharide. 
   
   
       9 . The data structure of  claim 6 , wherein the one or more properties comprise one or more conformations, each conformation being a conformation of a monosaccharide or disaccharide of the polysaccharide. 
   
   
       10 . The data structure of  claim 6 , wherein the one or more properties comprise one or more substituent identities, each substituent identity being an identity of a substituent of a monosaccharide or disaccharide of the polysaccharide. 
   
   
       11 - 13 . (canceled) 
   
   
       14 . The data structure of  claim 1 , wherein the one or more properties include one or more compositional ratios of substituents. 
   
   
       15 . The data structure of  claim 1 , wherein the one or more properties include one or more compositional ratios of iduronic versus glucuronic. 
   
   
       16 - 21 . (canceled) 
   
   
       22 . The data structure of  claim 1 , wherein the polysaccharide comprises disaccharide repeat units comprising hexosamine and glucuronic or iduronic acid that are linked by α/β 1→4 glycosidic linkages. 
   
   
       23 . A database, tangibly embodied in a computer-readable medium, for storing information descriptive of one or more polysaccharides, the database comprising:
 the data structure of  claim 1 .   
   
   
       24 . A computer-implemented method for generating a data structure, tangibly embodied in a computer-readable medium, representing a polysaccharide, the method comprising an act of:
 generating an identifier including one or more fields for storing values, each value corresponding to one or more properties of the polysaccharide,   wherein at least one field stores a non-character-based value.   
   
   
       25 . (canceled) 
   
   
       26 . A database, tangibly embodied in a computer-readable medium, for storing information descriptive of one or more polysaccharides, the database comprising:
 a data structure generated by the method of  claim 24 .   
   
   
       27 . A data structure, tangibly embodied in a computer-readable medium, representing a polysaccharide, the data structure comprising:
 an identifier including one or more fields, each field for storing a value corresponding to a monosaccharide or disaccharide of the polysaccharide.   
   
   
       28 - 32 . (canceled) 
   
   
       33 . A database, tangibly embodied in a computer-readable medium, for storing information descriptive of one or more polysaccharides, the database comprising:
 the data structure of  claim 27 .   
   
   
       34 . A data structure, tangibly embodied in a computer-readable medium, representing a monosaccharide or disaccharide of a polysaccharide, the data structure comprising:
 an identifier including one or more fields, each field for storing a value corresponding to one or more properties of the monosaccharide or disaccharide of the polysaccharide,   wherein at least one field stores a non-character-based value.   
   
   
       35 - 44 . (canceled) 
   
   
       45 . A database, tangibly embodied in a computer-readable medium, for storing information descriptive of one or more polysaccharides, the database comprising:
 the data structure of  claim 34 .