Syntactic tagging in a domain-specific context
First Claim
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1. A method for computationally determining navigational associations within an n-dimensional database, the method comprising:
- electronically storing a set of data entities in a database system, wherein the data entities represent elements of a biological system;
wherein one or more elements of the biological system comprise an organ system, a tissue, a cell, a genetic sequence, or a component thereof serving a common function;
electronically storing a computerized representation of a biological system syntax, wherein the biological system syntax can be an input to an algorithm executed on a computer processor to validate or generate a finite combination of the data entities;
electronically assigning syntactic tags to the data entities in a logical data model based on biological attributes of the elements of the biological system represented by the data entities;
wherein the logical data model comprises at least two fields ordered by a set of interrelationships among at least two elements of the biological system, the interrelationships corresponding to functional properties in a biological domain, and wherein the biological attributes comprise type, position, or expression of one or more elements of the biological system;
wherein one or more of the data entities represent one or more nodes or a property of a set of nodes, wherein a node represents a syntactic tag that has a range of values represented as coordinates in n-dimensional space with successive specialization of the functional properties as represented in the logical data model, wherein specialization is represented by a position of a tag in the syntactic structure;
wherein a set of connections among the nodes represents a set of the interrelationships corresponding to functional properties in the biological domain;
wherein the syntax describes a dimension in the n-dimensional space associated with a set of the elements of the biological system, wherein the finite combination of data entities describes a dimension which consists of regions and subregions within the n-dimensional space;
algorithmically identifying a set of syntactic positions in the n-dimensional space;
organizing and electronically storing the set of syntactic positions for use with a navigation function which identifies a set of associations among the nodes based on their locations in n-dimensional space, wherein the set of associations represent a plurality of the interrelationships corresponding to functional properties in the biological domain;
receiving an input query from a user, wherein the query corresponds to an attribute of the biological system; and
electronically traversing the n-dimensional space to retrieve a result regarding an element of the biological system.
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Abstract
This application relates generally to defining a domain-specific syntax characterizing a functional information system and performing operations on data entities represented by the domain-specific syntax, including defining a domain-specific syntax, receiving and storing a domain-specific data entity, assigning a syntactic tag to the domain-specific data entity, and electronically storing the tag assigned to the data entity in the electronic data store so that the tag is logically linked to the stored data entity.
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Citations
22 Claims
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1. A method for computationally determining navigational associations within an n-dimensional database, the method comprising:
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electronically storing a set of data entities in a database system, wherein the data entities represent elements of a biological system; wherein one or more elements of the biological system comprise an organ system, a tissue, a cell, a genetic sequence, or a component thereof serving a common function; electronically storing a computerized representation of a biological system syntax, wherein the biological system syntax can be an input to an algorithm executed on a computer processor to validate or generate a finite combination of the data entities; electronically assigning syntactic tags to the data entities in a logical data model based on biological attributes of the elements of the biological system represented by the data entities; wherein the logical data model comprises at least two fields ordered by a set of interrelationships among at least two elements of the biological system, the interrelationships corresponding to functional properties in a biological domain, and wherein the biological attributes comprise type, position, or expression of one or more elements of the biological system; wherein one or more of the data entities represent one or more nodes or a property of a set of nodes, wherein a node represents a syntactic tag that has a range of values represented as coordinates in n-dimensional space with successive specialization of the functional properties as represented in the logical data model, wherein specialization is represented by a position of a tag in the syntactic structure; wherein a set of connections among the nodes represents a set of the interrelationships corresponding to functional properties in the biological domain; wherein the syntax describes a dimension in the n-dimensional space associated with a set of the elements of the biological system, wherein the finite combination of data entities describes a dimension which consists of regions and subregions within the n-dimensional space; algorithmically identifying a set of syntactic positions in the n-dimensional space; organizing and electronically storing the set of syntactic positions for use with a navigation function which identifies a set of associations among the nodes based on their locations in n-dimensional space, wherein the set of associations represent a plurality of the interrelationships corresponding to functional properties in the biological domain; receiving an input query from a user, wherein the query corresponds to an attribute of the biological system; and electronically traversing the n-dimensional space to retrieve a result regarding an element of the biological system. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A system for computationally determining navigational associations within an n-dimensional database, the system comprising:
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a data storage device configured for; electronically storing a set of data entities in a database system, wherein the data entities represent elements of a biological system; wherein one or more elements of the biological system comprise an organ system, a tissue, a cell, a genetic sequence, or a component thereof serving a common function; electronically storing a computerized representation of a biological system syntax, wherein the biological system syntax can be an input to an algorithm executed on a computer processor to validate or generate a finite combination of the data entities; a computerized processor device configured for; electronically assigning syntactic tags to the data entities in a logical data model based on biological attributes of the elements of the biological system represented by the data entities; wherein the logical data model comprises at least two fields ordered by a set of interrelationships among at least two elements of the biological system, the interrelationships corresponding to functional properties in a biological domain, and wherein the biological attributes comprise type, position, or expression of one or more elements of the biological system; wherein one or more of the data entities represent one or more nodes or a property of a set of nodes, wherein a node represents a syntactic tag that has a range of values represented as coordinates in n-dimensional space with successive specialization of the functional properties as represented in the logical data model, wherein specialization is represented by a position of a tag in the syntactic structure; wherein a set of connections among the nodes represents a set of the interrelationships corresponding to functional properties in the biological domain; wherein the syntax describes a dimension in the n-dimensional space associated with a set of the elements of the biological system, wherein the finite combination of data entities describes a dimension which consists of regions and subregions within the n-dimensional space; algorithmically identifying a set of syntactic positions in the n-dimensional space; organizing and electronically storing the set of syntactic positions for use with a navigation function which identifies a set of associations among the nodes based on their locations in n-dimensional space, wherein the set of associations represent a plurality of the interrelationships corresponding to functional properties in the biological domain; receiving an input query from a user, wherein the query corresponds to an attribute of the biological system; and electronically traversing the n-dimensional space to retrieve a result regarding an element of the biological system. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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Specification