Intelligent molecular object data structure and method for application in heterogeneous data environments with high data density and dynamic application needs

• US 20020156756A1
• Filed: 12/06/2001
• Published: 10/24/2002
• Est. Priority Date: 12/06/2000
• Status: Abandoned Application

• Current Assignee: Biosentients Incorporated
• Original Assignee: Biosentients Incorporated
• Inventors: Gombocz, Erich A., Stanley, Robert A.
• Application Number:
  US10/010,724
• Publication Number:
  US 20020156756A1
• Time in Patent Office: Days
• US Class Current: 706/47
• CPC Class Codes: G06F 16/20 of structured data, e.g. relational data
• CPC Class Codes: Y10S 707/99944 Object-oriented database structure
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

Methods are provided to define and describe the creation, architecture and embodiment of Intelligent Molecular Object data (“IMO”, hereinafter “Intelligent Object”). The Intelligent Object is a software product invented to enable unified user presentation, accessing, routing and functionally integrated processing of potentially (but not necessarily) diverse data. Each Intelligent Object provides a unified, interactive user interface to uniquely identified, functionally integrated data from potentially heterogeneous, data content from potentially diverse database back-ends and/or data resources. Said data content includes but is not limited to data such as gene sequence data, protein expression data, 2D gel electrophoresis data, chemical structure data, bio-assay data, image data, text data, audio data or other data from an extensible variety of data types and structures. Intelligent Object technology improves data usability and rate of access to query-relevant elements, attributes and other meta-data, and provides means for functional multidimensional analysis. The technology provides real-time integrated access to previously incompatible data, including synchronized access to off-line and/or latent response data and significantly reduces response time for queries of large datasets. The technology provides data management and access across diverse hardware and software platforms and research applications. The technology secures data for global network use and exchange, and provides extensible options, including ownership management, data integrity, use-tracking, and selective access. Additionally, Intelligent Object handling and storage technology for customization, analysis, and exchange is provided. Methods including software processes, sets of instructions, procedural rules, and look-up tables are provided to define and describe: Intelligent Object creation; unified functional presentation; unique data object, content, user and session identification; user and session authentication and permission for data access; dynamic root data and meta-data routing of multidimensional, vectorized content information; data logging, auditing, status management and validation state alerting; raw data matrix and matrix structure definition; meta-data indexing and query optimization; functional content and attribute definition for database or application access and routing for said database or application; direct data-to-data information interchange; graphical data viewing and analysis; and text annotation integration for diversified data in networked Life Sciences applications environments.

Claims

1. A data structure (“

Intelligent Molecular Object, hereinafter “

Intelligent Object”

) providing methods for unified, functional integration and unified data content access and management, wherein the methods comprise;

a) at least one component comprising procedures for persistent data content and activity status management; and

b) at least one interface comprising procedures for functional integration and information interchange between the data, associated data and applications, components and interfaces.

2. An Intelligent Object as in claim 1, wherein the procedures for persistent data content and activity status management further comprise

a) at least one component comprising procedures for persistent data content and activity status management across diverse data types, content and computing environments;

and

b) at least one interface comprising procedures for direct data content addressing, definition and presentation of data content properties for information interchange between said data, associated data and applications, components and interfaces across diverse data types, content and computing environments.

3. An Intelligent Object as in claim 1, wherein said procedures for persistent data content and activity status management across diverse data types, content and computing environments further comprise

a) at least one set of procedural steps for data content access and processing synchronization;

b) at least one set of procedural steps for persistent data content access and processing logging and auditing;

c) at least one set of procedural steps for monitoring and verification of data integrity, command history, and regulatory validation states.

4. An Intelligent Object as in claim 1, wherein said interface procedures for direct data content addressing, definition, presentation and functional integration further comprise methods for:

a) vectorized access, routing, translation, linking and comparison of data content information such as data content and data content subsets (“

workspaces”

) defined to granularity from entire data content files to data content subsets as small as single byte workspaces;

b) and direct interchange of information not limited to said not limited to processing information, commands, queries, meta-data, data content and said defined workspace subsets;

i. between said data objects; and

ii. between said data objects, heterogeneous applications and a variety of components, access interfaces, and presentation layers.

5. An Intelligent Object as in claim 1, further comprising:

a) a set of unified presentation layers (“

property panes”

) comprising methods for user viewing and interactivity;

b) a set of unique components (and/or “

processing components”

) comprising methods for raw data matrix mapping, status management, data access and routing, data content translation and/or activation of external processing components for data processing; and

c) a set of functional interface layers (“

access interfaces”

) comprising methods for direct data content comparison and information interchange between addressed data content, meta-data, applications and components.

6. A data structure as in claim 1, further comprised as a core element within an information technology platform architecture (“

Sentient Platform”

) advantageously enabled in software, comprising methods for;

a) functional data integration, multidimensional data accessing and routing, viewing, querying, analyzing and other data-enabling operations

i. utilizing single data content files and/or high numbers of complex, heterogeneous and/or interdependent data content files which are functionally unified, although utilizing diverse and/or distributed data content resources; and

ii. capable of simultaneously utilizing data content stored in diverse and distributed database and/or data storage resources, diverse computational hardware and network environments with diverse and dynamic application needs.

7. The creation method of said data structure, which comprises methods and processes not limited to

a) automated detection of data content newly available locally and/or over networks that correspond to actions including user initiated and/or automated queries, user initiated and/or automated data acquisition activities and/or data import requests

b) invocation of a new unique object identifier property pane via a component comprised within an external object handler,

c) assignation of a globally unique identifier,

d) generation of functionally integrated property panes within the Intelligent Object;

e) identification of all user-defined and content attribute based connections to the data structure; and

f) listing within the unique object identifier property pane of information comprising the Intelligent Object'"'"'s creator, network and/or local routing information, content attribute information, information on connected users, access permissions, authentication information such as globally unique identification and public key encryption status, and current session information; and

g) state history recordation of all Intelligent Object activity over networks and/or within local computing environments.

8. A unique object identifier property pane (UID), for interactive user, data, session and machine authentication, comprising methods for

a) bi-directional information interchange with an external application for data handling and applications integration (“

IOH”

) and a comprised unique object identifier access interface; and

b) provision of globally unique identification of said Intelligent Object utilizing globally unique identifiers comprising an 128-bit alphanumeric string.

9. A unique object identifier property pane as in claim 8, wherein the procedures for identification further comprise methods for:

a) provision of additional identification information including;

i. data creation information, comprising time, date and machine identification information;

ii. ownership information, comprising unique identification information for the object creator;

iii. security setting information, comprising access permissions, read-only permission, write permission;

iv. routing information, comprising raw data content addressing information and Intelligent Object data addressing information; and

v. real-time information about locally or remotely connected users, comprising user'"'"'s unique identification information;

computer name;

login time;

network address or location information; and

session identification information; and

b) at least one rule or policy for object data security which either permits or denies access for information interchange between data objects, data content, users and applications, based on comprised criteria for session, user and data authentication.

10. An interactive content router component (ICR), for addressing of data content access and routing, comprising methods for

a) bi-directional information interchange with components and access interfaces including said object root router component, a status management component, an object pane descriptor component, and a unique object identifier Access Interface;

and

b) utilization of information provided by said object pane descriptor component and comprised meta-data index information to optimize linking, organization and direction of vectorized access and routing requests, processing commands, and information interchange between such as Intelligent Objects, heterogeneous and/or homogeneous data objects and data content, applications, data resources and/or databases.

11. An interactive content router component as in claim 10, further comprising methods for

a) implementation of read-only access to data content, and routing of said vectorized data to an external application for data handling, for cache-based processing according to non-destructive overlay methods;

b) addressing to multiple data content locations according to provided criteria;

c) direction of said vectorized data content access and routing within any local computing environment, local network, wide area network and/or global network;

d) direction of meta-data, data content and/or processing results routing within said computing environments;

e) Additionally, said comprised methods and processes report data content origination and routing information to a unique object identifier access interface.

13. An object root router component as in claim 12, further comprising methods for

a) definition of the origin of the Intelligent Object and for multiple addresses to said Intelligent Object, locally and/or over any local network and/or global network;

b) definition of the origin of associated data objects according to object description and relationship definitions; and

c) addressing for data management, accessing and routing of the Intelligent Object within local, distributed and/or remote database and data storage technology.

15. A unique object identifier access interface as in claim 14, further comprising methods for

a) fielding of electronic signatures for validated identification and authentication.

17. An object state engine property pane as in claim 16, further comprising methods for

a) detailed activity logging via a linked status management component of state attributes including:

globally unique user identification;

computer, instrument or device identification;

login date and time;

logout date and time;

user;

Intelligent Object and data content addressing information;

unique session identification;

data authentication information;

data integrity information;

user access authentication and/or denial of access;

session activity records;

data ranking status; and

/or validation states.

19. An always-on status management component as in claim 18, further comprising methods for

a) communication with an external object state engine to enable monitoring of data integrity, command history and regulatory validation states;

b) communication with an external object state engine to enable viewing of instrument parameters related to acquisition of data content and/or other instrument activities

c) communication with said object state engine to provide automated validation status verification according industry-specific validation requirements not limited to Good Practice (G*P)-compliance including GLP Laboratory Information Management Systems (LIMS);

U.S. Food and Drug Administration Center for Drug Evaluation and Research (FDA CDER);

Codebook for Forensic Investigation Requirements (CFIR); and

International Organization for Standardization (ISO

     9000); and

d) provision of information including data acquisition state;

calibration information;

applied transformation or analysis processes; and

validation state (Object State List—

Table

     1) to the object state engine property pane;

e) utilization of comprised state history information and non-destructive overlay processing techniques for data integrity protection and verification;

auditing;

logging; and

detailed rollback to previous Intelligent Object data states; and

f) functional integration of data and applications via interactive information exchange with external components that provide processes including data type translation and applications integration.

12. An object root router component (ORR), for addressing, accessing and routing of the Intelligent Object, comprising methods for

a) bi-directional information interchange with components and access interfaces such as a unique object identifier access interface, an interactive content router component, and a status management component;

b) definition of the origin of the Intelligent Object; and

c) addressing for access and routing of the Intelligent Object.

14. A unique object identifier access interface (UIDi), for authentication, validation, and gating permission or denial of access to said Intelligent Object and comprised data content, comprising methods for

a) bi-directional information interchange with components and access interfaces including an object root router component, interactive content routing component, status management component and said unique object identifier property pane;

and

b) permission or denial of access to said elements, components and access interfaces.

16. An object state engine property pane (OSE), for viewing and interactivity regarding Intelligent Object state information, comprising methods for

a) bi-directional information interchange with components and access interfaces including an external object handler user interface and a status management component;

and

b) interactive, real-time Intelligent Object activity viewing, activity alerting, auditing and manual activity synchronization.

18. An always-on status management component (SMC), for persistent data object state history and status management, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said object root routing component, said interactive content routing component, said unique object identification access interface, said object state engine property pane, an object graph preview component, an object pane descriptor component, and an external object state engine;

and

b) launching of and interaction with said external object state engine component.

20. An object query interface access interface (OQI), for massively parallel and direct Intelligent Object-to-Intelligent Object information interchange, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to an object pane descriptor component, a meta-data index access interface, and said status management component;

b) reception of query requests from the status management component and an external object state engine component;

c) implementation of queries across data subsets comprised within homogeneous and/or heterogeneous data content storage resources, based on query information provided by the object pane descriptor component, meta-data index interface and status management component;

d) initiation of direct object-to-object information interchange in parallel with corresponding Intelligent Objects via their comprised object query interfaces, by directing the interactive content routing of specified data vectors and/or meta-data index information directly between object query interfaces and of other Intelligent Objects for linking, comparison and relationship definition;

e) relaying said data content information to an external result aggregation engine for further processing and presentation to the user via the unified presentation layer user interface;

routing of results of Boolean comparisons and other algorithms applied to linked data content and/or meta-data compared back to the object pane descriptor property pane for presentation to the user; and

f) routing of results of said direct object-to-object information interchange to

i. update an object pane descriptor component and

ii. update a meta-data index access interface.

21. An object query interface access interface as in claim 20, further comprising methods for

a) implementation of queries across data subsets comprised within an external object data storage resources, based on query information provided by the object pane descriptor component, meta-data index interface and status management component;

22. A meta-data index property pane (MDX), for unified user viewing and interactivity with data object meta-data, comprising methods for:

a) bi-directional information interchange with components and access interfaces not limited to an external application for data handling and applications integration and a meta-data index access interface;

b) viewing of meta-data index information relating to said Intelligent Object and its data content and activity, said information comprising automatically generated and/or user-defined meta-descriptions and query relationship trees regarding information comprising specific data functionality and/or relationships to other data and/or data inter-dependencies.

23. A meta-data index property pane as in claim 22, further comprising methods for:

a) interactive user definition and updating of said meta-data index information relating to said Intelligent Object and its data content and activity.

25. A meta-data index access interface as in claim 24, further comprising methods for

a) extraction, integration and implementation of a variety of result aggregation, distributed learning and knowledge extraction algorithms, such as but not limited to external result aggregation engines;

distributed learning engines; and

knowledge extraction engines.

27. An object pane descriptor property pane as in claim 26, further comprising methods for

a) viewing of information highlighting functional relationships between Intelligent Object data properties, and related applications and data;

and

b) interactive “

drag and drop”

functionality to enable user definition of custom and/or automated analytical requirements.

29. An object pane descriptor component as in claim 28, further comprising methods for

a) provision of an overview of properties presented within said Intelligent Object'"'"'s property panes, such as data content attributes, data state, data location and/or locations, data environment definitions, data structure and/or structures, meta-data, locally available and/or remotely linked applications, processing components and access interfaces, linked databases and/or data resources

b) provision of information regarding functional relationships of data objects, data content and meta-data.

30. An object pane descriptor component as in claim 28, further comprising methods for

a) provision of functionally related data object, data content and meta-data information comprising:

data content attributes;

data content interrelationships;

data state;

data location and/or locations;

data environment definitions;

data structure and/or structures;

b) provision of said information for functional linking, vectorized accessing and routing of data content, meta-data and processing results;

c) functional integration of said data within a computing environment comprising locally available and/or remotely linked applications;

processing components;

access interfaces;

databases and/or data resources located within local computing environments, local networks, wide area networks and/or global networks; and

d) viewing and interactive user definition and updating of said information to provide integrated functionality of properties defined by the entity of object property panes.

24. A meta-data index access interface (MDXi), for functional integration of data object meta-data according to user activities, data properties and analytical requirements, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said object query interface, said meta-data index property pane, and an object pane descriptor component;

b) dynamic integration of meta-data information resulting from such as user-based and/or automated query histories, various applied analytical command and result histories, user-defined meta-data entries, and/or a combination thereof; and

aggregation and integration of results of multi-parametric clustering and/or other data analyses; and

c) provision of sets of rules to optimize access and routing and by said Intelligent Object.

26. An object pane descriptor property pane (OPD), for unified user viewing and interactivity with data object properties presented within the entity of property panes, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to an external application for data handling and applications integration and an object pane descriptor component;

and

b) provision of an overview of properties presented within said Intelligent Object'"'"'s property panes such as, but not limited to data content attributes, data state, data location and/or locations, data environment definitions, data structure and/or structures, meta-data, locally available and/or remotely linked applications, processing components and access interfaces, linked databases and/or data resources; and

c) provision of graphical data content and information views of linked data and applications.

28. An object pane descriptor component (OPD), for functional integration of data object properties presented within the entity of property panes, comprising methods for

a) bi-directional information interchange with components and access interfaces including said interactive content routing component, said status management component, said object query interface, said meta-data index access interface, said object pane descriptor property pane, an object graph preview property pane, an object graph preview access interface, an object access manager component, an applications/database definition router access interface, and a matrix structure descriptor component;

to provide

b) dynamic detection, updating, routing and presentation of information required for functionality defined by the entity of object property panes comprised by said Intelligent Object; and

c) direct linking of data with functionally related Intelligent Objects, data content and related applications;

to enable

d) unified analysis of data from homogeneous and/or heterogeneous data types from homogeneous and/or heterogeneous sources.

31. An applications/database definition router interface (ADDR), for definition and provision of application and database dependencies, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said object pane descriptor component and a matrix structure descriptor interface;

b) addressing and functional linking of data content for interactivity with heterogeneous applications, databases and/or data resources.

32. An applications/database definition router interface as in claim 31, further comprising methods for

a) detection, extraction and definition of required and/or available data content attributes, data state, data locations, data environment definitions, data structures required for interactivity with locally available and/or remotely linked applications, databases and/or data resources.

33. An object graph preview property pane (OGP), for unified user viewing of data content, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to an external application for data handling and applications integration user interface, said status management component, said object pane descriptor component and an object graph preview interface;

b) user reviewing of data content such as low-resolution graphical “

thumbnail”

data previews.

34. An object graph preview property pane as in claim 33, further comprising methods for

a) interactive user identification of data content subsets for accessing and user reviewing.

35. An object graph preview property pane as in claim 33, further comprising methods for

a) Interactive user identification of data content for access according to meta-data and vectorized data access protocols;

and

b) user reviewing of heterogeneous data content within a unified presentation environment comprising methods for detailed audio, graphic, digital video, review.

36. An object graph preview property pane as in claim 33, further comprising methods for

a) definition and selection of workspace subsets, which may include an entire data content file or a subset of said data content as small as a single byte, to applications such as pattern detection, normalization, comparison, 2D and 3D viewing and/or analysis;

b) interactive linking to external methods provided for detailed data relationship viewing, such as a data pool viewer; and

c) viewing of subsets of data content and/or linked data with corresponding content attributes.

38. An object graph preview interface as in claim 37, further comprising methods for

a) launching of functionally integrated applications according to correspondence of data content, queries and applications functionality via a comprised module launch component (MLC);

b) routing and linking of data content including content attribute information, data annotations, limited resolution graphic views of any selected data file content, and

c) linking of limited resolution image/graphics (“

thumbnail”

) views of data content from external applications and/or software systems such as operating systems, for passing said view to the object graph preview property pane.

40. An application translator link property pane as in claim 39, further comprising methods for

a) provision of a list of available and applicable applications, analytical components and related data resources;

b) manual linking of data content to related software modules and/or processing devices such as preferred analytical applications, processing devices and other interactive devices for actions not limited to viewing, analyzing and/or listening; and

c) manual launching of external components for analysis and/or processing of data.

41. An application translator link property pane as in claim 39, further comprising methods for

a) provision of a user interface for unified application and application component relationship definition, functional access, organization, translation, and integration;

and

b) interactive, unified user viewing of and interactivity with applications components and their required and/or available relationships;

i. depending on data content, functional data relationships, analytical requirements, available applications, available applications components, translation requirements and specific user queries;

c) provision of an interactive user interface for automated, instantaneous applications functionality integration via linking to an external component for automated applications assembly, to provide the assembly functionality for dynamic development of new and customized applications.

37. An object graph preview interface (OGPi), for accessing and directing graphical data content, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said object pane descriptor component, said object graph preview property pane, and an object access manager component;

b) routing and linking of data content between applications windows; and

c) linking of limited resolution image/graphics (“

thumbnail”

) views of data content to the object graph preview property pane.

39. An application translator link property pane (ATL), for interactive user modeling, linking, assembly, and integration of applications, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to an external application for data handling and applications integration and an object access manager component;

b) provision of a list of available and applicable applications, application components and related data resources; and

c) manual launching of external modules for cached non-destructive analysis and/or processing of data.

42. An object access manager component (OAM) for functional analytical application, component, interface and data integration, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said object pane descriptor component, said object graph preview property pane and an object access manager component;

and

b) defining parameters required for functional access, routing and presentation of data content within a given application or database environment.

43. An object access manager component, as in claim 42, further comprising methods for

a) provision of a messaging queue;

which

i. defines the applications window content required for data content transfer between the Intelligent Object and heterogeneous applications;

ii. governs functional presentation within homogeneous and/or heterogeneous application and database environments; and

iii. functionally integrates data content with a variety of applications;

b) direction of access and routing requests for specific data content to linked applications;

c) direction of information interchange between the Intelligent Object and external processing components and/or various applications such as text editors to allow for analysis, customization, formatting, processing, reviewing and unified presentation of said data content in a non-destructive manner, through said external components and applications;

d) interaction with external object translation engines to provide

i. data content translation for functional integration with a variety of applications; and

ii. data content and attribute-based algorithms for applications translation, integration and inter-application communication;

e) direct linking of data content and meta-data to external components comprising methods including data content translation and presentation according to requirements of heterogeneous software modules or plug-ins;

f) direct linking of data content and meta-data to external applications including applications running on hand-held electronic devices such as those used for data text entry; and

g) direct linking of data content and meta-data to external applications including laboratory instrument plug-ins for real-time viewing of instrument and/or data parameters related to acquisition of data content.

44. A raw data matrix property pane (RDM), for provision of detailed data storage and access information, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to an external application for data handling and applications integration user interface and a data link insertion component;

b) provision of information regarding originating data content matrices.

45. A raw data matrix property pane as in claim 44, further comprising methods for

a) user reviewing of data content information such as data source location, data source type, data storage information, data access;

data content path and vectorized data matrix structure information;

b) provision of information regarding originating data content matrices, across heterogeneous originating data and data resource type and/or structure.

47. A data link insertion component as in claim 46, further comprising methods for

a) detection and definition of data type, transport and routing protocols for the required communication mechanism to data content such as PPP over TC/IP, peer-to-peer, client/server, server/server, http and/or ftp.

49. A matrix structure descriptor component as in claim 48, further comprising methods for

a) linking of said data matrix structure information to meta-data and data description information;

b) linking of addressing definitions required to enable functional integration data content accessing; and

c) accessing of data content (“

workspaces”

) to levels of granularity including data subset overviews, data files, fields, rows, cells, pixels or bytes;

46. A data link insertion component (DLI), for synchronization of data content access and routing with required transport protocols, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said raw data matrix property pane;

and matrix structure descriptor access interface;

b) data content distinction by type membership such as file, database record, application, and live data acquisition; and

c) detection and activation of transport protocols required for specified data type accessing and routing requests.

48. A matrix structure descriptor component (MSD), for provision of vectorized data content mapping, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said status management component, said object pane descriptor component;

said Application/Database Definition Router interface; and

said data link insertion component;

b) matrix structure description of data content according to comprised vector mapping definitions; and

c) mapping of data according to data field, data format and/or data structure.

50. A text annotation property pane (TAN), for unified, interactive user text entry and linking of textual and other references, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to an external application for data handling and applications integration user interface and a text annotation access interface;

b) manual entry, viewing and linking of information such as text annotation;

c) activation of external components or applications such as text editors to allow for customization, formatting, reviewing and processing of said information through external editors; and

d) provision of functionality for linking of customized text annotations, external text resources, references, related data and information.

51. A text annotation access interface (TANi), for direct linking of external applications for text editing and for linking of textual and other reference files, comprising methods for

a) bi-directional information interchange with components and access interfaces not limited to said object access manager;

and said text annotation property pane;

b) linking of external components or applications such as text editors to allow for customization, formatting, reviewing and processing of said information through external editors; and

which allow for

c) passing of said information back to the text annotation property pane.