WO2006117770A1

WO2006117770A1 - An information management and control system

Info

Publication number: WO2006117770A1
Application number: PCT/IE2006/000048
Authority: WO
Inventors: Dante Borillo; Kevin Brendan Keenan; Richard Seán O'ROURKE; David Michael O'rourke; Barry James Neary
Original assignee: KINEMATIK RESEARCH Ltd; Kinematik Res Ltd
Current assignee: KINEMATIK RESEARCH Ltd; Kinematik Res Ltd
Priority date: 2005-05-05
Filing date: 2006-05-05
Publication date: 2006-11-09
Anticipated expiration: 2007-11-05
Also published as: IES20060357A2; IE20060356A1

Abstract

A scientific information management and control system comprises laboratory managers (5-8) each for exposing interfaces for managing lifecycles of dedicated objects to implement a work flow with state actions and object flow for management of laboratory experiments. A resource manager (6) for manages life-cycle of material and equipment resource objects. A classifications manager (5) manages life-cycle of resource classification objects containing the resource objects. A task manager (7) manages life-cycles of task objects. A procedure manager (8) manages life-cycles of procedure objects. A task comprises multiple procedures. The classification objects include equipment classification and material classification objects linked with resource classification objects, and the resource objects inherit from the resource classification objects. A design-of-experiment engine (2) interfaces with the objects managed by the laboratory managers (5-8) and generates experiment run objects. An experiment manager (3) generates low-level objects according to the run objects generated by the design-of-experiment engine (2) and according to the procedure objects generated by the procedure manager (8). The experiment manager (3) and the laboratory managers (5-8) comprise an interface to external systems. This interface parses mark-up language (ENML) received from external systems to determine data and instructions for experiment runs.

Description

"An information management and control system "

INTRODUCTION

Field of the Invention

The invention relate to information management and control, particularly for research experiments.

Prior Art Discussion

Our prior published PCT Patent Specification No. WO03/005249 describes a system having a design of experiment ("DOE") engine which generates a series of run objects, each for a particular experiment. This system provides an effective control structure and also allows considerable versatility.

US2005/0010370 (Medicel Oy) describes an information management system for managing biochemical information, which generates a first data set for describing biomaterial and/or biochemical entities and a second data set describing experiments.

The invention is directed towards achieving improved efficiency and versatility in management and control of scientific experiments.

SUMMARY OF THE INVENTION

According to the invention, there is provided a scientific information management and control system comprising: a plurality of laboratory managers each for exposing interfaces for managing lifecycles of dedicated objects to implement a work flow with state actions and object flow for management of laboratory experiments, said laboratory managers comprising:

a resource manager for managing life-cycle of material and equipment resource objects, a classifications manager for managing life-cycle of resource classification objects containing the resource objects, a task manager for managing life-cycle of task objects, and a procedure manager for managing life-cycle of procedure objects and in which a task comprises a plurality of procedures, wherein the classification objects include equipment classification and material classification objects linked with resource classification objects, and said resource objects inherit from said resource classification objects,

a design-of-experiment engine for interfacing with the objects managed by the laboratory managers and for generating experiment run objects; and

an experiment manager for generating low-level objects according to said run objects generated by the design-of-experiment engine and according to said procedure objects generated by the procedure manager, and

wherein the experiment manager and the laboratory managers comprise an interface to external systems, said interface comprising a parser for parsing mark-up language received from external systems to determine data and instructions for experiment runs. In one embodiment, the laboratory managers manage create, read, update, and delete stages of life-cycles of their dedicated objects.

In one embodiment, the resource objects contain material type and equipment type objects, a material type object contains a sample object, and an equipment type object contains an item object.

In one embodiment, at least some resource objects contain at least one parameter object.

In another embodiment, the parameter objects are grouped into intrinsic parameter objects which model an attribute of the parameters, and extrinsic parameter objects which model experiment-related attributes of a parameter.

In one embodiment, a task object contains a task configuration object, and a task configuration object instantiates a set of sample objects by defining target values and relationships between parameter objects.

In one embodiment, each sample object is linked to an experiment run object, and to an object for preparation of a sample.

In a further embodiment, the task manager creates a parameter object and associates the parameter object with handlers for visualisation, annotation, and searching.

In one embodiment, the resource manager creates a parameter object for a material type, the object parameters being inherited from a material classification.

In one embodiment, the procedure manager creates preparation procedure objects for preparation of sample objects belonging to a material type. In one embodiment, the task manager creates a plurality of sample objects greater than or equal to the number of runs of an experiment, in which each sample object is linked with an experiment run object generated by the design-of-experiment engine and is linked indirectly to resource objects for resources used during preparation of the sample, said links forming a tree structure representing genealogy of the sample object.

In one embodiment, the resource manager comprises means for instantiating at least one intrinsic parameter object according to a sample object.

DETAILED DESCRIPTION OF THE INVENTION

Brief Description of the Drawings

The invention will be more clearly understood from the following description of some embodiments thereof, given by way of example only with reference to the accompanying drawings in which: -

Fig. 1 is a UML (Unified Modeling Language) component view of the architecture of a scientific information management and control system of the invention;

Fig. 2 is a UML class diagram representing a domain model view of the object classes of the system; and

Fig. 3 is a UML activity view of operation of the system.

Description of the Embodiments Referring to Fig. 1, a scientific information management and control system provides an open framework for scientific methods. It includes a laboratory manager 1 modelling and operating on resources which are specific to a scientific laboratory. A design of experiment (DOE) engine 2 is linked with the laboratory manager 1 for generation of experiment runs. An experiment manager 3 operates at a lower level by generating Aim, Results, Analysis, Discussion and Conclusion objects and for using run and procedure objects to control execution of experiment runs.

The laboratory manager 1 and the experiment manager 3 expose to external systems 4 interfaces for communication based on a XML (extensible Markup Language) schema referred as ENML (E-Novator markup language) and available on the

Internet at the URI (Unified Resource Identifier) - http://www.enovator.com/ENML. The external systems 4 are, for example, laboratory information management systems (LIMS), scientific data management systems (SDMS), visualization and annotation software tools, search engines, or laboratory instrumentation controllers. Such systems communicate with the system

1, 2, 3 using the ENML interface, which is particularly versatile as it allows a wide range of data and commands to be communicated. The interfaces of the system automatically parse received ENML to determine data and instructions transmitted by the external systems.

Referring again to the laboratory manager 1 , this comprises a classification and roles manager 5 for managing the life-cycles of resource classification and resource role objects, a resource manager 6 for managing the life-cycles of material type and equipment type objects, a task manager 7 for managing the life-cycles of procedural task objects, and a procedure manager 8 for managing the life-cycles of procedure objects.

The managers 5-8 expose interfaces for the management of the life-cycle of their dedicated objects, each life-cycle including the following set of operations: create, read, update, delete (CRUD) and any additional operation required by the specific object work flow (refer to Fig. 2 for details on activity workflow).

In more detail the domain model diagram in Fig. 2 represents static relationships among different object classes in the system. A Resource object is a generalization of Material Type and Equipment Type objects (which represent its sub-classes in object- oriented terms). A Material Type contains one or more Sample objects, while an Equipment Type contains one or more Item.

Resource objects belongs to one and only one Resource Classification, which represents a generalization of either a Material Classification or an Equipment Classification. A Resource object has also one or more Resource Roles in the system.

Resource and Resource Classification objects contain at least one or more Parameter object. Parameter objects can be either Intrinsic (modeling an attribute or quality of the object) or Extrinsic (modeling an experiment related attribute of the object) and they have always an associated Parameter Type. Parameter Type objects can be extended to treat files (File Type), alphanumeric information (Categorical), numeric, information (Numerical) or be extended further into other user-defined types such as lists, or Boolean.

Because of the exposure of the system to third party software components through the ENML interface, Parameter objects can be associated to third party systems such as: visualization tools (Visualization Handler), for example 2D gel image visualization tools, chemical structure tools - annotation/ editing tools (Annotation Handler) - for example 2D Gel Image annotation tools, or genome structure annotation tools - search engines (Search Handler) - for example chemical structure and sub-structure search engines. Procedural Task objects may contain one or more Task Configuration objects. Each Task configuration instantiates a set of Sample objects and Item objects by defining target values and relationships between Parameter objects contained in the Resource or Resource Classification, which the Sample object or Item objects belong to (either directly or indirectly). Task Configuration may additionally instantiate Resource Role objects, which needs to be resolved into a Sample or Item object by the DOE engine 2.

Procedure objects represent a composition of one or more Task Configuration objects and they can be classified into Preparation or Characterization according to their purpose. The goal of Preparation Procedure objects is to create new Sample objects of a specified Material Type. The goal of Characterization Procedure objects is to determine or test attributes or qualities of a specified Intrinsic Parameter of a Resource obj ect.

One and only one Procedure object is used by a DOE 2 in order to generate a Results object for an Experiment object. A Results object is a collection of one or more Run Sets being a collection of one or more Run objects. Each Run object contains a copy of the Task Configuration objects composing the originating Procedure. Run object purpose is to record experimental values for Extrinsic Parameters or to determine or test Intrinsic Parameters. The purpose of Run objects purpose is to populate the system with new Sample objects.

Beside Procedure and Results objects an Experiment object is also composed by the following object classes: Aim, Analysis, Discussion and Conclusion following the scientific method. The Analysis object besides any other can contain a reference to a set of specific Parameter objects which are considered meaningful for the experimental analysis. Fig. 3 illustrates operations 50 for flow of information in terms of state actions and object flow of what is a typical dynamic behaviour of the system. A step 51 consists in the creation of one or more Parameter objects and their association with the appropriate handlers for visualization, annotation and searching. Handlers refer to third party components.

A second step, 52, is the creation of a Material Type. This process allows the composition of Parameter objects (both Intrinsic and Extrinsic) for the created Material Type. A Parameter can be inherited at this stage from the Material Classification which the Material Type belongs to. Even if not part of the diagram, it is assumed at this stage that appropriate Equipment Type, Items, and Task Configuration objects are in the system and they are appropriately composed with the newly created Material Type objects.

A step 53 involves the creation and definition (configuration) of one or more Preparation Procedure objects, the purpose of which is to prepare Sample objects belonging to the newly created Material Types. The Run DOE action state will allow for the creation of the Experiment object and its sub-components as shown in Fig. 2.

Finalization of a preparation experiment involves creating a number of Sample objects greater or equal to the number of Runs composing the experiment. Each Sample is linked to the appropriate Run and indirectly to any other Sample or Equipment Item used during the preparation of the Sample itself. This linking process forms a tree structure which is referred to as genealogy for a Sample object.

A final step, 54, characterizes one or more Intrinsic Parameter objects by using the newly created Sample objects. At this stage one or more Characterization Procedure objects are prepared and the DOE is run against them to produce a characterization Experiment object. Identified Intrinsic Parameter objects can be then determined for the first time or tested by using one of the handlers associated to them in step 51. In the case of a Search Handler, new Material Types can be identified and created in the system.

Parameters considered to be interesting can be referenced by the Analysis object of the Experiment prior to its finalization and a Report can be generated using the ENML interface. Generated Report objects are XML components which can either be used for communication with third party components (such as LIMS, SDMS, or other software) or to generate human readable output in one of a variety of standard formats. Other formats can be added to this list upon use of the appropriate converter from ENML.

It will be appreciated that the system provides excellent versatility for automated experiment run control. The system can handle a wide variety of resource, parameter, and procedure types. The use of laboratory managers each of which manages life-cycle of dedicated objects imposes an efficient structure on the system, even though relationships between the objects can become complex where the experiment runs involve many different resources and procedures. Also, the overall system structure of the laboratory managers 5-8, the DOE engine 2 and the experiment manager 3 is efficient because of its modularity, and the fact that the laboratory managers 5-8 and the experiment manager 3 can each individually interface with external systems with their ENML interfaces.

The invention is not limited to the embodiments described but may be varied in construction and detail.

Claims

1. A scientific information management and control system comprising:

a plurality of laboratory managers (5-8) each for exposing interfaces for managing lifecycles of dedicated objects to implement a work flow with state actions and object flow for management of laboratory experiments, said laboratory managers comprising:

a resource manager (6) for managing life-cycle of material and equipment resource objects, a classifications manager (5) for managing life-cycle of resource classification objects containing the resource objects, a task manager (7) for managing life-cycle of task objects, and a procedure manager (8) for managing life-cycle of procedure objects and in which a task comprises a plurality of procedures, wherein the classification objects include equipment classification and material classification objects linked with resource classification objects, and said resource objects inherit from said resource classification objects,

a design-of-experiment engine (2) for interfacing with the objects managed by the laboratory managers (5-8) and for generating experiment run objects; and

an experiment manager (3) for generating low-level objects according to said run objects generated by the design-of-experiment engine (2) and according to said procedure objects generated by the procedure manager (8), and

wherein the experiment manager (3) and the laboratory managers (5-8) comprise an interface to external systems, said interface comprising a parser for parsing mark-up language received from external systems to determine data and instructions for experiment runs.

2. A system as claimed in claim 1, wherein the laboratory managers (5-8) manage create, read, update, and delete stages of life-cycles of their dedicated objects.

3. A system as claimed in claims 1 or 2, wherein the resource objects contain material type and equipment type objects, a material type object contains a sample object, and an equipment type object contains an item object.

4. A system as claimed in any of claims 1 to 3, wherein at least some resource objects contain at least one parameter object.

5. A system as claimed in claim 4, wherein the parameter objects are grouped into intrinsic parameter objects which model an attribute of the parameters, and extrinsic parameter objects which model experiment-related attributes of a parameter.

6. A system as claimed in any preceding claim, wherein a task object contains a task configuration object, and a task configuration object instantiates a set of sample objects by defining target values and relationships between parameter objects.

7. A system as claimed in claim 6, wherein each sample object is linked to an experiment run object, and to an object for preparation of a sample.

8. A system as claimed in any preceding claim, wherein the task manager (7) creates a parameter object and associates the parameter object with handlers for visualisation, annotation, and searching.

9. A system as claimed in claim 8, wherein the resource manager (6) creates a parameter object for a material type, the object parameters being inherited from a material classification.

10. A system as claimed in claims 8 or 9, wherein the procedure manager (8) creates preparation procedure objects for preparation of sample objects belonging to a material type.

11. A system as claimed in any of claims 8 to 10, wherein the task manager (7) creates a plurality of sample objects greater than or equal to the number of runs of an experiment, in which each sample object is linked with an experiment run object generated by the design-of-experiment engine (2) and is linked indirectly to resource objects for resources used during preparation of the sample, said links forming a tree structure representing genealogy of the sample object.

12. A system as claimed in claim 11, wherein the resource manager (6) comprises means for instantiating at least one intrinsic parameter object according to a sample object.