Semantic Grid Group Members: Phạm Đức Đệ Võ Bảo Hùng Hồ Phương.

Semantic GridSemantic Grid

Group Members: Phạm Đức Đệ Võ Bảo Hùng Hồ Phương

2

Outline

IntroductionSemantic WebS-OGSAImplementation ( e-Science & myGrid )

3

What is Grid?

The "Grid”◦ flexible, secure, coordinated resource sharing

among dynamic collections of individuals, institutions, and resources - virtual organizations.

4

What is the Semantic Grid ?

An extension of the current Grid in which information and services are given well-defined and explicitly represented meaning, so that it can be shared and used by humans and machines, better enabling them to work in cooperation

6

Example: To illustrate, consider if a machine’s operating system is described as “SunOS” or “Linux.” To query for a machine that is “Unix” compatible, a user either has to:

1. Explicitly incorporate the Unix compatibility concept into the request requirements by requesting a disjunction of all Unix-variant operating systems, e.g., (OpSys=“SunOS” || OpSys=“Linux”)

2. Wait for all interesting resources to advertise their operating system as Unix as well as either Linux or SunOS, e.g., (OpSys=“SunOS,” “Unix”), and then express a match as set-membership of the desired Unix value in the OpSys value set, e.g., hasMember(OpSys, “Unix”).

Why we need the Semantic Grid?

7

Example (cont) Apply Semantics…

- Knowledge base: “SunOS and Linux are types of Unix operating system”

- Request: “Need the Unix compatibility OS”

Why we need the Semantic Grid?

8

Semantic WebCurrent Web ( WWW )

◦ Is a huge library of interlinked documents that are transferred by computers and presented to people

◦ Anyone can contribute to it◦ Quality of information or even the persistence of

documents cannot be generally guaranteed◦ Contains a lot of information and knowledge, but machines

usually serve only to deliver and present the content of documents describing the knowledge

◦ People have to connect all the sources of relevant information and interpret them themselves

Machine can Process the content

ButMachine can’t Understand content

9

Definition

The Semantic Web is an extension of the current web in which the semantics of information and services on the web is defined, making it possible for the web to understand and satisfy the requests of people and machines to use the web content.

--- Tim Berners-Lee

Semantic Web

10

Ontology is a formal representation of the knowledge by a set of concepts within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to describe the domain.

Implement by XML, XML Namespace, XML Schema, RDF, RDF Schema và OWL

Ontology

11

Ontology example

12

Semantic Web Architecture (1)

13

Semantic Grid

Scale of data and computation

Sca

le o

f In

tero

pera

bilit

y SemanticWeb

ClassicalWeb

SemanticGrid

ClassicalGrid

Based on an idea by Norman Paton

14

What is Semantic Grid

An extension of the Grid Rich metadata is exposed and handled

explicitly, shared, and managed via Grid protocols

15

What is Semantic Grid

The Semantic Grid uses metadata to describe information in the Grid.

Turning information into something more than just a collection of data means understanding the context, format, and significance of the data.

Therefore:◦ Understand information◦ Discovery and reuse

16

S-OGSA

A Grid usually consist of several different services by OGSA:◦ VO management service◦ Resource discovery and Management service◦ Job Management service◦ Security service◦ Data Management service

The S-OGSA should (will) provide the metadata + semantic services to those services.

17

S-OGSA

The Solution:◦ Attached the semantic to Grid entities.◦ Binding them together by semantic binding

service.◦ Normal grid services can be “semantic” by the

semantic binding service.

18

S-OGSA

19

S-OGSA

Defined by ◦Information model

New entities

◦Capabilites New functionalities

◦Mechanisms How it is delivered

Model

Capabilities Mechanisms

provide/consume

expose

use

20

S-OGSA Model

21

S-OGSA Model

Grid Entities: Grid resources and services Knowledge Entities: represent/operate with some form of knowledge (e.g

ontologies, rules, knowledge bases …) Semantic Bindings: entities associate of a Grid Entity with one or more

Knowledge Entities

22

METADATAas SemanticAnnotations

S-OGSA Model Example

23

Optimization

Execution Management

Resourcemanagement

Data

Security

Information Management

Infrastructure Services

Application 1 Application N

OG

SA

Sem

antic

-OG

SA

Semantic Provisioning

Services

From OGSA to the S-OGSA

Ontology

ReasoningKno

wle

dge

Metadata

Annotation

Sem

antic

bin

ding

Semantic Provisioning Services

24

Semantic ProvisioningService

Knowledge Resource

Grid Entity

Semantic Binding

Grid ServiceIs-a

0..m0..m

1..m1..m

Semantic aware Grid Service

consume

produce

0..m0..m

1..m1..m

uses

WebMDS

SAMLfile

DFDL file

JSDL file

Is-a

Knowledge Entity

Is-a

Ontology Service

Is-a

Reasoning Service

Semantic BindingProvisioning Service

Annotation Service

Metadata Service

Grid Resource

OGSA-DAI

CASIs-a Is-a

Is-a

Is-a

Knowledge Service

Is-a

Ontology

Rule set

Knowledge Semantic Grid Grid

S-OGSA Capabilities

25

S-OGSA Capabilities

Semantic Provisioning Services – SPS provisioning and management of explicit

semantics and its association with Grid entities creation, storage, update, removal and access of

different forms of knowledge and metadata ◦ Knowledge provisioning services

ontology services , reasoning services .◦ Semantic binding provisioning services

metadata services, annotation services .

26

S-OGSA Capabilities

Semantically Aware Grid Services ◦ Be able to consume Semantics Bindings and being

able to take actions based on knowledge and metadata

◦ Sample Actions : Metadata aware authorization of a given identity by a VO

Manager service Execution of a search request over entries in a semantic

resource catalogue Incorporation of a new concept in to an ontology hosted by an

ontology service

27

S-OGSA Mechanisms

Treating Knowledge Entities and Semantic Bindings as Grid Resources ◦ Common Information Model (CIM) Resource

Model ◦ Grid Entities : class CIM-ManagedElement in the

CIM Model. ◦ Knowledge Entities : class S-OGSA-

KnowledgeEntity◦ S-OGSA-SemanticBinding:Semantic Binding, the

association between a Grid Entity (CIM-ManagedElement) and a Knowledge Entity (S-OGSA-KnowledgeEntity)

28

S-OGSA Mechanisms

29

Lifetime

State/properties/metadata access port

. . . MetadataService

OntologyService

Service

Resource

MetadataSeekingClient

3

1

2

Semantic Binding Ids Retrieval Request

Semantic Binding Ids

Metadata Retrieval/Query Request

4

Query/Retrieval Result

5 Obtain schema for Semantic Bindings

Access Patterns to Grid Resource Metadata

• Deliver Metadata pointers through resource properties• Zero impact on existing protocols

Resource Specific

30

Outline

• e-Science• myGrid project

Introduction myGrid Services và Architecture myGrid workbench

31

e-Science (1)

‘e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it.’

‘e-Science will change the dynamic of the way science is undertaken.’

John Taylor, DG of UK OST ‘[The Grid] intends to make access to

computing power, scientific data repositories and experimental facilities as easy as the Web makes access to information.’

Tony Blair, 2002

32

e-Science (2)

Requirements of e-Science Grid Application Projects determine services required by Grid middleware

UK Projects focus more on Grid Data Services than Teraflop/s HPC systems

33

UK UK e-Science Initiative Initiative

$180M Programme over 3 years$130M is for Grid Applications in all areas of

science and engineeringParticle Physics and Astronomy (PPARC)

Engineering and Physical Sciences (EPSRC)Biology, Medical and Environmental Science$50M ‘Core Program’ to encourage

development of generic ‘industrial strength’ Grid middleware

34

e-Science core program core program

Network of e-Science CentresUK e-Science Grid

Support for e-Science ApplicationsGrid Network IssuesGeneric/Industrial Grid Middlewaree-Health Grid ‘Grand Challenges’ Outreach/International Activities

35

UK e-Science Grid Grid

36

UK e-Science GridUK e-Science Grid

All e-Science Centres donating resources plus four JCSR funded dedicated compute/data clusters– Supercomputers, clusters, storage, facilities

All Centres run same Grid Software– Starting point is Globus 2 and Condor: Storage Resource Broker (SRB) being evaluated

37

Some UK e-Science Projects (1)Some UK e-Science Projects (1)

Climateprediction.com (NERC)

Oceanographic Grid (NERC) Molecular Environmental

Grid (NERC) NERC DataGrid (NERC +

OST-CP) Biomolecular Grid (BBSRC) Proteome Annotation

Pipeline (BBSRC) High-Throughput Structural

Biology (BBSRC) Global Biodiversity (BBSRC)

GRIDPP (PPARC) ASTROGRID (PPARC) Comb-e-Chem (EPSRC) DAME (EPSRC) DiscoveryNet (EPSRC) GEODISE (EPSRC) myGrid (EPSRC) RealityGrid (EPSRC)

38

Some UK e-Science Projects (2)Some UK e-Science Projects (2)

Biology of Ageing (BBSRC + MRC)

Sequence and Structure Data (MRC)

Molecular Genetics (MRC) Cancer Management

(MRC + PPARC) Clinical e-Science

Framework (MRC) Neuroinformatics Modeling

Tools (MRC)

Interdisciplinary Research Collaborations ‘Grand Challenge’◦ Advanced Knowledge

Technologies◦ Meical Images and Signals◦ Equator◦ DIRC (Dependability

39

Support for e-Science ProjectsSupport for e-Science Projects

Grid Support Centre in operation◦ supported Grid middleware & users◦ see www.grid-support.ac.uk

National e-Science Institute ◦ Research Seminars◦ Training Programme ◦ See www.nesc.ac.uk

National Certificate Authority◦ Issue digital certificates for projects◦ Goal is ‘single sign-on'

40

myGrid projectmyGrid project

41

myGrid (1)myGrid (1)

The goal is to design, develop and demonstrate higher level functionalities over an existing Grid infrastructure

An e-science research projectDevelop open source high-level service-base

middleware Using database and computation analysisThe project is pioneering the use of semantic

web technology, to manage annotation, ontologies and sematic discovery

42

myGrid (2)

The ultimate is to supply collection of services as a toolkit to build end applications.

43

Outline

1. Introduction

2. myGrid Services and Architecture • Tools• Forming and executing experiments• Semantic service• Supporting the e-science scientific method• Applications and application services

3. myGrid workbench

44

myGrid service and architecture (1)myGrid service and architecture (1)

• The myGrid middleware framwork employs service-base

• Firstly prototype with web service but with an anticipated migration to the OGSA

• The primary services to support routine in silico experiments fall into fours categories: Services that are the tools that will contitute the

experiments Service for forming and executing experiments Semantic services Service for supporting the e-science scientific

method

45


46

Tools (1)Tools (1)

• Development of domain services that can deliver data and computation analysis

• To access bioinformatices tools and data• Bioinformatics service

Retrieval database and analysis tools EMBOSS application suite of over eight

analysis tools: MEDLINE, SRS, OMIM, NCBI and WU BLAST sequence alignment tools, …

Soaplab, connector for command line based system and provides a universal glue to web service

47

Tools (2)Tools (2)

Text extraction services AMBIT is system for Acquiring Medical and

Biological Information AMBIT provides an information extraction service

based on natural language processing

48

myGrid service and architecture myGrid service and architecture

49

Forming & executing experiments (1)Forming & executing experiments (1)

FreeFluo workflow enactment engine Can handle WSDL based web service invocation Supporting two XML workflow language: IBM’s web

service flow language and Xscufl

OGSA distributed query processor Distributed query processing Query language initiate OQL The initial prototype is to be release in

August 2003

50


myGrid information repository An information model tailored to e-science Include experiment data and provenance

records of its origin Store workflow specifications, information

about person and project Metadata storageo Annotations are stored in an RDF triple, such as The Jena

Semantic Web Toolkito Annotation is a key tool used to link related objects

51


myGrid information repository An organisation have a single mIR OGSA-DAI service supports to access repository

local and remote The first version of mIR has been built over the

relational database product DB2 primarily The second extras a federated architecture, using

mediator and extensive use of annotation and shared identifiers

52


53

discovery & metadata management (1)discovery & metadata management (1)

Registries and registry views Service descriptions are centrally published To extend the idea of a registry in three way:oPersonalised views over distributed registriesoExtensible metadata storageo Addition semantic descriptionso DAML+OIL semantic descriptiono Semantic description of workflow has been

used to discover revelant workflows

54


Discovery components To enable more sophisticated semantic

discovery Indexing and searches over DAML+OIL A service browser module with the

workbenchAnnotation components

myGrid is using semantic web annotation tools

55


Ontology services To provide a single

point of reference for concepts and to support description logic reasoning of concept expressions

DAML+OIL

56


57

Service for supporting e-science (1)Service for supporting e-science (1)

Notification services When new or update data analytical

software become available A notification service to mediate an

asynchronous interaction between services Servers may register type of notification

events Be used to automatically trigger workflow Be defined with ontological descriptions in

metadata

58


Provenance management Provence information is used to determine

whether a notification service needs to be re-run

Freefluo generates provenanece logs in the form of xml file which is stored in mIR

Provenance attributes: start time, end time and attribute service instance

59


Personalisation opportunities Difference users can be provided with

appropriate views of the mIR the registry view gives a user perspective

over the services

60


Ontology services To provide a single

point of reference for concepts and to support description logic reasoning of concept expressions

DAML+OIL

61

Applications and application servicesApplications and application services

Applications can interact with services directly or via a Gateway

The Gateway provides an optional unified single point of programmatic access to the whole system

To create client software

62

Outline Outline

1. Introduction

2. myGrid Services and Architecture• Tools• Forming and executing experiments• Semantic service• Supporting the e-science scientific method• Applications and application services

3. myGrid workbench

63

myGrid workbenchmyGrid workbench

NetBean platform and JAVAGraves Disease is caused by an

autoimmune response against the thyroid, causing hyperthyroidism

64

Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (1)Autoimmune disease of the thyroid (1)

65


As soon as the identity of the relevant genes is known the myGrid workbench is used to run workflows that gather information about those genes, help design new molecular biology experiments to focus on the genes of interest, and to predict the 3D structure of the protein products of the genes

67


68


69

Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (5)Autoimmune disease of the thyroid (5)(1) The notification service informs the

user via a notification client in the workbench that new data has been added to the mIR which can be browsed in the workBench (2)

In this case it is the identity of a new gene with changed expression in Graves’ Disease

70

Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (6)Autoimmune disease of the thyroid (6)(3) The user can then discover workflows via a

wizard in the workbench The wizard itself makes use of a semantic find

service, which finds relevant services and workflows in the myGrid registry using description logic reasoning over associated semantic descriptions

A registry browser is also available in the workbench to allow the user to browse more freely for a workflow or service using a hierarchical categorisation based on each individual semantic description (4)

71


If an appropriate workflow does not exist, a new one can be created in the Taverna editor (5)

The workflow and associated data are submitted to the FreeFluo enactor

The enactor provides a detailed provenance record stored in the mIR describing what was done, with what services and when. This can also be viewed within the workbench (6)

THANK YOU FOR YOUR ATTENTIONTHANK YOU FOR YOUR ATTENTION

Semantic Grid Group Members: Phạm Đức Đệ Võ Bảo Hùng Hồ Phương.

Documents

Transcript of Semantic Grid Group Members: Phạm Đức Đệ Võ Bảo Hùng Hồ Phương.