Semantic Grid
Group Members:
 Phạm Đức Đệ
 Võ Bảo Hùng
 Hồ Phương
Outline
Introduction
 Semantic Web
 S-OGSA
 Implementation ( e-Science & myGrid )

1
What is Grid?

The "Grid”
◦ flexible, secure, coordinated resource sharing
among dynamic collections of individuals,
institutions, and resources - virtual organizations.
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What is the Semantic Grid ?

3
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
Why we need the Semantic Grid?

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”).
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Why we need the Semantic Grid?

Example (cont)
Apply Semantics…
- Knowledge base: “SunOS and Linux are types of
Unix operating system”
- Request: “Need the Unix compatibility OS”
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Semantic Web

Current 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
But
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Machine can’t Understand content
Semantic Web

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
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Ontology
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

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Ontology example
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Semantic Web Architecture (1)
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Scale of
Interoperability
Semantic Grid
Semantic
Web
Semantic
Grid
Classical
Web
Classical
Grid
Scale of data and computation
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Based on an idea by Norman Paton
What is Semantic Grid
An extension of the Grid
 Rich metadata is exposed and handled
explicitly, shared, and managed via Grid
protocols

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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
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S-OGSA

A Grid usually consist of several different
services by OGSA:
◦
◦
◦
◦
◦
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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.
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.
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S-OGSA
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S-OGSA

Defined by
◦ Information model
 New entities
◦ Capabilites
 New functionalities
◦ Mechanisms
 How it is delivered
Model
provide/
consume
expose
Capabilities
Mechanisms
use
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S-OGSA Model
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S-OGSA Model
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
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
S-OGSA Model Example
METADATA
as Semantic
Annotations
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From OGSA to the S-OGSA
Application N
Optimization
Data
Semantic Provisioning
Services
Execution
Management
Resource
management
Semantic
Ontology
Provisioning
Services
Reasoning
Information
Management
Infrastructure Services
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Semantic binding
Security
Knowledge
Semantic-OGSA
OGSA
Application 1
Metadata
Annotation
S-OGSA Capabilities
Annotation
Service
Ontology
Service
Reasoning
Service
Metadata
Service
WebMDS
Is-a
Knowledge
Service
Semantic Binding
Provisioning Service
Grid Service
Is-a
Is-a
1..m
Semantic Provisioning
Service
1..m
CAS
Grid Entity
SAML
file
uses
Is-a
Ontology
Is-a
Semantic aware
Grid Service
Knowledge
Resource
1..m
0..m
0..m
Knowledge
Grid Resource
1..m
consume
produce
Rule set
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OGSA-DAI
Is-a
Is-a
Knowledge
Entity
Is-a
0..m
Semantic Binding
Semantic Grid
DFDL
file
JSDL
file
0..m
Is-a
Grid
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 .
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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
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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-OGSAKnowledgeEntity
◦ S-OGSA-SemanticBinding:Semantic Binding, the
association between a Grid Entity (CIMManagedElement) and a Knowledge Entity (SOGSA-KnowledgeEntity)
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S-OGSA Mechanisms
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Access Patterns to Grid Resource Metadata
Query/Retrieval Result
4
3
Metadata
Service
Metadata Retrieval/Query
Request
Ontology
Service
5 Obtain schema for Semantic
Bindings
Metadata
Seeking
Client
Semantic Binding Ids Retrieval Request
1
Resource
Specific
Lifetime
2
State/properties/metadata
access port
Resource
Semantic Binding Ids
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...
• Deliver Metadata pointers
through resource properties
• Zero impact on existing protocols
Service
Outline
• e-Science
• myGrid project
 Introduction
 myGrid Services và Architecture
 myGrid workbench
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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
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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
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UK e-Science Initiative
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$180M Programme over 3 years
$130M is for Grid Applications in all areas of
science and engineering
Particle 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
e-Science core program
Network of e-Science Centres
UK e-Science Grid
 Support for e-Science Applications
 Grid Network Issues
 Generic/Industrial Grid Middleware
 e-Health Grid ‘Grand Challenges’
 Outreach/International Activities

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UK e-Science Grid
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UK 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
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Some UK e-Science Projects (1)

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GRIDPP (PPARC)
ASTROGRID (PPARC)
Comb-e-Chem (EPSRC)
DAME (EPSRC)
DiscoveryNet (EPSRC)
GEODISE (EPSRC)
myGrid (EPSRC)
RealityGrid (EPSRC)

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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)
Some UK e-Science Projects (2)



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Biology of Ageing (BBSRC  Interdisciplinary Research
Collaborations ‘Grand
+ MRC)
Challenge’
Sequence and Structure
Data (MRC)
◦ Advanced Knowledge
Molecular Genetics (MRC)
Technologies
Cancer Management
◦ Meical Images and Signals
(MRC + PPARC)
◦ Equator
Clinical e-Science
◦ DIRC (Dependability
Framework (MRC)
Neuroinformatics Modeling
Tools (MRC)
Support 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'
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myGrid project
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myGrid (1)

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The goal is to design, develop and
demonstrate higher level functionalities over
an existing Grid infrastructure
An e-science research project
Develop open source high-level service-base
middleware
Using database and computation analysis
The project is pioneering the use of semantic
web technology, to manage annotation,
ontologies and sematic discovery
myGrid (2)

41
The ultimate is to supply collection of
services as a toolkit to build end
applications.
Outline
Introduction
2. myGrid Services and Architecture
1.
•
•
•
•
•
3.
42

Tools
Forming and executing experiments
Semantic service
Supporting the e-science scientific method
Applications and application services
myGrid workbench
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
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myGrid service and architecture (2)
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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
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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
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myGrid service and architecture
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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
48
Forming & executing experiments (2)

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 storage
o Annotations are stored in an RDF triple, such as The Jena
Semantic Web Toolkit
o Annotation is a key tool used to link related objects
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Forming & executing experiments (3)

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
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myGrid service and architecture (2)
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discovery & metadata management (1)

Registries and registry views
 Service descriptions are centrally published
 To extend the idea of a registry in three way:
o Personalised views over distributed registries
o Extensible metadata storage
o Addition semantic descriptions
o DAML+OIL semantic description
o Semantic description of workflow has been
used to discover revelant workflows
52
discovery & metadata management (2)

Discovery components
 To enable more sophisticated semantic
discovery
 Indexing and searches over DAML+OIL
 A service browser module with the
workbench

Annotation components
 myGrid is using semantic web annotation
tools
53
discovery & metadata management (3)

Ontology services
 To provide a single
point of reference
for concepts and to
support description
DAML+OIL
logic reasoning of
concept
expressions
54
myGrid service and architecture (2)
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Service for supporting e-science (1)

56
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
Service for supporting e-science (2)
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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
Service for supporting e-science (3)

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Personalisation opportunities
 Difference users can be provided with
appropriate views of the mIR
 the registry view gives a user perspective
over the services
discovery & metadata management (3)

Ontology services
 To provide a single
point of reference
for concepts and to
support description
DAML+OIL
logic reasoning of
concept
expressions
59
Applications 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

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Outline
Introduction
2. myGrid Services and Architecture
1.
•
•
•
•
•
3.
61
Tools
Forming and executing experiments
Semantic service
Supporting the e-science scientific method
Applications and application services
myGrid workbench

myGrid workbench
NetBean platform and JAVA
 Graves Disease is caused by an
autoimmune response against the
thyroid, causing hyperthyroidism

62
Graves Disease
Autoimmune disease of the thyroid (1)
63
Graves Disease
Autoimmune disease of the thyroid (2)

64
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
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Graves Disease
Autoimmune disease of the thyroid (3)
66
Graves Disease
Autoimmune disease of the thyroid (4)
67
Graves Disease
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

68
Graves Disease
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)

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Graves Disease
Autoimmune disease of the thyroid (7)
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)
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THANK YOU FOR YOUR ATTENTION