Semantic Semantic Grid Grid Group Members: Phạm Đức Đệ Võ Bảo Hùng Hồ Phương
Jan 19, 2016
Semantic GridSemantic Grid
Group Members: Phạm Đức Đệ Võ Bảo Hùng Hồ Phương
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Outline
IntroductionSemantic WebS-OGSAImplementation ( e-Science & myGrid )
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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 ?
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
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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?
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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?
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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
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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
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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
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Ontology example
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Semantic Web Architecture (1)
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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
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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:◦ 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.
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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
Capabilities Mechanisms
provide/consume
expose
use
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S-OGSA Model
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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
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METADATAas SemanticAnnotations
S-OGSA Model Example
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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
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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
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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-OGSA-
KnowledgeEntity◦ S-OGSA-SemanticBinding:Semantic Binding, the
association between a Grid Entity (CIM-ManagedElement) and a Knowledge Entity (S-OGSA-KnowledgeEntity)
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S-OGSA Mechanisms
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Lifetime
State/properties/metadata access port
. . . MetadataService
OntologyService
Service
Resource
MetadataSeekingClient
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1
2
Semantic Binding Ids Retrieval Request
Semantic Binding Ids
Metadata Retrieval/Query Request
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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
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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 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
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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
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UK e-Science Grid Grid
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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
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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)
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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
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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'
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myGrid projectmyGrid project
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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
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myGrid (2)
The ultimate is to supply collection of services as a toolkit to build end applications.
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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
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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
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myGrid service and architecture (2)myGrid service and architecture (2)
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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
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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
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myGrid service and architecture myGrid service and architecture
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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
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Forming & executing experiments (2)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 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
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Forming & executing experiments (3)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)myGrid service and architecture (2)
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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
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discovery & metadata management (2)discovery & metadata management (2)
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
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discovery & metadata management (3)discovery & metadata management (3)
Ontology services To provide a single
point of reference for concepts and to support description logic reasoning of concept expressions
DAML+OIL
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myGrid service and architecture (2)myGrid service and architecture (2)
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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
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Service for supporting e-science (2)Service for supporting e-science (2)
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
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Service for supporting e-science (3)Service for supporting e-science (3)
Personalisation opportunities Difference users can be provided with
appropriate views of the mIR the registry view gives a user perspective
over the services
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discovery & metadata management (3)discovery & metadata management (3)
Ontology services To provide a single
point of reference for concepts and to support description logic reasoning of concept expressions
DAML+OIL
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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
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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
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myGrid workbenchmyGrid workbench
NetBean platform and JAVAGraves Disease is caused by an
autoimmune response against the thyroid, causing hyperthyroidism
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Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (1)Autoimmune disease of the thyroid (1)
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Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (2)Autoimmune disease of the thyroid (2)
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 DiseaseGraves DiseaseAutoimmune disease of the thyroid (3)Autoimmune disease of the thyroid (3)
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Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (4)Autoimmune disease of the thyroid (4)
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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
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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)
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Graves DiseaseGraves DiseaseAutoimmune disease of the thyroid (7)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)
THANK YOU FOR YOUR ATTENTIONTHANK YOU FOR YOUR ATTENTION