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David De RoureUniversity of Southampton
The Story of the Semantic Grid
OGF Semantic Grid Research Group
www.semanticgrid.org
WWWFG Singapore 2007 04/12/2023 | | Slide 2
1. The search for the missing link • Data• Services• Collaboration
Overview
2. Evolution of the Web
WWWFG Singapore 2007 04/12/2023 | | Slide 3
The Semantic Grid Report 2001
John Taylor
There are a number of grid applications being developed and there is a whole raft of computer technologies that provide fragments of the necessary functionality. However there is currently a major gap between these endeavours and the vision of e-Science in which there is a high degree of easy-to-use and seamless automation and in which there are flexible collaborations and computations on a global scale.
Us
e-Science is about global collaboration in key areas of science and the next generation of infrastructure that will enable it
WWWFG Singapore 2007
Missing Link
Grid Infrastructure04/12/2023 | | Slide 4
ScientistsNeed something here
WWWFG Singapore 2007
Why Semantic Web?
Huge potential for Science– making data reusable,
interlinked– making connections
between decoupled content
– generating new intelligence Automation requires machine-
processable descriptions Grid community talking about
metadata and knowledge
04/12/2023 | | Slide 5
Grid Computing
The Semantic
Web
The Semantic
Grid
Web Services
WWWFG Singapore 2007 04/12/2023 | | Slide 6
Building bridges
RDF…RDF…RDF…
WWWFG Singapore 2007 04/12/2023 | | Slide 8
Semantic Grid = Grid + Semantic Web for e-Science
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
WWWFG Singapore 2007 04/12/2023 | | Slide 9
Semantic Grid
The Semantic Web is an extension of the current Web in which information and services are given well-defined meaning, better enabling computers and people to work in cooperation www.semanticgrid.org
Grid
Grid
Free the data!Free the services!
WWWFG Singapore 2007 04/12/2023 | | Slide 10
My Chemistry Experiment
Box of Chemists
WWWFG Singapore 2007 26/2/2007 | myExperiment | Slide 11
X-Raye-Lab
Analysis
Properties
Propertiese-Lab
SimulationVideo
Diff
ract
omet
er
Grid Middleware
StructuresDatabase
CombeChem pilot project
www.combechem.org
Learning & Teaching workflows
Research & e-Science workflows
Aggregator services: national, commercial
Repositories : institutional, e-prints, subject, data, learning objects
Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules
Harvestingmetadata
Data creation / capture / gathering: laboratory experiments, Grids, fieldwork, surveys, media
Resource discovery, linking, embedding
Deposit / self-archiving
Peer-reviewed publications: journals, conference proceedings
Publication
Validation
Data analysis, transformation, mining, modelling
Resource discovery, linking, embedding
Deposit / self-archiving
Learning object creation, re-use
Searching , harvesting, embedding
Quality assurance bodies
Validation
Presentation services: subject, media-specific, data, commercial portals
Resource discovery, linking, embedding
The scholarly knowledge cycle.
Liz Lyon, Ariadne, July 2003.
This work is licensed under a Creative Commons LicenseAttribution-ShareAlike 2.0
© Liz Lyon (UKOLN, University of Bath), 2003
Reducing Time-to-Discovery by Reducing Time-to-Experiment
WWWFG Singapore 2007 04/12/2023 | | Slide 13
The key observation!
“Publication at Source” describes the need to capture data and its context from the outset and maintain a complete end-to-end connection between the laboratory bench and the intellectual chemical knowledge that is published as a result of the investigation
e-Science = Record and Reuse. Reuse needs provenance
The details of the origins of data are just as important to understanding as their actual values
WWWFG Singapore 2007 26/2/2007 | myExperiment | Slide 14
WWWFG Singapore 2007 26/2/2007 | myExperiment | Slide 15
1 1 2 2 1 3 1 4
Sample of 4-flourinatedbiphenyl
Add CoolReflux
Butanone Sample ofK2CO3Powder
Weigh
grammes0.9031
Measure
40 ml
Add
Weigh
2.0719 g
text
3 5
Add
g
Sample ofBr11OCB
2 6
Reflux
2 7
Cool
Water
Measure
30 ml
9
Liquid-liquid
extraction
DCM
Measure
3 of 40 ml
10
Dry
MgSO4
11
Filter(Buchner)
12
RemoveSolvent
by RotaryEvaporation
13
Fuse
Silica
14
ColumnChromatography
Ether/PetrolRatio
Butanone dried via silica column andmeasured into 100ml RB flask.
Used 1ml extra solvent to wash outcontainer.
Started reflux at 13.30. (Had tochange heater stirrer) Only reflux
for 45min, next step 14:15.
Inorganics dissolve 2layers. Added brine
~20ml.
Organics are yellowsolution
Washed MgSO4 withDCM ~ 50ml
Measure
excess
Observation Types
weight - grammes
measure - ml, drops
annotate - text
temperature - K, °C
Key
Process
Input
Literal
Observation
Add CoolRefluxAddAdd Reflux Cool Dry Filter Remove
Solventby Rotary
Evaporation
Fuse ColumnChromatography
Dissolve 4-flourinatedbiphenyl inbutanone
Add K2CO3powder
Heat at refluxfor 1.5 hours
Cool and addBr11OCB
Heat atreflux untilcompletion
Cool and addwater (30ml)
Combine organics,dry over MgSO4 &filter
Removesolvent invacuo
Liquid-liquid
extraction
Extract withDCM(3x40ml)
Fuse compound to silica &column in ether/petrol
4 8
Add
Add
text
Annotate
Annotate
text
Weigh
Annotate
g
Annotate Annotate
text text
Future Questions
Whether to have many subclasses of processes or fewer with annotations
How to depict destructive processes
How to depict taking lots of samples
What is the observation/process boundary? e.g. MRI scan
1.5918
Combechem
30 January 2004gvh, hrm, gms
Ingredient List
Fluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml
image
To D
oLis
tP
lan
Pro
cess
Record
The RDF Graph
WWWFG Singapore 2007 26/2/2007 | myExperiment | Slide 16
WWWFG Singapore 2007
CombeChem Principles
It’s a Semantic DataGrid
Think Holistic – we’re working in the context of the Scholarly Knowledge Cycle
In the Wild – Integrating 3rd party data sources
Power of Provenance
Publish don’t warehouse
Users add value
A little Semantics goes a long way
04/12/2023 | | Slide 17
WWWFG Singapore 2007 26/2/2007 | myExperiment | Slide 18Taverna Workflow Workbench
WWWFG Singapore 2007
myGrid Principles
Reuse, reuse and reuse
In the Wild – Integrating 3rd party services
Power of Provenance
Users add value
A little Semantics goes a long way
04/12/2023 | | Slide 19
Open – services “Come As You Are”. Your desktop app. Spectrum of Capability Appropriate abstractions. Different user and machine viewpoints.
Customise rather than be too Generic. Act local, think global. Specific solutions are widely applicable.
Cooperate. Get Users to Add Value. Jam Today and more / better Jam Tomorrow. Just Enough. Preferably, Just In Time. Understand the rewards system of stakeholders.
WWWFG Singapore 2007 23/3/2007 | Semantic Web in e-Science | Slide 20
agentslogic
grids
semantic web
grids
semantic web
applications
applications
hybrid
p2p
hybrid
GGF5 Semantic Grid BOFEdinburgh, July 2002
GGF9 Semantic Grid WorkshopChicago, October 2003
GGF11 Semantic Grid Applications WorkshopHawaii, June 2004
Dagstuhl SeminarJuly 2005
GGF16 3rd GGF Semantic Grid WorkshopAthens, February 2006
OGF19 Web 2.0 and the Grid WorkshopNorth Carolina, January 2007
WWWFG Singapore 2007 21
Wave 2 – start 2006
Degree
DataminingGrid
data, knowledge, semantics
OntoGrid
InteliGridK-WF Grid
Chemomen tum
A-Ware Sorma
platforms, user environments
CoreGRIDvirtual laboratories
UniGrids HPC4U
g-Eclipse
Gredia
GridComp
QosCosGrid
Grid4all
Provenance
AssessGridGridTrust
trust, security
Grid services, business models
ArguGrid Edutain@ Grid
GridEconGridCoord
Nessi-GridChallengers
NextGRIDservice
architecture
Akogrimomobile services
BREINagents & semantics
BeinGridbusiness
experiments
supporting the Grid community
SIMDATindustrial
simulations
XtreemOS
Linux based Grid
operating system
BeinGridbusiness
experiments
KnowArc
EC-GinBridge
Grid@Asia EchoGrid
international cooperation
Specific support action
Integrated project
Network of excellence
Specific targeted research projectWave 1 – start 2004
EU Funding: 130 M€
Grid Research Projects under FP6
WWWFG Singapore 2007
Grid Ontology
Semantic OGSA
• Semantic Grid Reference Architecture
• A low-impact extension of OGSA
• Everything is OGSA compliant
• Mixed ecosystem of Grid and Semantic Grid services
• Services ignorant of bindings
• Services binding aware but unable to process them
• Services binding aware and capable of processing
23
Optimization
Execution Management
Resourcemanagement
Data
Security
Information Management
Infrastructure Services
Application 1 Application N
Semantic Services
WWWFG Singapore 2007
A utility is a directly and immediately useable service with established functionality, performance and dependability, illustrating the emphasis on user needs and issues such as trust
Services are knowledge-assisted (‘semantic’) to facilitate automation and advanced functionality, the knowledge aspect reinforced by the emphasis on delivering high level services to the user
Service-Oriented Knowledge UtilityNGG3
The architecture comprises services which may be instantiated and assembled dynamically, hence the structure, behaviour and location of software is changing at run-time
WWWFG Singapore 2007 04/12/2023 | | Slide 26
Transformative Application - to
enhance discovery & learning
R&D to enhance technical and social dimensions of future CI
systems
Provisioning -Creation,
deployment and operation of advanced CI
Dan Atkins
WWWFG Singapore 2007 04/12/2023 | | Slide 29
Key collective activities in e-science
interpretation of data/events
following through decisions/coordinating activities
producing documents& other artifacts
archiving/recovering information
informal and formalcommunication
meetings
http://www.aktors.org/coakting/
WWWFG Singapore 2007 04/12/2023 | | Slide 30
How can we weave together distributed discourse and documents?
Add notational and hypermedia structure to discussions & documents
Add notational and hypermedia structure to discussions & documents
Add indices to events in meetings so the meetings themselves become indexed documents
Add indices to events in meetings so the meetings themselves become indexed documents
Make meetings persistent and replayable
Make meetings persistent and replayable
Mike Daw
WWWFG Singapore 2007 November 2005SNAC 31
Images from NASA
WWWFG Singapore 2007 November 2005SNAC 32
Images from NASA
WWWFG Singapore 2007
WorkflowExecution
And MonitoringInstrument
TrackingAnd utilisation
Resource+ Floor
Management
Run-time tracking and control
ActionRealisation+ RationaleFeedback
Comb-e-Chem: Facility e-Science in Action
PresenceAwareness + Remote
Participation
WWWFG Singapore 2007 04/12/2023 | | Slide 34
Workshop 1: Kyra Norman and Orchestra Cube
Angela Piccini
performativity, place, space
WWWFG Singapore 2007
The Collaborative Semantic Grid, CTS 2006
WWWFG Singapore 2007
Collaboration Principles
e-Science as sense-making
Supporting formal and informal scientific process
Collaboration over artefacts
Scaling up from project to community
04/12/2023 | | Slide 37
WWWFG Singapore 2007 04/12/2023 | | Slide 39
Evolution
Time
WWWFG Singapore 2007 04/12/2023 | | Slide 40
Joint Information Systems Committee 04/12/2023 | | Slide 41
Geoffrey Fox
WWWFG Singapore 2007
Web 2.0 Design Patterns
http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html
26/2/2007 | myExperiment | Slide 42
1. The Long Tail
2. Data is the Next Intel Inside
3. Users Add Value
4. Network Effects by Default
5. Some Rights Reserved
6. The Perpetual Beta
7. Cooperate, Don't Control
8. Software Above the Level of a Single Device
04/12/2023 | | Slide 43
Too sophisticated for its own good?
WWWFG Singapore 2007 04/12/2023 | | Slide 45
Overengineering of standards
Assumption that users will come
Divorces computation from content provision
Service provider mentality
– users seen as consumers not producers
So it’s a long haul
When Grids go bad
WWWFG Singapore 2007 04/12/2023 | | Slide 46
The Grid Problem
The Web 2.0 community decided Web Services are too complicated so they use HTTP instead.
The Grid community decided Web Services aren’t complicated enough so they invented OGSA.
S M NTICW B CLUB
You are a member of the
WWWFG Singapore 2007
Missing Link
Grid Infrastructure04/12/2023 | | Slide 49
ScientistsReally simple interfaces to computation,
storage, content and annotation
WWWFG Singapore 2007 04/12/2023 | | Slide 53
Semantic Grid – metadata management and automation through annotation
The Grid community can learn from Web 2.0 in terms of how developers and users engage with the new capabilities
– simplicity of interface for developers
– bring new functionality to the users rather than expecting them to come to it
– Web 2.0 is compatible with Grid in that it requires robust services underlying it
If we were writing the report now...Semantic Grid 2.0 ?!
Messages
WWWFG Singapore 2007 04/12/2023 | | Slide 54
semanticgrid.org
David De Roure
Carole Goble
Geoffrey Fox
Marlon Pierce
Semantic Grid Research Group
See the Call for Participation for the OGF21 Grid and Web 2.0 WorkshopOGF21 Seattle, October 15-19, 2007
WWWFG Singapore 2007 04/12/2023 | | Slide 55
Credits, Links and Contacts
Slides
– Stephen Downie
– Liz Lyon
– Geoffrey Fox
– Jeremy Frey
– Carole Goble
– Angela Piccini
David De Roure
Carole Goble