The Story of the Semantic Grid

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


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


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


Building bridges

RDF…RDF…RDF…


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


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!


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


Deposit / self-archiving

Learning object creation, re-use

Searching , harvesting, embedding

Quality assurance bodies

Validation

Presentation services: subject, media-specific, data, commercial portals


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

http://creativecommons.org/licenses/by-sa/2.0/


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



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



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


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


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


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


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


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/


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


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


Workshop 1: Kyra Norman and Orchestra Cube

Angela Piccini

performativity, place, space


The Collaborative Semantic Grid, CTS 2006


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


Evolution

Time


Joint Information Systems Committee 04/12/2023 | | Slide 41

Geoffrey Fox


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?


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


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


Missing Link

Grid Infrastructure04/12/2023 | | Slide 49

ScientistsReally simple interfaces to computation,

storage, content and annotation


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


semanticgrid.org

David De Roure

[email protected]

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


Credits, Links and Contacts

Slides

– Stephen Downie

– Liz Lyon

– Geoffrey Fox

– Jeremy Frey

– Carole Goble

– Angela Piccini

David De Roure

[email protected]

Carole Goble

[email protected]

Documents

The Story of the Semantic Grid