National e-Science Centre, Edinburgh 27/11/06 (Ontology-based) Metadata: What is it, Where and How...

National e-Science Centre, Edinburgh 27/11/06

(Ontology-based) Metadata: What is it,

Where and How can we use it, and How can we share it?

www.ontogrid.eu

Oscar CorchoUniversity of Manchester

[email protected]

Free text and tags also allowed

Controlled and systematicmanagement

And many other Wh-questions

2Edinburgh, 27 November 2006

Outline

Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge (Reasoning) Web

Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use

Ongoing work Conclusions


Organisation

News

Research

Grant Application

Videocast

Events

Gene Database

Annotation assert facts using terms (metadata in RDF)Represent terms and their relationships (ontology in RDFS/OWL)


Types of vocabularies. Formality

Lassila O, McGuiness D. The Role of Frame-Based Representation on the Semantic Web. Technical Report. Knowledge Systems Laboratory. Stanford University. KSL-01-02. 2001.

BIRNLex GO GALENAdd your vocabularies here


Metadata annotation

Different types of annotation depending on the type of vocabulary used

Based on Dublin CoreThe contributor and creator is the flight booking service “www.flightbookings.com”.The date would be January 1st, 2003, in case that the HTML page has been generated on that specific date.The description would be something like “flight details for a travel between Madrid and Seattle via Chicago on February 8th, 2004”.The document format is “HTML”.The document language is “en”, which stands for English

Based on thesauriMadrid is a reference to the term with ID 7010413 in the thesaurus, which refers to the city of Madrid in Spain.Spain is a reference to the term with ID 1000095, which refers to the kingdom of Spain in Europe.Chicago is a reference to the term with ID 7013596, which refers to the city of Chicago in Illinois, US.United States of America is a reference to the term “United States” with ID 7012149, which refers to the US nation.Seattle is a reference to the term with ID 7014494, which refers to the city of Seattle in Washington, US.

Based on ontologiesConcept instances relate a part of the document to one or several concepts in an ontology. For example, “Flight details” may represent an instance of the concept Flight, and can be named as AA7615_Feb08_2003, although concept instances do not necessarily have a name.Attribute values relate a concept instance with part of the document, which is the value of one of its attributes. For example, “American Airlines” can be the value of the attribute companyName.Relation instances that relate two concept instances by some domain-specific relation. For example, the flight AA7615_Feb08_2003 and the location Madrid can be connected by the relation departurePlace

Ontology-based document annotation: trends and open research problems. Corcho, O. International Journal of Metadata, Semantics and Ontologies 1(1):47-57. 2006


Outline

Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge Web




Data mining

Knowledge Discovery

Smart search

Social networking

Smart portals

Agents

Information Integration and aggregation

Integration use a uniform common model in RDFConnecting through shared terms and shared instancesPreserving context and provenance

D2RR2OBIRN Mediator


urn:data:f2urn:data:f2

urn:data1urn:data1

urn:data2urn:data2

urn:compareinvocation3urn:compareinvocation3

urn:data12urn:data12

Blast_report

[input]

[output]

[input]

[distantlyDerivedFrom]

SwissProt_seq[instanceOf]

Sequence_hit

[hasHits]

urn:hit2….urn:hit2….

urn:hit1…urn:hit1…

urn:hit50…..

urn:hit50…..

[instanceOf]

[similar_sequence_to]

Data generated by services/workflows

Concepts

[ ]

[performsTask]

Find similar sequence[contains]

Services

urn:data:3urn:data:3

urn:hit8….urn:hit8….

urn:hit5…urn:hit5…

urn:hit10…..

urn:hit10…..

[contains]

[instanceOf]

urn:BlastNInvocation3urn:BlastNInvocation3

urn:invocation5urn:invocation5urn:data:f1urn:data:f1[output]

New sequenceMissed sequence

[hasName][hasName]

literalsDatumCollection

[type]

LSDatum

[type]Properties

[instanceOf]

[output]

[output]

[directlyDerivedFrom]

Resource Description Framework


Metadata Matters

Flexible and extensible self describing schemas that don’t have to be nailed down “Lets describe my data set, or the output format of my tool, that

changes all the time” Open world

“I need to comment on that experiment” “That fact is now incorrect because …”

Data fusion across different data modelscross linked by shared instances and shared concepts

Global naming schemeE.g. LSID: Life Science Identifiers


Don’t Prescribe, Describe!!

The tyranny of the table •The tyranny of the tree

“Not everything fits in onetaxonomy” -- Maryanne Martone (US BIRN)


Seamark Demo:

ID new drug candidates for

BRKCB-1

GO2Keyword.rdf

UniProt.rdf

GO.rdf

Keywords.rdf

Taxonomy.rdfPubMed.xml

Citation

IntAct.rdf

Organism

Enzymes.rdf

OMIM.rdf

GO2OMIM.rdf

GO2Enzyme.rdf

MIM Id

KEGG.rdf

KeywordGO2UniProt.rdf

Protein

Enzyme

ProbeSet.rdf

Gene

Probe

Pathway

Compound

Courtesy Joanne Luciano


RDF for Proteomic Standards

http://www.naturebiotechnology.org


Outline

Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data WebSemantic Knowledge (Reasoning) Web



14Edinburgh, 27 November 2006James Hendler Science and the Semantic Web Science 299: 520-521, 2003

Rearrangement of a DNA sequence homologous to a cell-virus junction fragment in several Moloney murine leukemia virus-induced rat thymomas

8q24PVT1

Inference Logic-based classification and validity checking using OWLRules using SWRL (Semantic Web Rule Language)RDF queries Just making connections because so much stuff is connected!


In summary

OWL

Integration

RDF(S)

RDF

XML

Annotation

Integration

Inference

SWRL

Extensible metadata schemas that you don’t have to nail down

Controlled vocabularies

Data fusion

Expressive models

Model fusion


Outline





EU-STREP Project OntoGrid

Middleware for the Semantic GridP2P Metadata Storage & Querying

(Atlas).Ontology Access: WS-DAIOnt-

RDF(S)Annotation:

• Data and provenanceKnowledge Parser

• ServicesODE-SGS

Business process monitoringNegotiation Coordination

Applications Insurance SettlementSatellite Image Quality

Analysis

SEMANTIC OGSACapabilites & Behaviors for

Semantic GridsPrincipled way of realization

Disclaimer: Talking about Grid does not necessarily mean High Performance Computing and Parallelisation, but mainly management of distributed systems


S-OGSA

Semantic-OGSA (S-OGSA) is...Our proposed Semantic Grid reference architectureA low-impact extension of OGSA

• Mixed ecosystem of Grid and Semantic Grid servicesServices ignorant of semanticsServices aware of semantics but unable to process themServices aware of semantics and able to process (part of) them

• Everything is OGSA compliant

Defined by • Information model

New entities

• CapabilitesNew functionalities

• Mechanisms How it is delivered

Model

Capabilities Mechanisms

provide/consume

expose

use


METADATAas SemanticAnnotations

S-OGSA Model


S-OGSA Model: Metadata is a first-class resource

Benefits of treating Metadata as a first-class resource:-- Clear AuthZ mechanisms-- Clear lifetime-- Metadata can be also distributed-- ...


Optimization

Execution Management

Resourcemanagement

Data

Security

Information Management

Infrastructure Services

Application 1 Application N

OG

SA

Sem

antic

-OG

SA

Semantic Services

S-OGSA Capabilities: From OGSA to S-OGSA


Optimization

Execution Management

Resourcemanagement

Data

Security

Information Management

Infrastructure Services

Application 1 Application N

OG

SA

Sem

antic

-OG

SA

Semantic Services

S-OGSA Capabilities: From OGSA to S-OGSA

Ontology

ReasoningKno

wle

dge

Metadata

Annotation

Sem

antic

bin

ding

Semantic Provisioning Services


S-OGSA Patterns. Semantic Aware and Capable Service

Deployed in Globus Toolkit 4

Lifetime

MetadataService

Service

ResourceMetadataSeekingClient

Properties

Others…

Access/Query Semantic Bindings1Semantics

1.1

Farm out request

Semantic aware interface

OntologyService


S-OGSA Scenario. Satellite Image Quality Analysis

Scenes: Routine operations Metadata generation Report retrieving

Satellite Routine Operations

Satellite LifeCycle: Launch and Early Orbit

Phase (~ 3 days) Calibration and Validation

campaign (~ 6-9 months) Routine operations (~ 5-9

years) Satellite de-orbiting.

Product processing continues


Outline





S-OGSA Metadata Access/Management Protocols

SB Factory

Client

Semantic Binding

Metadata Query

SBSB

SB

create

Query w/o Inference, UpdateContent

Query( over unified view)

WS-RP: Get/Set/Query Properties

WS-Addressing: epr

RDFRDF

create

query

Inspect-props . . .

query

Semantic Binding Service Suite

WS-RL: Destroy , SetTerminationTime

WS-RL ++: archive

WS-Notif: Subscribe / Notify


S-OGSA Metadata Lifecycle

Metadata is normally in stable situation

If the entity it refers to or the knowledge entity it uses change, then it may move to a stale situationChecks neededPossibly reannotation

Metadata can be archived or deleted from the system

Stable

Stale

GEchanged

KEchanged

Archived Deleted

“Periodically, we will have to reannotate everything” -- Maryanne Martone (US BIRN)


Data Integration

Information integration from gLite and GT4 information servicesBDIIRGMAMDS

Trade-off between...Continuous update or on-

demand access, fresh information

Consolidated data but possibly non-fresh information


Outline





Conclusions

Metadata can be used for many purposesSimply for the sake of annotation

• Reuse and sharing Look at the Web 2.0 successFor integration

• Open and flexible schemas. Describe, not prescribeFor reasoning

• Complex applications

S-OGSA Metadata as a first-class citizen Semantic BindingSemantic Binding Service already available for use

• Robust metadata management• Distributed

Metadata lifecycle


Access to S-OGSA

PublicationsAn overview of S-OGSA: a Reference Semantic Grid

Architecture. Corcho O, Alper P, Kotsiopoulos I, Missier P, Bechhofer S, Goble C. Journal of Web Semantics 4(2):102-115. June 2006

Source code http://www.ontogrid.net/, For Downloading DistributionsAccess to CVS

Connection type: pserveruser: ontogridpassword: not neededHost: rpc262.cs.man.ac.ukPort: 2401Repository path: /local/ontogrid/cvsrootmodule: prototype


Questions

Thank you for your attention!

Questions?

Acknowledgements Carole Goble OntoGrid team members at Manchester

• Pinar Alper, Ioannis Kotsiopoulos, Sean Bechoffer, Ian Dunlop, Wei Xing

OntoGrid Consortium

National e-Science Centre, Edinburgh 27/11/06

(Ontology-based) Metadata: What is it,

Where and How can we use it, and How can we share it?

www.ontogrid.eu

Oscar CorchoUniversity of Manchester

[email protected]

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National e-Science Centre, Edinburgh 27/11/06 (Ontology-based) Metadata: What is it, Where and How...

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