Ontology and Ontology Libraries: a Critical Study

Indian Statistical Institute Documentation Research and Training Centre

Seminar (2) MSLIS 2012-2014

Outline

• Introduction and Overview• Languages for expressing Ontologies• Tools for building Ontologies• Ontology Libraries• Evaluation criteria• Transitions to the future

What is Ontology?

• The term "ontology" can be defined as an explicit specification of conceptualization.

1. Ontology is a term in philosophy and its meaning is ``theory

of existence''.

2. Ontology is a body of knowledge describing some domain.

Ontology-Definition

Ontologies to capture human knowledge based on common sense.

- Lenat y Guha (1990)

Source: http://www.emiliosanfilippo.it/wp-content/uploads/2011/11/Ontology-3.jpg

How are Ontologies currently being used to Librarians?

• Standardize vocabulary.• Provide better routes.• Provide better search.

Source: http://gonereading.com/newshop/wpcontent/uploads/2012/01/Librarian-Gift-446x446.png

Languages for Expressing Ontologies

XML RDF RDF Schema OWL

Tools for Building ontology

• The are many Ontology tools are available in the present times such as Protégé, OntoEdit, Ontolingua, OilEd, pOWL etc.

Source: http://www.colourbox.com/preview/2456889-245207-three-3d-people-with-the-tools-in-the-hands-of.jpg

Protégé

• Free, open source• Web client and format• Strong community

Source: http://www.racer-systems.com/img//logo/protege.gif

Ontology built using Protégé

Source: http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/attachment/4658809/2/jbddhbbc.png

What is Ontology Libraries (OL)?

Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies.

Source: http://semanticweb.com/files/2013/09/9685321345_afc5296f95.jpg

Need for ontology libraries

• Enables and facilitates interoperability• Well-established and well-tested ontologies• Integrates the data much more easily

(Contd.)

Need for ontology libraries

• Find and determine the domain• Ontology in specific format• Publish their ontology

Characteristics of ontology libraries

Purpose and Coverage

What is it for?

-Domain

-Intended scope

Library content

What is in it?

-Ontology and how they are collected

-Gatekeeping

-Mappings and other inter-ontology relations

-Metadata

Main function for users

What does it let you do?

-Finding, Search and evaluating ontologies

-Browsing

-Programmatic access

Other features

What else is there?

-Versioning

-Reasoning

-User management

-Notifications

What OL offers!!

Ontology library systems o er functions for ffmanaging, adapting and standardizing groups of ontologies, for indexing content with ontologies, and for utilizing ontologies in applications.

Source: http://assets.fiercemarkets.com/public/newsletter/fiercehealthit/telehealth4.jpg

Structure of Ontology Library Systems

Source: http://origin-ars.els-cdn.com/content/image/1-s2.0-S0169023X02000411-gr4.jpg

Lists of Ontology librariesDomain General Mixed

• BioPortal• OBO Foundry• OLS• oeGov

• Cupboard• ODP• OntoSelect• OntoSearch2• Schema-Cache• TONES• SHOE

• ONKI• COLOR• Ontohub • WebOnto• DAML• IEEE Standard Upper Ontology (SUO)• MMI• SHOE

Ontology Libraries-Domain

• Biomedical- BioPortal

- OBO (Open Biological and Biomedical Ontologies ) Foundry

- OLS (Ontology Lookup Service).

• e-Government

- oeGov (Ontologies for e-Government)

Ontology Libraries-General

- Cupboard

- ODP(Ontology Design Pattern)

- OntoSelect

- OntoSearch2

- TONES(Thinking ONtologiES)

- Schema-Cache

Ontology Libraries-Mixed

• ONKI Ontology Server • COLOR (Common Logic Ontology Repository)• Ontohub • WebOnto• DAML Ontology library system• IEEE-SUO (Standard Upper Ontology)• MMI-ORR (Marine Metadata Interoperability-Ontology Registry and Repository )• SHOE (Simple HTML Ontology Extensions)

BioPortal- Biomedical

• Browse, search and visualize ontologies.• Multiple formats support• Add notes• Add review• NCBO annotator• NCBO Resource Index

Source: http://ontolog.cim3.net/file/work/OOR/OOR-Logo/OOR-Logo-candidates/BioPortal-1.jpg

Where can I access the BioPortal?

oeGov- e-Government

• Distributed creation and maintenance of information• RDF/OWL formats• Semantics and controlled vocabularies• Schemas and several datasets• Blog system and review

Source: http://oegov.org/images/oegov_logo.jpg

Where can I access the oeGOV Ontologies?

TONES-General

• Browsing ontology• Empirical studies • RDF/XML format• Collection of OWL ontologies

Source: http://webont.org/owled/2007/TonesLogo.png

Where can I access the TONES?

SHOE-Mixed

• Management - Storage

- Versioning

• Adaptation - Searching

• Standardization - Language

- Upper-level ontology

Source: http://www.cs.umd.edu/projects/plus/SHOE/SHOEtitle.gif

Where can I access the SHOE?

Evaluation Criteria

1. Domain

2. Number of ontologies

3. Dynamics

4. Search metadata

5. Search within ontology

6. Browsing ontologies

7. Architecture

8. Components

9. Collection

10. Gatekeeping

11. Search across ontologies

12. Metrics

13. Comments and reviews

14.Ranking

15. Navigation criteria

16. SPARQL endpoint

17. Content available

18. Read or write

19. Intended use

20. Storage

21. Web service access

22. Accepted formats

OL

Features

BioPortal Cupboard OBOFoundry

oeGov OLS ODP Schema-Cache

Domain Biomedical General Biomedical e-Govt. Biomedical General General

No. of ontologies

270 150 86 31 79 125 157

Dynamics Growing Growing Stable Growing Stable Growing Stable

Search metadata

Yes Yes Yes Blog-based No Wiki-based No

Search within ontology

Yes, with autocomple

te

Advanced search

No No Yes, terms and terms

IDs

No Keyword-based

Browsing ontologies

Yes Yes No No Yes No Yes

Components

Protégé, LexGrid

Watson Sourceforge Wordpress OBO API MediaWiki Talis platform

Architecture

Single server

REST-based communicat

ion

CVS-based Single server

Single server

Single server

Cloud-based

Transitions to the future

Challenges and opportunities for an ontology developer-Role of an ontology libraries in massive adoption and reuse.

-Community service as provided by ontology libraies through appropriate endorsements.

(contd.)

Transitions to the future

Challenges and opportunities for an ontology user- Important for ontologies to be validated by a given community

- An Ontologies be considered to one particular domain, one particular format

References

1. Mathieu, d’Aquin, F. Noy, Natalya (2012). Where to publish and find ontologies? A survey of ontology libraries. Web Semantics: Science, Services and Agents on the World Wide Web, 11, 96–111

2. http://obitko.com/tutorials/ontologies-semantic-web/ontologies.html

3. Curras, E (2010), Ontologies, Taxonomies and Thesauri in system science and systematics. Great Abinton, CB: Woodhead Publishing.

4. King, Brandy . E , Reinold, Kathy (2008). Finding the concept, not just the word: a librarian’s guide to ontologies and semantics. Witney, OX: Chandos Publishing.

5. Bechhofer, S. Goble, C and Horrocks, I (2002). Requirements of Ontology Languages. IST Project IST-2000-29243 OntoWeb.

6. http://www.dur.ac.uk/p.h.shaw/teaching/ais/lectures/patricia/ais13-rdfs.pdf

References (Contd.)

7. Heflin, J , an introduction to the owl web ontology language

8. http://protege.stanford.edu/

9. http://en.wikipedia.org/wiki/Ontology_Libraries_(computer_science)

10.http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html

11. Y. Ding, D. Fensel, Ontology library systems. The key to successful ontology reuse, in: First Semantic Web Working Symposium, Stanford University, 2001, pp. 93–112.

12. http://rpc295.cs.man.ac.uk:8080/repository/13. http://semanticweb.com/oegov-open-government-through-semantic-

web-technologies_b1399014. http://oegov.org/

Thank You