OWL and OBO

OWL: Web Ontology Language An overview Dr. Duncan Hull, Software engineer, EBI Chemoinformatics and Metabolism

OWL: The Web Ontology Language ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10

OWL (not WOL) Web Ontology Language Ontogenesis 25.02.10 A. A. Milne (1926) Winnie the Pooh (fictional characters who often had trouble spelling…)

ChEBI example: ontology of small molecules ,[object Object],Ontogenesis 25.02.10 is-a (subclass of) base-of is-a (subclass of) acid-of has-role ChEBI:15365

OWL is a W3C standard for expressing this: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10 (Classes) (Relations between classes)

A key feature of OWL is reasoning ,[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10

Why use OWL? ,[object Object],[object Object],[object Object],Ontogenesis 25.02.10

Why OWL? 1. Big data ,[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10

Why OWL? 2. Suite of web standards ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10 Picture via http://www.codinghorror.com/blog/archives/001145.html

Why OWL? 3. Active research area ,[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Who? Ontogenesis 25.02.10 OWL is managed by a Working Group at the W3C http://www.w3.org/2007/OWL/ A large group of people chaired by : http://web.comlab.ox.ac.uk/ian.horrocks/ http://sciencecommons.org/about/whoweare/ruttenberg/ Ian Horrocks, The University of Oxford Alan Ruttenberg, Science Commons

Who? ,[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10

When was OWL created? ,[object Object],[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10

Where does OWL fit? Ontogenesis 25.02.10 Class: ChEBI:Acetylsalicylic_acid SubClassOf: ChEBI:Salicyclic_acid, ChEBI:acid-of some ChEBI:Acetylsalicylate, ChEBI:has-role some ChEBI:anti-inflammatory_drug For humans For machines Using existing XML, RDF and OWL tools

Where does OWL fit with related technology? Ontogenesis 25.02.10 Robert Hoehndorf, What is an ontology? ,[object Object],[object Object],[object Object],Life Scientists vs. Computer Scientists communities have different languages and goals

Ontogenesis 25.02.10 Capulets (Biologists) Like to use OBO Montagues (Computer Scientists) Like to use OWL The Montagues and the Capulets (2004) Carole Goble, Chris Wroe Comparative and Functional Genomics , Vol. 5, No. 8. pp. 623-632. http://dx.doi.org/10.1002/cfg.442

Montagues and Capulets Ontogenesis 25.02.10 Montagues (OWL) Capulets (OBO) Generic (“top down”) Specific (“bottom up”) Describe any domain (in theory) : Technology driven Describe biology (in practice) “ Application pull” Focus on automated reasoning using logic Focus on supporting existing users Background in Artificial Intelligence Background in genome annotation (e.g. with Gene Ontology)

In an ideal world we could easily “round-trip” OWL and OBO 25.02.10 Without gaining or losing information OBO version 1.2 OWL 2.0

But there are crucial differences ,[object Object],[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Key differences: OBO vs. OWL ,[object Object],[object Object],[object Object],[object Object],Ontogenesis 25.02.10

Quantified relations (not in OBO) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Cardinality (not in OBO) ,[object Object],[object Object],[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Necessary & Sufficient conditions (not in OBO) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Identity crisis ,[object Object],[object Object],[object Object],OWL and OBO 25.02.10

How can you use OWL… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],OWL and OBO 25.02.10

Acknowledgements ,[object Object],Ontogenesis 25.02.10

OWL and OBO

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