owl and obo

EBI is an Outstation of the European Molecular Biology Laboratory.

OWL: Web Ontology Language

Dr. Duncan Hull, Software engineer, EBI Chemoinformatics and Metabolism

An overview

OWL: The Web Ontology Language

• What is OWL?• Examples from ChEBI• When was OWL created?• Who is responsible for OWL?

• Why would you want to use OWL• Where does OWL fit with related technology?

• Other web standards• OBO (Open Biomedical Ontologies)

• How can you use OWL?

• Disclaimer: this is a (superficial) introduction only!

Ontogenesis12.04.232

OWL (not WOL) Web Ontology Language


A. A. Milne (1926) Winnie the Pooh (fictional characters who often had trouble spelling…)

ChEBI example: ontology of small molecules

Chemical Entities of Biological Interest


is-a (subclass of)

base-of

is-a (subclass of)

acid-of

has-role

ChEBI:15365

OWL is a W3C standard for expressing this:

Class: ChEBI:Acetylsalicylic_acid

SubClassOf:

ChEBI:Salicyclic_acid,

ChEBI:acid-of some ChEBI:Acetylsalicylate,

ChEBI:has-role some ChEBI:anti-inflammatory_drug

Class: ChEBI:Acetylsalicylate

SubClassOf:

ChEBI:Organic_Molecular_Entity,

ChEBI:base-of some ChEBI:Acetylsalicylic_acid

Class: ChEBI:Salicyclic_acid

SubClassOf:

ChEBI:Organic_Molecular_Entity


(Classes)

(Relations between classes)

A key feature of OWL is reasoning

• Key feature is automated reasoning (aka classification), with a reasoner using Description Logic (DL) which can perform several tasks including

• Subsumption, automatically organise classes in an ontology into a hierarchy of sub / super-classes

• Consistency, highlight inconsistent statements e.g. a given compound can’t be organic and inorganic at the same time because these are disjoint

• Querying, answering questions about an ontology… (e.g. query languages like SPARQL and SPARQL-DL)


Why use OWL?

1 Big data: need for more automation

2 A Web standard standard (W3C)

3 Active area of research: funding


Why OWL? 1. Big data

• Managing big data, manual data curation is not always possible – automation is required for handling quality and quantity of data. Current examples of OWL usage:• ChEBI (~500,000 compounds)

http://www.ebi.ac.uk/chebi

• National Cancer Institute (NCI) Thesaurus http://cancer.gov defines 10,000 cancers using 50,000 concepts managed by ~20 people, provides terminology for cancer image database.

• SNOMED-CT (Systematised Nomenclature of Medicine: Clinical Terms) 373,731 classes and over 1 million terms used by National Health Servicehttp://en.wikipedia.org/wiki/SNOMED_CT


Why OWL? 2. Suite of web standards• URI:

• E.g. http://www.ebi.ac.uk is a URI• Standard way of naming and identifying things since ~1990

• XML and namespaces: • Standard way of describing data, since 1998

• RDF• Describing graphs, since ~1999

• So what?• Active community of global users • Choice of tools, both open-source and

otherwise• Interoperability, no “vendor lock-in”• Re-use rather than re-invent wheels


Picture via http://www.codinghorror.com/blog/archives/001145.html

Why OWL? 3. Active research area

• The paint isn’t quite dry yet but if you’re looking to secure research funding OWL and ontologies are very active areas of research…

• This is both a blessing and a curse!

• See e.g. http://www.bio-ontologies.org.uk/ , http://iswc.semanticweb.org/, http://icbo.buffalo.edu/ and many others

OWL and OBO12.04.2310

Who?


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?

• Every year developers and users of OWL gather at OWLED (OWL Experiences and Directions)http://www.webont.org/owled/

• 6th International Workshop in Shanghai, China…

• Co-located with ISWC 2010 The 9th International Semantic Web Conference (Nov 7th – 11th, 2010), at Shanghai International Convention Center, China.

• http://iswc.semanticweb.org/


When was OWL created?

• OWL 1.0 became a W3C recommendation in 2004(also OBO Flat File Format Specification, version 1.0)

• OWL 2.0 became a W3C recommendation in 2009

• But OWL has roots in a range of Knowledge Representation (K.R.) systems from Artificial Intelligence (A.I.) research:

• From 1990’s: KRIS, SB-one, Cyc-L, Loom, K-rep, Classic , Back, Candide, GRAIL, DAML, OIL etc

• From 1980’s: KL-ONE, Nikl and Krypton


Where does OWL fit?


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?


Robert Hoehndorf, What is an ontology?

1. Philosophy

2. Biology

3. Computer Science / Artificial Intelligence

Life Scientists vs. Computer Scientists communities have different languages and goals


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

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”


Without gaining or losing information

OBO version 1.2

OWL 2.0

But there are crucial differences

• OBO does things OWL can’t do• OWL does things OBO can’t do• We’ll look at some of them…

• More details in OBO & OWL: Roundtrip Ontology Transformations Syed Hamid Tirmizi, Stuart Aitken, Dilvan A. Moreira, Chris Mungall, Juan Sequeda, Nigam H. Shah, Daniel P. Miranker. Proceedings of Semantic Web Applications and Tools for the Life Sciencses (SWAT4LS) 2009 http://ceur-ws.org/Vol-559/Paper6.pdf


Key differences: OBO vs. OWL

• Quantified relations• Cardinality• Necessary and sufficient conditions• Identity, using unique and stable URI’s


Quantified relations (not in OBO)

Class: ChEBI:Acetylsalicylate

SubClassOf:

ChEBI:Organic_Molecular_Entity,

ChEBI:base-of some ChEBI:Acetylsalicylic_acid

“Some” means at least one “Existential quantification” here but might want to say:

ChEBI:base-of only ChEBI:Acetylsalicylic_acid

“Only” means all of the things Acetylsalicylate is base-of are Acetylsalicylic_acid “Universal quantification”: not in OBO


Cardinality (not in OBO)

Class: ChEBI:Acetylsalicylic_acid

SubClassOf:

ChEBI:Salicyclic_acid,

ChEBI:has-part exactly 1 ChEBI:carboxyl-group

Cardinality can be very useful e.g. saying a hand has five digits etc but is not currently possible in OBO


Necessary & Sufficient conditions (not in OBO)

Class: ChEBI:Organic_Molecular_Entity

SubClassOf:

ChEBI:Molecular_Entity

Class: ChEBI:Organic_Molecular_Entity

EquivalentTo:

ChEBI:Molecular_Entity that ChEBI:has-part some CarbonAtom and

that ChEBI:has-part some HydrogenAtom

Can use a reasoner to infer that Acetylsalicylic-Acid is organic but Diamond is inorganic


Identity crisis

• OBO uses ID’s in the form e.g. GO:0006534(cysteine metabolic process)

• Rules for transforming OBO ID’s into URI’s e.g.http://purl.obolibrary.org/obo/GO_006534http://purl.org/obo/owl/GO#GO_006534and back again are still being finalised…

• By default, everything (classes, relations and instances) gets a URI in an OWL ontology: WEB Ontology Language


How can you use OWL…

• Today is mostly about languages (not tools) but…• Protégé http://protege.stanford.edu (see over)• Top Braid http://www.topquadrant.com • Many others e.g. http://owl.cs.manchester.ac.uk/

• Also OWL API http://owlapi.sourceforge.net/ programmatically read/write ontologies (for software engineers)

• If people want to know more we can arrange hands-on tutorials…


Conclusions

• Introduced the Web Ontology Language• What it is• Why you might want to use it• How it relates to other web technology • How it relates to OBO

• It would be great if everyone used the same ontology language (and that’s the point) but…

• Developers of biomedical ontologies look likely to continue using both OWL and OBO

• We’ll be struggling with converting between the two for a while...


Acknowledgements

• Janna Hastings, Midori Harris, Nico Adams, David Osumi-Sutherland, Ulrike Sattler, Bijan Parsia, Paula de Matos, Christoph Steinbeck.


owl and obo

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