OWL and OBO

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

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!
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
Ch emical E ntities of B iological I nterest
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:
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
Ontogenesis 25.02.10 (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?
Big data: need for more automation
A Web standard standard (W3C)
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 Service http://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
Ontogenesis 25.02.10 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 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?
Every year developers and users of OWL gather at OWLED ( OWL E xperiences and D irections) 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? 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?
Philosophy
Biology
Computer Science / Artificial Intelligence
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
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_006534 http://purl.org/obo/owl/GO#GO_006534 and 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

by Duncan Hull on Feb 25, 2010

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OWL and OBO — Presentation Transcript