OWL and OBO
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OWL and OBO

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Part of a joint presentation with Midori Harris comparing OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) as ontology languages, This presentation concentrates on OWL, Midori......

Part of a joint presentation with Midori Harris comparing OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) as ontology languages, This presentation concentrates on OWL, Midori Harris presented OBO.

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  • 1. OWL: Web Ontology Language An overview Dr. Duncan Hull, Software engineer, EBI Chemoinformatics and Metabolism
  • 2. 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
  • 3. OWL (not WOL) Web Ontology Language Ontogenesis 25.02.10 A. A. Milne (1926) Winnie the Pooh (fictional characters who often had trouble spelling…)
  • 4. 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
  • 5. 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)
  • 6. 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)
    Ontogenesis 25.02.10
  • 7. Why use OWL?
    • Big data: need for more automation
    • A Web standard standard (W3C)
    • Active area of research: funding
    Ontogenesis 25.02.10
  • 8. 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
    Ontogenesis 25.02.10
  • 9. 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
  • 10. 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
  • 11. 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
  • 12. 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/
    Ontogenesis 25.02.10
  • 13. 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
    Ontogenesis 25.02.10
  • 14. 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
  • 15. 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
  • 16. 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
  • 17. 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)
  • 18. 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
  • 19. 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
    OWL and OBO 25.02.10
  • 20. Key differences: OBO vs. OWL
    • Quantified relations
    • Cardinality
    • Necessary and sufficient conditions
    • Identity, using unique and stable URI’s
    Ontogenesis 25.02.10
  • 21. 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
    OWL and OBO 25.02.10
  • 22. 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
    OWL and OBO 25.02.10
  • 23. 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
    OWL and OBO 25.02.10
  • 24. 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
    OWL and OBO 25.02.10
  • 25. 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…
    OWL and OBO 25.02.10
  • 26. OWL and OBO 25.02.10
  • 27. 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...
    OWL and OBO 25.02.10
  • 28. Acknowledgements
    • Janna Hastings, Midori Harris, Nico Adams, David Osumi-Sutherland, Ulrike Sattler, Bijan Parsia, Paula de Matos, Christoph Steinbeck.
    Ontogenesis 25.02.10