The OBO Foundry Towards Gold Standard Terminology Resources in the Biomedical Domain

1. The OBO FoundryTowards Gold Standard Terminology Resources in  the Biomedical Domain Thomas Bittner(based on a presentation by Barry Smith)

2. how create broad-coverage semantic annotation systems for biomedicine? • UMLS, Semantic Web, Moby, wikis, etc. • let a million flowers bloom • integration relies on post hoc mappings

3. O2 O3 O1 On O4

4. O2 O3 O1 On O4

5. for science a new approach • create an evolutionary path towards evidence-based terminology

6. O2 O3 O1 On O4

7. Shared Organizatorial, Scientific, and Ontological principles Cell Ontology TLO ChEBI RNAO FMA PaTO

8. for science a new approach • create an evolutionary path towards evidence-based terminology • Terminologies/ontologies that • have proven their usefulness through applications • based on/ verified through scientific methodology • structured/formalized according to ontological principles

9. First step (Oct. 11, 2001) • a shared portal for (so far) 58 ontologies • originally called ‘GOBO’ (for Global Open Biological Ontologies)

10. GOBO Principles • All ontologies will be welcome if, and only if, they conform to the following principles of gobo: • 1. They are ‘open’ • 2. They are in, or can be instantiated in, the GO syntax or extensions of this syntax. • 3. They are orthogonal to other ontologies already lodged with gobo.  • 4. Shared ID space. • 5. Terms are defined.

11. Second step (March 2004) • Initiation by the Gene Ontology Consortium - logical reforms of the GO and related ontologies

12. e.g. linking GO logically to other OBO ontologies via cross-products id: CL:0000062 name: osteoblast def: "A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." is_a: CL:0000055 relationship: develops_from CL:0000008 relationship: develops_from CL:0000375 GO + Cell type (CL) = Osteoblast differentiation: Processes whereby an osteoprogenitor cell or a cranial neural crest cell acquires the specialized features of an osteoblast, a bone-forming cell which secretes extracellular matrix. New Definition

13. Third step (2005-6) The OBO Foundryfurther principles added + intense collaborative development

14. The OBO Foundry • a family of interoperable gold standard biomedical reference ontologies to serve the annotation of • scientific literature • model organism databases • clinical data à la Ida • experimental results • etc.

15. A prospective standard designed to guarantee interoperability of ontologies from the very start (contrast to: post hoc mapping à la UMLS) several ontologies now being constructed ab initio

16. Initial set of 10 principles • = 5 GOBO principles (with broadened family of allowable types of syntax, including OWL-DL syntaxes) plus: • 6. Collaborative development • 7. Intelligible documentation. • 8. Plurality of independent users. • 9. Clearly specified content. • 10. Uses relations which are formally defined

17. Ontology • Scope • URL • Custodians • Cell Ontology • (CL) • cell types from prokaryotes • to mammals • obo.sourceforge.net/cgi- • bin/detail.cgi?cell • Jonathan Bard, Michael • Ashburner, Oliver Hofman • Chemical Entities of Bio- • logical Interest (ChEBI) • molecular entities • ebi.ac.uk/chebi • Paula Dematos, • Rafael Alcantara • Common Anatomy Refer- • ence Ontology (CARO) • anatomical structures in • human and model organisms • (under development) • Melissa Haendel, Terry • Hayamizu, Cornelius Rosse, • David Sutherland, • Foundational Model of Anatomy (FMA) • structure of the human body • fma.biostr.washington. • edu • JLV Mejino Jr., • Cornelius Rosse • Functional Genomics • Investigation Ontology • (FuGO) • design, protocol, data • instrumentation, and analysis • fugo.sf.net • FuGO Working Group • Gene Ontology • (GO) • cellular components, • molecular functions, • biological processes • www.geneontology.org • Gene Ontology Consortium • Phenotypic Quality • Ontology • (PaTO) • qualities of biomedical entities • obo.sourceforge.net/cgi • -bin/ detail.cgi? • attribute_and_value • Michael Ashburner, Suzanna • Lewis, Georgios Gkoutos • Protein Ontology • (PrO) • protein types and • modifications • (under development) • Protein Ontology Consortium • Relation Ontology (RO) • relations • obo.sf.net/relationship • Barry Smith, Chris Mungall • RNA Ontology • (RnaO) • three-dimensional RNA • structures • (under development) • RNA Ontology Consortium • Sequence Ontology • (SO) • properties and features of • nucleic sequences • song.sf.net • Karen Eilbeck

18. RELATION TO TIME GRANULARITY OBO Foundry coverage

19. Building out from the original GO

20. Current state of OBO Foundry • 1. Ontologies already mature but still undergoing continuous reform: • Cell Ontology (CL) • Foundational Model of Anatomy (FMA) • Gene Ontology (GO) • Zebrafish Anatomy Ontology (ZAO)

21. 2. Early versions exist • Clinical Trial Ontology (CTO, part of OBI) • Common Anatomy Reference Ontology (CARO, DB1 & DB2) • Mosquito Anatomy Ontology (MAO) • Ontology for Biomedical Investigations (OBI) • Phenotypic Quality Ontology (PATO, DB1 & DB2) • Protein Ontology (PRO) • Relation Ontology (RO) • RNA Ontology (RnaO)

22. 3. Still in need of thorough review • Chemical Entities of Biological Interest (ChEBI) • Disease Ontology (DO) • Sequence Ontology (SO) • various other OBO ontologies (Mammalian Phenotype Ontology ...)

23. 4. Still in planning phase Biobank/Biorepository Ontology (BrO, part of OBI) Environment Ontology (EnvO) – inaugural meeting August, 2007 organized by NERC in OERC (Oxford E-Research Center) Fish Multi-Species Anatomy Ontology (funding received; no acronym yet) Infectious Disease Ontology (IDO) Mouse Adult Neurogenesis Ontology (MANGO) Xenopus Anatomy Ontology (XAO)

24. OBO Foundry Listservs (Jan. 2007)

25. Foundry developers have agreed in advance to accept a common set of principles designed to ensure • compatibility • interoperability • formal robustness http://obofoundry.org/

26. CRITERIA • The ontology isopenand available to be used by all. • The ontology is in, or can be instantiated in, a common formal language. • The developers of the ontology agree in advance to collaboratewith developers of other OBO Foundry ontology where domains overlap. CRITERIA http://obofoundry.org/

27. UPDATE: The developers of each ontology commit to its maintenance in light of scientific advance, and to soliciting community feedback for its improvement. • ORTHOGONALITY: They commit to ensuring that there is community convergence on a single controlled vocabulary for each domain CRITERIA http://obofoundry.org/

28. CRITERIA CRITERIA • IDENTIFIERS: The ontology possesses a unique identifierspace within OBO. • VERSIONING: The ontology provider has procedures for identifying distinct successive versions. • The ontology includes textual definitions for all terms. http://obofoundry.org/

29. CRITERIA • CLEARLY BOUNDED: The ontology has a clearly specified and clearly delineated content. • DOCUMENTATION: The ontology is well-documented. • USERS: The ontology has a plurality of independent users. http://obofoundry.org/

30. CRITERIA • COMMON ARCHITECTURE: The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.* • * Smith et al., Genome Biology 2005, 6:R46 http://obofoundry.org/

31. The Foundational Model of Anatomy (FMA)

32. The Foundational Model of Anatomy (FMA) FMA Uni-Washington Protégé – frame system http://fme.biostr.washington.edu:8089/FME/index.html Human anatomy

33. Digital Anatomist Foundational Model of Anatomy (FMA) High level scheme FMA= (At, ASA, ATA, Mk) where: At= Anatomy taxonomy ASA = Anatomical Structural Abstraction ATA = Anatomical Transformation Abstraction Mk= Metaknowledge Mejino & Rosse, KR-Med 04

34. Physical Anatomical Entity Non-physical Anatomical Entity Spatial entity (located in space) Non-spatial entity (not located in space) Anatomy Taxonomy (Mejino & Rosse, KR-Med 04) Anatomical Entity -is a-

35. Physical Anatomical Entity Non-physical Anatomical Entity Material Physical Anatomical Entity Non-material Physical Anatomical Entity Space Surface Line Anatomy Taxonomy (Mejino & Rosse, KR-Med 04) Anatomical Entity -is a-

36. Anatomical spaces (is-a hierarchy)

37. Physical Anatomical Entity Non-physical Anatomical Entity Material Physical Anatomical Entity Non-material Physical Anatomical Entity Body Substance Space Surface Line Anatomical Structure Anatomy Taxonomy (Mejino & Rosse, KR-Med 04) Anatomical Entity -is a-

38. Physical Anatomical Entity Non-physical Anatomical Entity Material Physical Anatomical Entity Non-material Physical Anatomical Entity Body Substance Space Surface Line Anatomical Structure Human Body Biological Macromolecule Body Part Acellular Anatomical Structure Cell Part Cell Tissue Organ Part Organ Organ System Anatomy Taxonomy (Mejino & Rosse, KR-Med 04) Anatomical Entity -is a-

39. Universal parthood: The universal human body The universal human head Human anatomy Human heads are parts of human bodies

40. The semantics of universal parthood X PART-OF Y iff For every instance x of X there exists an instance y of Y such that x part-of y AND For every instance y of Y there exists an instance x of X such that x part-of y