The OBO Foundry Towards Gold Standard Terminology Resources in by qvs59240

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

            Thomas Bittner
(based on a presentation by Barry Smith)
                                           1
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




                                              2
      O2    O3
O1




 O4        On

                 3
      O2    O3
O1




 O4        On

                 4
         for science
      a new approach
create an evolutionary path towards
   evidence-based terminology




                                      5
      O2    O3
O1




 O4        On

                 6
                         FMA


                                     Cell
           PaTO                    Ontology

                         TLO
Shared
Organizatorial,
                  RNAO         ChEBI
Scientific, and
Ontological
principles
                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
                                                      8
     First step (Oct. 11, 2001)




       a shared portal for (so far) 58 ontologies

originally called ‘GOBO’ (for Global Open
           Biological Ontologies)
                                                    9
               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.

                                                                  10
Second step (March 2004)
Initiation by the Gene Ontology
Consortium - logical reforms of the GO
and related ontologies




                                         11
      e.g. linking GO logically to other OBO
           ontologies via cross-products

                                                                          GO

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."                                                               Cell type (CL)
is_a: CL:0000055
relationship: develops_from CL:0000008
relationship: develops_from CL:0000375
                                                                           =
Osteoblast differentiation: Processes whereby an
osteoprogenitor cell or a cranial neural crest cell
acquires the specialized features of an osteoblast, a                New Definition
bone-forming cell which secretes extracellular matrix.                                12
                    Third step
                     (2005-6)



  The OBO Foundry
     further principles added +
intense collaborative development

                                    13
       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.


                                               14
       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




                                                       15
      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

                                                 16
     Ontology                        Scope                          URL                     Custodians
     Cell Ontology           cell types from prokaryotes    obo.sourceforge.net/cgi-     Jonathan Bard, Michael
          (CL)                       to mammals                bin/detail.cgi?cell      Ashburner, Oliver Hofman

Chemical Entities of Bio-                                                                    Paula Dematos,
                                 molecular entities             ebi.ac.uk/chebi
logical Interest (ChEBI)                                                                     Rafael Alcantara
                                                                                         Melissa Haendel, Terry
Common Anatomy Refer-         anatomical structures in
                                                             (under development)       Hayamizu, Cornelius Rosse,
 ence Ontology (CARO)       human and model organisms
                                                                                           David Sutherland,

 Foundational Model of                                      fma.biostr.washington.            JLV Mejino Jr.,
                            structure of the human body
    Anatomy (FMA)                                                    edu                     Cornelius Rosse

  Functional Genomics
                                design, protocol, data
 Investigation Ontology                                           fugo.sf.net             FuGO Working Group
                            instrumentation, and analysis
         (FuGO)
                                cellular components,
    Gene Ontology
                                molecular functions,        www.geneontology.org       Gene Ontology Consortium
        (GO)                    biological processes
  Phenotypic Quality                                        obo.sourceforge.net/cgi
                               qualities of biomedical                                 Michael Ashburner, Suzanna
      Ontology                                                  -bin/ detail.cgi?
                                       entities                                         Lewis, Georgios Gkoutos
       (PaTO)                                                attribute_and_value
   Protein Ontology              protein types and
                                                             (under development)       Protein Ontology Consortium
         (PrO)                     modifications
Relation Ontology (RO)                relations             obo.sf.net/relationship     Barry Smith, Chris Mungall
    RNA Ontology              three-dimensional RNA
                                                             (under development)        RNA Ontology Consortium
      (RnaO)                         structures
  Sequence Ontology          properties and features of
                                                                  song.sf.net                 Karen Eilbeck
        (SO)                    nucleic sequences
      RELATION TO              CONTINUANT                     OCCURRENT
      TIME
               INDEPENDENT               DEPENDENT
GRANULARITY
                         Anatomical
             Organism                  Organ                 Organism-Level
 ORGAN AND                  Entity
               (NCBI                  Function                  Process
 ORGANISM                   (FMA,
             Taxonomy)              (FMP, CPRO) Phenotypic       (GO)
                           CARO)
                                                 Quality
                                                  (PaTO)
  CELL AND                 Cellular   Cellular
               Cell                                          Cellular Process
  CELLULAR               Component Function
               (CL)                                               (GO)
 COMPONENT               (FMA, GO)      (GO)

                  Molecule                                     Molecular
                                      Molecular Function
 MOLECULE        (ChEBI, SO,                                    Process
                                            (GO)
                 RnaO, PrO)                                      (GO)


              OBO Foundry coverage
    RELATION
     TO TIME                     CONTINUANT                     OCCURRENT


                 INDEPENDENT               DEPENDENT
GRANULARITY

                           Anatomical
                Organism                 Organ
 ORGAN AND                    Entity
                 (NCBI                  Function
 ORGANISM                     (FMA,
               Taxonomy)              (FMP, CPRO) Phenotypic      Biological
                             CARO)
                                                   Quality         Process
                                                    (PaTO)          (GO)
  CELL AND                   Cellular   Cellular
                 Cell
  CELLULAR                 Component Function
                 (CL)
 COMPONENT                 (FMA, GO)     (GO)

                    Molecule
                                        Molecular Function     Molecular Process
  MOLECULE         (ChEBI, SO,
                                              (GO)                  (GO)
                   RnaO, PrO)



          Building out from the original GO
   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)
                                         20
        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)
                                               21
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 ...)

                                           22
   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)

                                                    23
OBO Foundry Listservs (Jan. 2007)




                                24
   Foundry developers have agreed in advance to
   accept a common set of principles designed to
   ensure
        compatibility
        interoperability
        formal robustness



                                                   25
http://obofoundry.org/
                         CRITERIA
                         CRITERIA
    The ontology is open and 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 collaborate with developers of other OBO
     Foundry ontology where domains overlap.


                                                        26
http://obofoundry.org/
                         CRITERIA
    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



                                                        27
http://obofoundry.org/
                         CRITERIA
                         CRITERIA
    IDENTIFIERS: The ontology possesses a unique
     identifier space within OBO.
    VERSIONING: The ontology provider has
     procedures for identifying distinct successive
     versions.
    The ontology includes textual definitions for all
     terms.


                                                         28
http://obofoundry.org/
                         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.



                                                         29
http://obofoundry.org/
                          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




                                                         30
http://obofoundry.org/
The Foundational Model of
     Anatomy (FMA)




                            31
   The Foundational Model of
        Anatomy (FMA)
FMA
Uni-Washington
Protégé – frame
  system
http://fme.biostr.washi
  ngton.edu:8089/FM
  E/index.html


                          Human anatomy
                                          32
              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 0433
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
                        Anatomical Entity


        Physical                                 Non-physical
    Anatomical Entity           -is a-         Anatomical Entity


 Spatial entity                             Non-spatial entity
 (located in space)                         (not located in space)




                                                                     34
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
                        Anatomical Entity


       Physical                                Non-physical
   Anatomical Entity            -is a-       Anatomical Entity


    Material Physical                       Non-material Physical
    Anatomical Entity                         Anatomical Entity


                                               Space       Surface   Line




                                                                            35
Anatomical spaces (is-a
      hierarchy)



               QuickTime™ and a
           TIFF (LZW) decompressor
        are needed to see this picture.




                                          36
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
                        Anatomical Entity


       Physical                                Non-physical
   Anatomical Entity            -is a-       Anatomical Entity


    Material Physical                       Non-material Physical
    Anatomical Entity                         Anatomical Entity

        Body                                   Space       Surface   Line
      Substance             Anatomical
                             Structure




                                                                            37
      Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
                                    Anatomical Entity


                  Physical                                        Non-physical
              Anatomical Entity             -is a-              Anatomical Entity


              Material Physical                                Non-material Physical
              Anatomical Entity                                  Anatomical Entity

                   Body                                           Space       Surface       Line
                 Substance              Anatomical
                                         Structure
                                                                                          Human
  Biological
                                                                                           Body
Macromolecule

  Acellular
                                                                                           Body
 Anatomical                                                                                Part
  Structure
                Cell                                    Organ                           Organ
                             Cell       Tissue                        Organ
                Part                                    Part                            System
                                                                                                   38
    Universal parthood:
 The universal
 human body


  The universal
  human head      Human heads
                  are parts of
                  human bodies
Human anatomy
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

								
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