1 The OBO Foundry Towards Gold Standard Terminology Resources in the Biomedical Domain Thomas Bittner (based on a presentation by Barry Smith)
Jan 13, 2016
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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)
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UMLS, Semantic Web, Moby, wikis, etc.
let a million flowers bloom
integration relies on post hoc mappings
how create broad-coverage semantic annotation systems for biomedicine?
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O1
O2
O4
O3
On
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O1
O4
O2 O3
On
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for science
create an evolutionary path towards evidence-based terminology
a new approach
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O1
O2
O4
O3
On
FMA
RNAO ChEBI
Cell OntologyPaTO
SharedOrganizatorial,Scientific, and Ontologicalprinciples
TLO
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for science
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
a new approach
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a shared portal for (so far) 58 ontologies
originally called ‘GOBO’ (for Global Open Biological Ontologies)
First step (Oct. 11, 2001)
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GOBO PrinciplesAll 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.
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Second step (March 2004)
Initiation by the Gene Ontology Consortium - logical reforms of the GO and related ontologies
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e.g. linking GO logically to other OBO ontologies via cross-products
id: CL:0000062name: osteoblastdef: "A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." is_a: CL:0000055relationship: develops_from CL:0000008relationship: develops_from CL:0000375
GO
Cell type (CL)
New Definition
+
=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.
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The OBO Foundryfurther principles added +
intense collaborative development
Third step (2005-6)
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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.
The OBO Foundry
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A prospective standarddesigned to guarantee interoperability of ontologies from the very start (contrast to: post hoc mapping à la UMLS)
several ontologies now being constructed ab initio
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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
Karen Eilbecksong.sf.netproperties and features of
nucleic sequencesSequence Ontology
(SO)
RNA Ontology Consortium(under development)three-dimensional RNA
structuresRNA Ontology
(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium
(under development)protein types and
modificationsProtein Ontology
(PrO)
Michael Ashburner, Suzanna
Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi-bin/ detail.cgi?
attribute_and_value
qualities of biomedical entities
Phenotypic Quality Ontology
(PaTO)
Gene Ontology Consortium
www.geneontology.org
cellular components, molecular functions, biological processes
Gene Ontology (GO)
FuGO Working Groupfugo.sf.netdesign, protocol, data instrumentation, and
analysis
Functional Genomics Investigation Ontology
(FuGO)
JLV Mejino Jr.,Cornelius Rosse
fma.biostr.washington.edu
structure of the human body
Foundational Model of Anatomy (FMA)
Melissa Haendel, Terry Hayamizu, Cornelius Rosse,
David Sutherland, (under development)
anatomical structures in human and model
organisms
Common Anatomy Refer-ence Ontology (CARO)
Paula Dematos,Rafael Alcantara
ebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)
Jonathan Bard, Michael Ashburner, Oliver Hofman
obo.sourceforge.net/cgi-bin/detail.cgi?cell
cell types from prokaryotes to mammals
Cell Ontology (CL)
CustodiansURLScopeOntology
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
Cellular Process
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
OBO Foundry coverage
GRANULARITY
RELATION TO TIME
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Building out from the original GO
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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)
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2. Early versions existClinical 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)
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3. Still in need of thorough reviewChemical Entities of Biological Interest
(ChEBI)
Disease Ontology (DO)
Sequence Ontology (SO)
various other OBO ontologies (Mammalian Phenotype Ontology ...)
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4. Still in planning phaseBiobank/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)
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OBO Foundry Listservs (Jan. 2007)
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Foundry developers have agreed in advance to accept a common set of principles designed to ensure
compatibility
interoperability
formal robustness
http://obofoundry.org/http://obofoundry.org/
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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.
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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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
http://obofoundry.org/http://obofoundry.org/
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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.
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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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.
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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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
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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The Foundational Model of Anatomy (FMA)
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The Foundational Model of Anatomy (FMA)
FMAUni-WashingtonProtégé – frame
systemhttp://
fme.biostr.washington.edu:8089/FME/index.html
Human anatomy
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High level scheme
Digital Anatomist Foundational Model of Anatomy (FMA)
Mejino & Rosse, KR-Med 04
FMA= (At, ASA, ATA, Mk)
where:
AtAt = Anatomy taxonomy
ASAASA = Anatomical Structural Abstraction
ATAATA = Anatomical Transformation Abstraction
MkMk = Metaknowledge
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity -is a--is a- Non-physical
Anatomical Entity
Non-physicalAnatomical Entity
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
Non-spatial entity(not located in space)
Spatial entity(located in space)
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity -is a--is a- Non-physical
Anatomical Entity
Non-physicalAnatomical Entity
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
SpaceSpace SurfaceSurface LineLine
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
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QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
Anatomical spaces (is-a hierarchy)
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity -is a--is a- Non-physical
Anatomical Entity
Non-physicalAnatomical Entity
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
AnatomicalStructure
AnatomicalStructure
BodySubstance
BodySubstance SpaceSpace SurfaceSurface LineLine
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity -is a--is a- Non-physical
Anatomical Entity
Non-physicalAnatomical Entity
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
AnatomicalStructure
AnatomicalStructure
BodySubstance
BodySubstance
BiologicalMacromolecule
BiologicalMacromolecule
AcellularAnatomicalStructure
AcellularAnatomicalStructure
CellPart
CellPart CellCell TissueTissue
BodyPart
BodyPart
HumanBody
HumanBody
SpaceSpace SurfaceSurface LineLine
OrganOrgan OrganSystem
OrganSystem
OrganPart
OrganPart
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
Universal parthood:
Human anatomy
The universal human body
The universalhuman head Human heads
are parts of human bodies
The semantics of universal parthood
X PART-OF Y iffFor every instance x of X there exists an instance y of Y such thatx part-of y
ANDFor every instance y of Y there exists an instance x of X such thatx part-of y