Transcript The OBO Foundry Towards Gold Standard Terminology Resources in the Biomedical Domain Thomas Bittner (based on a presentation by Barry Smith)

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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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
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O2
O3
O1
O4
On
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O2
O3
O1
O4
On
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for science
a new approach
create an evolutionary path towards
evidence-based terminology
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O2
O3
O1
O4
On
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FMA
Cell
Ontology
PaTO
TLO
Shared
Organizatorial,
Scientific, and
Ontological
principles
RNAO
ChEBI
for science
a new approach
create an evolutionary path towards evidencebased terminology
Terminologies/ontologies that
• have proven their usefulness through applications
• based on/ verified through scientific methodology
• structured/formalized according to ontological
principles
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First step (Oct. 11, 2001)
a shared portal for (so far) 58 ontologies
originally called ‘GOBO’ (for Global Open
Biological Ontologies)
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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.
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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
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."
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
bone-forming cell which secretes extracellular matrix.
+
Cell type (CL)
=
New Definition
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Third step
(2005-6)
The OBO Foundry
further principles added +
intense collaborative development
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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.
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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
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Initial set of 10 principles
= 5 GOBO principles (with broadened family
of allowable types of syntax, including OWLDL syntaxes) plus:
6. Collaborative development
7. Intelligible documentation.
8. Plurality of independent users.
9. Clearly specified content.
10. Uses relations which are formally defined
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Ontology
Scope
URL
Custodians
Cell Ontology
(CL)
cell types from prokaryotes
to mammals
obo.sourceforge.net/cgibin/detail.cgi?cell
Jonathan Bard, Michael
Ashburner, Oliver Hofman
Chemical Entities of Biological Interest (ChEBI)
molecular entities
ebi.ac.uk/chebi
Paula Dematos,
Rafael Alcantara
Common Anatomy Reference 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
RELATION TO
TIME
GRANULARITY
INDEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
MOLECULE
CONTINUANT
DEPENDENT
Anatomical
Organ
Entity
Function
(FMA,
(FMP, CPRO) Phenotypic
CARO)
Quality
(PaTO)
Cellular
Cellular
Component Function
(FMA, GO)
(GO)
Molecule
(ChEBI, SO,
RnaO, PrO)
OCCURRENT
Molecular Function
(GO)
OBO Foundry coverage
Organism-Level
Process
(GO)
Cellular Process
(GO)
Molecular
Process
(GO)
RELATION
TO TIME
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
MOLECULE
Anatomical
Organ
Entity
Function
(FMA,
(FMP, CPRO) Phenotypic
CARO)
Quality
(PaTO)
Cellular
Cellular
Component Function
(FMA, GO)
(GO)
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Biological
Process
(GO)
Molecular Process
(GO)
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)
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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)
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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 ...)
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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)
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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/
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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.
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/
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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.
http://obofoundry.org/
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CRITERIA
 CLEARLY BOUNDED: The ontology has a
clearly specified and clearly delineated content.
 DOCUMENTATION: The ontology is welldocumented.
 USERS: The ontology has a plurality of
independent users.
http://obofoundry.org/
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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/
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The Foundational Model of
Anatomy (FMA)
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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
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Digital Anatomist
Foundational Model of Anatomy (FMA)
High level scheme
FMA= (At, ASA, ATA, Mk)
where:
At
ASA
ATA
Mk
=
=
=
=
Anatomy taxonomy
Anatomical Structural Abstraction
Anatomical Transformation Abstraction
Metaknowledge
Mejino & Rosse, KR-Med 0433
Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
Anatomical Entity
Physical
Anatomical Entity
Spatial entity
(located in space)
-is a-
Non-physical
Anatomical Entity
Non-spatial entity
(not located in space)
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Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
Anatomical Entity
Physical
Anatomical Entity
Material Physical
Anatomical Entity
-is a-
Non-physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Space
Surface
Line
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Anatomical spaces (is-a
hierarchy)
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
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Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
Anatomical Entity
Physical
Anatomical Entity
-is a-
Material Physical
Anatomical Entity
Body
Substance
Non-physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Anatomical
Structure
Space
Surface
Line
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Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)
Anatomical Entity
Physical
Anatomical Entity
Non-physical
Anatomical Entity
-is a-
Material Physical
Anatomical Entity
Body
Substance
Non-material Physical
Anatomical Entity
Anatomical
Structure
Space
Surface
Line
Human
Biological
Macromolecule
Body
Body
Acellular
Anatomical
Structure
Part
Cell
Part
Cell
Tissue
Organ
Part
Organ
Organ
System
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Universal parthood:
The universal
human body
The universal
human head
Human anatomy
Human heads
are parts of
human bodies
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