Transcript Presentation

OBO Foundry Update: April 2010
Barry Smith
OBO Foundry: The Underlying Idea
 We have lots and lots of ontologies
 Most of them are stand alone
 Yet the biology is inherently interconnected
 Across granular levels (molecules, cells, organisms, ...)
 Across different basic types (objects, processes,
functions ...)
 Rigorously enforced modularity
RELATION
TO TIME
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
CELL AND
CELLULAR
COMPONENT
MOLECULE
Organism
(NCBI
Taxonomy)
Cell
(CL)
Anatomical
Organ
Entity
Function
(FMA,
(FMP, CPRO) Phenotypic
CARO)
Quality
(PaTO)
Cellular
Component
(FMA, GO)
Molecule
(ChEBI, SO,
RNAO, PRO)
Biological
Process
(GO)
Cellular
Function
(GO)
Molecular Function
(GO)
Molecular Process
(GO)
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OBO Foundry
 Open Biological/Biomedical Ontologies Foundry
 International open initiative since 2006 (Nat Biotech
2007)
 Coordinating editors: Michael Ashburner, Chris
Mungall, Suzanna Lewis, Alan Ruttenberg, Richard H.
Scheuermann, Barry Smith
 http://obofoundry.org
 Create a suite of orthogonal and interoperable
ontologies
 Maintain a framework for governance and testing of
best practices
 Initiate a formal, peer review process for wellstructured biological accurate ontologies
Why OBO Foundry ontology
standards?
 Operational efficiencies
 Eliminate duplication of effort, code once, retrieve and
reuse efficiently
 Unbiased, neutral perspective
 Considering biology/biomedical domain as a whole
 Homesteading by experts
 who have an incentive to ensure adequate
terminology resources for their respective disciplines
OBO Foundry Principles
Revised Proposals
February 2010
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OBO Foundry Principles
 open (Creative Commons 3.0 CC-by license or equivalent)
 common formal language (OBO Format, OWL 2, Common
Logic)
 commitment to collaboration
 maintenance in light of scientific advance
 unique identifier space (URIs)
 naming conventions (Susanna / EBI)
 versioning (metadata for changes)
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OBO Foundry Principles
 ontologies should be conceivable as the result of
populating downwards from some fragment of (BFO2.0)
 clearly delineated content (coherent natural language
definitions of top-level term(s) incorporating crossproduct links to other OBO Foundry ontologies)
 the ontology is well-documented (e.g. in a published
paper describing the ontology or in manuals for
developers and users)
 plurality of mutually independent users (documented
e.g. via pointers in external URIs, use in cross-products)
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OBO Foundry Principles
 single locus of authority, tracker (SOP), responsive
help desk
 textual definitions (SOP) for all terms, plus
equivalent formal definitions (for at least a
substantial number of terms)
 all definitions of the genus-species form, utilizing
(some) cross-products
 single is_a inheritance (= each ontology should be
conceived as consisting of a core of asserted single
inheritance links, with further is_a relations
inferred)
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Results of peer review process
2nd OBO Foundry meeting in Hinxton, UK in June 2009
Special mention:
 CL (Cell Ontology)
 FMA (Foundational Model of Anatomy Ontology)
 EnvO: Environment Ontology
 HPO: Human Phenotype Ontology
 OBI: Ontology for Biomedical Investigations
 SO: Sequence Ontology
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Approved for full membership






CHEBI: Chemical Entities of Biological Interest
GO: Gene Ontology
PATO: Phenotypic Quality Ontology
PRO: Protein Ontology
XAO: Xenopus Anatomy Ontology
ZFA: Zebrafish Anatomy Ontology
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Goals of the peer review process
 identify problems in ontologies
 identify, nurture and recommend best practices
 education: provide illustrations of good practice
and flagposts for those new to the domain
 motivation
 of ontology authors
 of ontology reviewers
 of ontology users, publishers, vendors
 analogous to scientific journal peer review
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Linking ontologies via cross
products
Compound terms are formed out of simpler
constituents
{cysteine, leucine, collagen,..}
X {biosynthesis, metabolism,..}
LEGO examples: GO+CL
ChEBI PRO
CC
cell
anat
envo
PATO
MF
BP
ChEBI
PRO
16
GO-CC
14
Cell
174
8
70
13
Gross anat
19
Envo
phen
MP
273
WP
115
TO
127
disease
GO-MF
GO-BP
2407
10
GO:germ cell nucleus
654
3300
=def?
?
45
432
GO:nucleus
2
355
19
that is part_of
CL:germ cell
511
1085
28
5815
1040
1450
686
1
55
LEGO examples: CL+PATO
ChEBI PRO
CC
cell
anat
envo
PATO
MF
BP
ChEBI
PRO
16
GO-CC
Cell
174
14
8
70
19
CL:spiny neuron
654
3300
=def
45
432
CL:neuron
2
355
that has_quality
PATO:spiny
28
13
Gross anat
Envo
phen
MP
273
WP
115
TO
127
disease
GO-MF
GO-BP
2407
10
511
1085
5815
1040
1450
686
19?
1
55
LEGO examples: CL+ChEBI
ChEBI PRO
CC
cell
anat
envo
PATO
MF
BP
ChEBI
PRO
16
GO-CC
14
Cell
174
8
70
13
Gross anat
19
Envo
phen
MP
273
WP
115
TO
127
disease
GO-MF
GO-BP
2407
CL:estradiol secreting cell
10
654
3300
=def
45
432
CL:secretory
cell355
2
19?
that has_output
CHEBI:estradiol
511
1085
28
5815
1040
1450
686
1
55
LEGO examples: EnvO+ChEBI
ChEBI PRO
CC
cell
anat
envo
PATO
MF
BP
ChEBI
PRO
16
GO-CC
14
Cell
174
8
70
13
Gross anat
19
Envo
phen
MP
273
WP
115
TO
127
disease
GO-MF
GO-BP
2407
ENVO:xylene contaminated28soil
10
654
3300
5815
=def
45
432
1450
ENVO:soil2
355
19?
that has_contaminant
CHEBI:xylene
511
1085
55
1040
686
1
LEGO examples: GO+Anatomy
ChEBI PRO
CC
cell
anat
envo
PATO
MF
BP
ChEBI
19
GO:heart development
=def
16
GO:developmental
process 70
8
that results_in_development_of
FMA:heart
28
MP
273
10
WP
TO
PRO
GO-CC
14
Cell
Gross anat
Envo
phen
GO-BP
13
654
3300
5815
1040
115
45
432
1450
686
127
2
355
511
1085
19?
1
disease
GO-MF
174
2407
55
LEGO examples: Diseases
circulating
glucose
ChEBI MP:abnormal
PRO
CC
cell
anat
envo
PATO
ChEBI
PRO
GO-CC
14
Cell
Gross anat
19
Envo
phen
MP
273
WP
TO
=def
PATO:concentration
that inheres_in
16
MA:blood
8
towards
CHEBI:glucose
10
GO-BP
BP
174
70
13
gluconeogenesis
28
diabetes
654
3300
5815
1040
115
45
432
1450
686
127
2
355
511
1085
19
1
disease
GO-MF
MF
2407
55
Sustainable standards policy
requires
 Openness
 Readily available to access and open to participation
 Separation of Duties
 Ontology is vetted by multiple groups
 Generational Compliance
 Initially support backward compatibility so no one is
stranded
 Enforce a more rigorous set of criteria in successive
generation of products
Varieties of application ontology
•
•
•
•
cross-border national parks
slims
cross-product ontologies
template ontologies:
– Infectious Disease Ontology
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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)
cross-border national parks: an ontology for studying
the effects of viral infection on cell function22in shrimp
http://www.infectiousdiseaseontology.org/
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