1. OBO Foundry Update: April 2010
Barry Smith

2. 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

3. Biological Process Cellular Component Molecular Function
RELATION
TO TIME
GRANULARITY
CONTINUANT
OCCURRENT
INDEPENDENT
DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO)
Phenotypic Quality (PaTO)
Biological Process
(GO)
CELL AND CELLULAR COMPONENT
Cell
(CL)
Cellular Component
(FMA, GO)
Cellular Function
MOLECULE
Molecule
(ChEBI, SO,
RNAO, PRO)
Molecular Function
Molecular Process

4. 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
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 well-structured biological accurate ontologies

5. 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

6. OBO Foundry Principles Revised Proposals February 2010

7. 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)

8. 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 cross-product 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)

9. 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)

10. 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

11. 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

12. 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

13. Linking ontologies via cross products
Compound terms are formed out of simpler constituents
{cysteine, leucine, collagen,..}
X {biosynthesis, metabolism,..}

14. LEGO examples: GO+CL GO:germ cell nucleus =def GO:nucleus
ChEBI
PRO CC
cell
anat
envo
PATO MF BP
GO-CC 16
174
Cell 14 8 70 13
Gross anat
Envo 19 28
phen MP
273 10 ?
654
3300
5815
1040 WP
115 45
432
1450
686 TO
127 2
355 1
disease
GO-MF
2407
GO-BP
511
1085 55
GO:germ cell nucleus
=def
GO:nucleus
that is part_of
CL:germ cell

15. LEGO examples: CL+PATO
ChEBI
PRO CC
cell
anat
envo
PATO MF BP
GO-CC 16
174
Cell 14 8 70 13
Gross anat
Envo 19 28
phen MP
273 10
654
3300
5815
1040 WP
115 45
432
1450
686 TO
127 2
355
19? 1
disease
GO-MF
2407
GO-BP
511
1085 55
CL:spiny neuron
=def
CL:neuron
that has_quality
PATO:spiny

16. LEGO examples: CL+ChEBI
PRO CC
cell
anat
envo
PATO MF BP
GO-CC 16
174
Cell 14 8 70 13
Gross anat
Envo 19 28
phen MP
273 10
654
3300
5815
1040 WP
115 45
432
1450
686 TO
127 2
355
19? 1
disease
GO-MF
2407
GO-BP
511
1085 55
CL:estradiol secreting cell
=def
CL:secretory cell
that has_output
CHEBI:estradiol

17. LEGO examples: EnvO+ChEBI
PRO CC
cell
anat
envo
PATO MF BP
GO-CC 16
174
Cell 14 8 70 13
Gross anat
Envo 19 28
phen MP
273 10
654
3300
5815
1040 WP
115 45
432
1450
686 TO
127 2
355
19? 1
disease
GO-MF
2407
GO-BP
511
1085 55
ENVO:xylene contaminated soil
=def
ENVO:soil
that has_contaminant
CHEBI:xylene

18. LEGO examples: GO+Anatomy
ChEBI
PRO CC
cell
anat
envo
PATO MF BP
GO-CC 16
174
Cell 14 8 70 13
Gross anat
Envo 19 28
phen MP
273 10
654
3300
5815
1040 WP
115 45
432
1450
686 TO
127 2
355
19? 1
disease
GO-MF
2407
GO-BP
511
1085 55
GO:heart development
=def
GO:developmental process
that results_in_development_of
FMA:heart

19. LEGO examples: Diseases
MP:abnormal circulating glucose
=def
PATO:concentration
that inheres_in
MA:blood
towards
CHEBI:glucose
ChEBI
PRO CC
cell
anat
envo
PATO MF BP
GO-CC 16
174
Cell 14 8 70 13
Gross anat
Envo 19 28
phen MP
273 10
654
3300
5815
1040 WP
115 45
432
1450
686 TO
127 2
355 1
disease
GO-MF
2407
GO-BP
511
1085 55
gluconeogenesis
diabetes

20. 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

21. Varieties of application ontology
cross-border national parks
slims
cross-product ontologies
template ontologies:
Infectious Disease Ontology

22. RELATION
TO TIME
GRANULARITY
CONTINUANT
OCCURRENT
INDEPENDENT
DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO)
Phenotypic Quality (PaTO)
Biological Process
(GO)
CELL AND CELLULAR COMPONENT
Cell
(CL)
Cellular Component
(FMA, GO)
Cellular Function
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
Molecular Process
cross-border national parks: an ontology for studying the effects of viral infection on cell function in shrimp