OBO-Foundry

OBO was conceived and announced in in 2001

10 october 2001

Michael Ashburner and Suzanna Lewis with acknowledgements of others in the GO community.

open biology ontologies - obo.org

The success of GO leads us to propose the formation of an umbrella body which we call OBO - open biology ontologies. OBO would act as an umbrella site for GO and other ontologies within the broad domain of biology.

It is critical that ontologies are developed cooperatively

so thattheir classification

strategies augment one another.

Open Biomedical Ontology

Original OBO Criteria

1. The ontology must be OPEN and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

2. The ontologies are in, or can be instantiated in, a COMMON SHARED SYNTAX. This may be either the OBO syntax, extensions of this syntax, or OWL.

3. The ontology must be ORTHOGONAL to other ontologies already lodged within OBO.

4. The ontologies possesses a UNIQUE IDENTIFIER space within the OBO Foundry.

5. The ontologies include TEXTUAL DEFINITIONS for all terms.

Implicit ontologies

cysteine biosynthesis (ChEBI) myoblast fusion (Cell Type Ontology) hydrogen ion transporter activity (ChEBI) snoRNA catabolism (Sequence Ontology) wing disc pattern formation (Drosophila anatomy) epidermal cell differentiation (Cell Type Ontology) regulation of flower development (Plant anatomy) interleukin-18 receptor complex (not yet in OBO) B-cell differentiation (Cell Type Ontology)

B-cell

differentiation

lymphocytedifferentiati

onlymphocyte

B-cell

GO CL

is_a

cell differentiation bloodcell

B-cellactivatio

n

Relations to Other Ontologies

[Term]id: GO:0030183name: B-cell differentiationis_a: GO:0042113 ! B-cell activationis_a: GO:0030098 ! lymphocyte differentiationintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000236 ! B-cell

[Term]id: CL:0000236name: B-cellis_a: CL:0000542 ! lymphocytedevelops_from: CL:0000231 ! B-lymphoblast

Augmented GO

CELL Ontology

Bone length short very Compound observable (disease?)

observable attribute value units qualifier assay conditions

obesity body mass 30 BMI increased body fat analysis

normal

obesity blood triglyceride levels

400 ? blood test

normal

hypertension artery elasticity 140/90 mm Hg

elevated

Observable Attribute Value Qualifier

Assay

Environmental contribution

Genetic contribution

Conditions Units

TIGR, December 6-7, 2002

There are many ontologies needed

Anatomy Cell Chemical

Drug

Disease Environmental

context . . .

Qualifier Unit GO - biological

process GO - molecular

function GO - cellular

component

Latest OBO Criteria

1. The ontology is OPEN and available to be used by all.2. The ontology is in, or can be instantiated in, a

COMMON FORMAL LANGUAGE.3. ORTHOGONALITY: They commit to working with

other Foundry members to ensure that, for any particular domain, there is community convergence on a single controlled vocabulary.

4. IDENTIFIERS: The ontology possesses a unique identifier space within OBO.

5. The ontology includes TEXTUAL DEFINITIONS and where possible equivalent formal definitions of its terms.

New OBO Criteria

6. The developers of the ontology agree in advance to COLLABORATE with developers of other OBO Foundry ontology where domains overlap.

7. UPDATE: The developers of each ontology commit to its maintenance in light of scientific advance, and to soliciting community feedback for its improvement.

8. VERSIONING: The ontology provider has procedures for identifying distinct successive versions to ensure BACKWARDS COMPATIBITY with annotation resources already in common use

9. CLEARLY BOUNDED: The ontology has a clearly specified and clearly delineated content.

10. DOCUMENTATION: The ontology is well-documented.11. USERS: The ontology has a plurality of independent users.12. COMMON ARCHITECTURE: The ontology uses relations

which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.*

The success of ontology alignment demands that ontological relations (is_a, part_of, ...) have the same meanings in the different ontologies to be aligned.

Genome Biology 6:R46, 2005.

Agree on relations

Orthogonality of ontologies implies

additivity of annotations

If we annotate a database or body of literature with one high-quality biomedical ontology, we should be able to add annotations from a second such ontology without conflicts

To create the conditions for a step-by-step evolution towards robust gold standard reference ontologies in the biomedical domain.

To introduce some of the features of scientific peer review into biomedical ontology development.

obofoundry.org

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)

MOLECULE Molecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Building out from the original GO

Why Survey

Improve

Domain covered

?

Public?

Active?

Applied?

Community?

DevelopSalvage

Collaborate & Learn (Listen to Barry)

yes

no

Necessary character of a computational environment for

biological research Sustainable There must be mechanism for maintaining the

environment (that is less than the initial cost). Adaptable

It must work for the complete spectrum of data types, from genomics to clinical trials

It must continually adapt to new knowledge and new technologies

Interoperable The capability of easily integrating data from a variety of

sources. Evolvable

Mechanisms must be put in place to respond to the needs of the biomedical research community. They provide the primary selection pressure on the evolution of the technology.

There is no requirement that ontology construction

be done using any particular technology.

The Scientific Method

A body of techniques for investigating phenomena and acquiring new knowledge, as well as for correcting and integrating previous knowledge. It is based on observable, empirical, measurable evidence, and subject to rules of reasoning.

Isaac Newton (1687, 1713, 1726). "Rules for the study of natural philosophy", Philosophiae Naturalis Principia Mathematica, Book 3, The System of the World. Third edition, the 4 rules as reprinted on pages 794-796 of I. Bernard Cohen and Anne Whitman's 1999 translation, University of California Press ISBN 0-520-08817-4, 974 pages.

No text search can retrieve all of the correct results, and

nothing more

Negative Regulator of the PHO system

CDK5 protein

Hypothetical protein

Cyclin-dependent protein kinase 5

Cell division protein kinase 5

Protein kinase

CDC2-like serine/threonine-protein kinase CRP

Hypothetical protein T27E9.3

ENSANGP00000018692

Serine/threonine-protein kinase pef1

Contrast—two types of ontology

Natural-science ontologies capture terminology-level knowledge underlying the best current science (e.g. GO, PATO, SO)

Administrative ontologies prepared for specific, local purposes (e.g. billing, bloodbank, lab workflow, literature indices)

Scientific ontologies are realism-based

Elements for Success 2

Keep It Simple: lowest possible barrier to entry

Technology independence “With new data, we change our minds”

An ontology must adapt to reflect current understanding of reality

Plan for and anticipate changes Stay close to your users

biologists and medical researchers

Truth springs from arguments amongst

friends.

David Hume

With thanks

to*

Seth Carbon John Day-Richter Karen Eilbeck Mark Gibson Chris Mungall Shu Shengqiang Nicole

WashingtonBerkeley

BOP

BIRN DictyBase FlyBase MGI NESCENT ZFIN And more…

Others… Mark Musen Barry Smith Monte Westerfield Michael

Ashburner Daniel Rubin And more…

NCBO*Without even going into our other projects: Apollo, SO, Chado, GMOD, DAS, Reactome…

Michael Ashburner

Judith Blake J. Michael Cherry David Hill Midori Harris Rex Chisholm And many more…

GO