OBO-Foundry. OBO was conceived and announced in in 2001 10 october 2001 Michael Ashburner and...
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Transcript of OBO-Foundry. OBO was conceived and announced in in 2001 10 october 2001 Michael Ashburner and...
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.
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
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