Transcript OBOFoundry_FuGO - Buffalo Ontology Site

The OBO Foundry
http://obofoundry.org/
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A prospective standard
designed to guarantee interoperability of ontologies from
the very start (contrast to: post hoc mapping)
established March 2006
11 initial candidate OBO ontologies – focused primarily on
1. basic science domains of natural objects
2. investigation domains (of equipment and other artifacts)
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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 anatomical
structures
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
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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)
Organism-Level
Process
(GO)
Cellular Process
(GO)
Molecular
Process
(GO)
Annotations plus ontologies yield an ever-growing
computer-interpretable map of biological reality.
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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)
Building out from the original GO
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Under consideration:
Natural
 Disease Ontology (DO)
 Drug Ontology (DrO)
 Environment Ontology (EnvO)
 Systems Biology Ontology (SBO)
 Upper Biomedical Ontology (OBO UBO)
Artifactual
 Clinical Trial Ontology (CTO)
 Biomedical Imaging Ontology (BIO)
 (Upper-Level) Investigation Ontology (IO)
 Unit Ontology (UO)
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RELATION
TO TIME
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
CELL AND
CELLULAR
COMPONENT
MOLECULE
Anatomica Organ
Organism
l Entity
Function
NCBI
(FMA,
(FMP,
Taxonomy?
CARO)
CPRO)
Cell
(CL)
Cellular
Compone
nt
(FMA,
GO)
Molecule
(ChEBI, SO,
RnaO, PrO)
Phenotypic
Quality
(PaTO)
Biological
Process
(GO)
Pathological
Cellular
Function
(GO)
Molecular Function
(GO)
Molecular
Process
(GO)
Investigation
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Investigation
Ontology
Functional
Genomic
Investigation
Ontology
Clinical Trial
Ontology
Imaging
Ontology
Unit
Ontology
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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.
The OBO Foundry
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 working with
other Foundry members to ensure that, for any
particular domain, there is community
convergence on a single controlled vocabulary.
The OBO Foundry
http://obofoundry.org/
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for science
orthogonality of ontologies
implies additivity of annotations
if we annotate a database or body of literature or
images with one high-quality biomedical ontology,
we should be able to add annotations from a
second such ontology without conflicts
The OBO Foundry
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 to ensure BACKWARDS COMPATIBITY
with annotation resources already in common use
 The ontology includes TEXTUAL DEFINITIONS
and where possible equivalent formal definitions of
its terms.
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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.
The OBO Foundry
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
The OBO Foundry
http://obofoundry.org/
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OBO Relation Ontology
Foundational
is_a
part_of
Spatial
located_in
contained_in
adjacent_to
Temporal
transformation_of
derives_from
preceded_by
Participation
has_participant
has_agent
The OBO Foundry
http://obofoundry.org/
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IT WILL GET HARDER
Further criteria will be added over time in light of
lessons learned in order to bring about a gradual
improvement in the quality of Foundry ontologies
ALL FOUNDRY ONTOLOGIES WILL BE SUBJECT
TO CONSTANT UPDATE IN LIGHT OF
SCIENTIFIC ADVANCE
The OBO Foundry
http://obofoundry.org/
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IT WILL GET HARDER
But not everyone needs to join
The Foundry is not seeking to serve as a check on
flexibility or creativity
ALL FOUNDRY ONTOLOGIES WILL ENCOURAGE
COMMUNITY CRITICISM, CORRECTION AND
EXTENSION WITH NEW TERMS
The OBO Foundry
http://obofoundry.org/
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PROPOSED NEW CRITERIA
Single inheritance
All terms in ontology are singular nouns
Term-by-term versioning
Uniform naming conventions
Independence of ontology from computational idiom
The OBO Foundry
http://obofoundry.org/
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GOALS
 to introduce some of the features of SCIENTIFIC
PEER REVIEW into biomedical ontology
development
 CREDIT for high quality ontology development work
 KUDOS for early adopters of high quality ontologies /
terminologies e.g. in reporting clinical trial results
The OBO Foundry
http://obofoundry.org/
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GOALS
 to providing a FRAMEWORK OF RULES to
counteract the current policy of ad hoc creation
of new annotation schemas by each clinical
research group by
 REUSABILITY: if data-schemas are formulated
using a single well-integrated framework
ontology system in widespread use, then this
data will be to this degree itself become more
widely accessible and usable
The OBO Foundry
http://obofoundry.org/
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GOALS

to serve as BENCHMARK FOR IMPROVEMENTS in
discipline-focused terminology resources

once a system of interoperable reference ontologies is
there, it will make sense to calibrate existing
terminologies in its terms in order to achieve more robust
alignment and greater domain coverage

exploit the avenue of EVIDENCE-BASED MEDICINE
(NIH CLINICAL RESEARCH NETWORKS) to foster their
use by clinicians
The OBO Foundry
http://obofoundry.org/
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MICheck
June 2006: establishment of MICheck:
reflects growing need for prescriptive checklists
specifying the key information to include when
reporting experimental results (concerning
methods, data, analyses and results).
The OBO Foundry
http://obofoundry.org/
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MICheck Foundry
 MICheck: ‘a common resource for minimum
information checklists’ analogous to OBO /
NCBO BioPortal
 MICheck Foundry: will create ‘a suite of selfconsistent, clearly bounded, orthogonal,
integrable checklist modules’ *
* Taylor CF, et al. Nature Biotech, in press
The OBO Foundry
http://obofoundry.org/
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From OBO to OBD: Open
Biomedical Data
OBD is part of NCBO BioPortal:
houses data annotated using ontologies
– open to all
– with a flexible ontology-based schema
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OBD Foundry
The OBD Foundry
– data annotated using OBO Foundry ontologies
– emphasis on coordination especially with
NCBO Driving Biological Projects
• linking genes to disease via model organism
mutant phenotypes
• high-quality clinical trial data
• additivity of annotations implies additivity of data
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