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Workshop
description
Transcript of Workshop
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Workshop7.00 Welcoming Remarks
7.15 Barry Smith (Buffalo, NY)
7.40 Lindsay Cowell (Duke University, NC)
8.05 Nigam Shah (Stanford University, CA)
8.30 Break
8.40 Dave Parrish (Immune Tolerance Network, PA)
9.05 Yannick Legre (Healthgrid, France)
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The OBO Foundry: From Basic Biology to Genomic Medicine
Barry SmithUniversity at Buffalo
National Center for Biomedical Ontologyhttp://ontology.buffalo.edu/smith
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where in the body ? where in the cell ?
what kind of disease process ?
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UMLS, Semantic Web, Moby, wikis, etc.
let a million flowers bloom
integration relies on post hoc mappings
how create broad-coverage semantic annotation systems for biomedicine?
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for science
create an evolutionary path towards evidence-based terminology
a new approach
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a shared portal for 60+ ontologies (low regimentation)
http://obo.sourceforge.net
First step (2001)
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Second step (2004):logic-based reform efforts
GO linked to other OBO ontologies
id: CL:0000062name: osteoblastdef: "A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." is_a: CL:0000055relationship: develops_from CL:0000008relationship: develops_from CL:0000375
GO
Cell type
New Definition
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=Osteoblast differentiation: Processes whereby an osteoprogenitor cell or a cranial neural crest cell acquires the specialized features of an osteoblast, a bone-forming cell which secretes extracellular matrix.
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The OBO FoundryThe OBO Foundryhttp://obofoundry.org/http://obofoundry.org/
Third step (2006)Third step (2006)
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a family of interoperable gold standard biomedical reference ontologies to serve the annotation of
model organism databases scientific literature clinical data experimental results
http://obofoundry.org/http://obofoundry.org/
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Foundry developers have agreed in advance to accept a common set of principles designed to ensure
compatibility
interoperability
formal robustness
http://obofoundry.org/http://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)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Building out fron the original GO
http://obofoundry.org/http://obofoundry.org/
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Ontology Scope URL Custodians
Cell Ontology (CL)
cell types from prokaryotes to mammals
obo.sourceforge.net/cgi-
bin/detail.cgi?cell
Jonathan Bard, Michael Ashburner, Oliver Hofman
Chemical Entities of Bio-
logical Interest (ChEBI)
molecular entities ebi.ac.uk/chebiPaula Dematos,Rafael Alcantara
Common Anatomy Refer-
ence 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
analysisfugo.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)
relationsobo.sf.net/
relationshipBarry 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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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.
CRITERIA
http://obofoundry.org/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 ensuring that there is community convergence on a single controlled vocabulary for each domain
http://obofoundry.org/http://obofoundry.org/
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CRITERIA
IDENTIFIERS: The ontology possesses a unique identifier space within OBO.
VERSIONING: The ontology provider has procedures for identifying distinct successive versions.
The ontology includes textual definitions for all terms.
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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CLEARLY BOUNDED: The ontology has a clearly specified and clearly delineated content.
DOCUMENTATION: The ontology is well-documented.
USERS: The ontology has a plurality of independent users.
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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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
CRITERIA
http://obofoundry.org/http://obofoundry.org/
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Ontology of Biomedical Investigations
with thanks to Trish Whetzel (FuGO Working Group)
FuGO = Functional Genomics Investigation Ontology
OBI née FuGO
http://obofoundry.org/http://obofoundry.org/
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controlled vocabulary for biomedical investigations including
protocols instrumentationmaterialdata types of analysis and statistical tools
applied to the data
OBI
http://obofoundry.org/http://obofoundry.org/
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OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP),Environmental genomics MGED RSBI Group, www.mged.org/Workgroups/rsbiGenomic Standards Consortium (GSC),
www.genomics.ceh.ac.uk/genomecatalogueHUPO Proteomics Standards Initiative (PSI), psidev.sourceforge.netImmunology Database and Analysis Portal, www.immport.orgImmune Epitope Database and Analysis Resource (IEDB),
http://www.immuneepitope.org/home.doInternational Society for Analytical Cytology, http://www.isac-net.org/Metabolomics Standards Initiative (MSI), Neurogenetics, Biomedical Informatics Research Network (BIRN),Nutrigenomics MGED RSBI Group, www.mged.org/Workgroups/rsbiPolymorphismToxicogenomics MGED RSBI Group, www.mged.org/Workgroups/rsbiTranscriptomics MGED Ontology Group
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Clinical Trial Ontology
To serve merger of data schemasTo serve flexibility of collaborative clinical
trial researchTo serve design and management of
clinical trialsTo serve data access and reuse – send
me all trials which ...
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Randomized controlled trials
http://rctbank.ucsf.edu/ontology/outline/index.htm
RCT Schema – a ‘frame-based ontology’
supporting TrialBank
RCT
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RCT Top-Level Class Hierarchy
Root – Secondary-study – Trial-details – Trial – Concept
• Generic-concept • Population-concept • Protocol-concept • Design-concept • Outcome-concept • Administrative-concept • Intervention-concept
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RCT: Trial Details
Trial-details • Erratum • Publication-details • Conclusion-details • Background-details • Stopping-details • Retraction-details • Correction-details • Fraud-details
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– Concept • Generic-concept
– Term-information – Time-entity – Rule-concept – Situation
• Population-concept – Subgroup – Population – Recruitment
• Protocol-concept – Follow-up-activity
RCT: Concept
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Ontology vs. Schema
Separate development of medical ontologies and terminologies such as SNOMED
and medical information models and database schemas
Rector, et al., Binding Ontologies and Coding Systems to Electronic Health Records and Messages
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Ontology vs. Schema
diabetes => disease
diabetes => string
temperature => quality
temperature => integer
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Valid Specifications for data structures“Valid diabetic data structures have: a topic of code for diabetes, a diagnosis code that is diabetes or one of its subcodes, and a brittleness code that is one of the subcodes for diabetic brittlenes and nothing else”
Ontology“All diabetes are metabolic diseases”“John has diabetes & it is brittle and long-standing”
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– Concept • Administrative-concept
– Publication-concept – Study-site – Person
• Intervention-concept – Blinding-concept – Intervention-step – Intervention
RCT: Concept
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Two kinds of entities
occurrents (processes, events, happenings)
continuants (objects, qualities, states...)
You are a continuant
Your life is an occurrent
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An instrument is a continuantA protocol is a continuant
A trial is an occurrentA selection process is an occurrent
Two kinds of entities
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OBI Top Level
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OBO Occurrent
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CTO
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CTO Continuant
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CTO Occurrent
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Clinical Trial Ontology Working Group
http://www.bioontology.org/wiki/
Workshop on May 16-17, 2007
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