An Ontology-Based Approach for Computational Phenomics ... · 10/7/2009 · A controlled...
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Stanford Center for Biomedical Informatics Research An Ontology-Based Approach for Computational Phenomics: Application to Autism Spectrum Disorder
Transcript of An Ontology-Based Approach for Computational Phenomics ... · 10/7/2009 · A controlled...
Stanford Center
for Biomedical Informatics Research
An Ontology-Based Approach for
Computational Phenomics:
Application to Autism Spectrum
Disorder
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Psychiatric Genetics
Phenotyping
Terminology
Ontology
Logic
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Hasler G,et al. Toward constructing
an endophenotype strategy for
bipolar disorders. Biological
Psychiatry (2006)
Represent
findings and
their links
using
structured
knowledge
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Freimer & Sabatti, Nature Genetics (2003)
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Mailman, M.D. Nature Genetics (2007)
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Query and Reporting
BIRN Services
& Resources
NDAR System
Security
Portal
Grid
Computing
Collaboration
Data Storage
ManagementData Integration
ToolsAuditingUser
Management
Subject Tracking
& Management
Clinical Assessments
(OpenClinica)
Common
Measures
Study
Management
Neuroimaging
Image Analysis
Image
Processing
Image data
access
Genomics
Genomics data
access
Data Integration
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Tu, S. W. AMIA Annual Proceedings (2008)
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Clinical Research Study
Clinical Trial StudyCase Study
Controlled Case Study Study Arms
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SubjectGenotype
Phenotype
mutIn-
RELN
Macro-
encephaly
011451
hasResult
isBearerOf
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A controlled terminology for annotation of
BIRN data sources, focusing on imaging
data from human subjects and mouse
models
Terms cover neuroanatomy, molecular
species, behavioral and cognitive
processes, subject information,
experimental practice and design
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CONTINU ANT OCCURRENT RELATI ON TO
TIM E
GRAN ULAR ITY INDE PENDENT DEPENDENT
ORGAN AN D
ORGAN ISM
Orga nism
(NCBI
Taxonomy)
Anatomical Entit y
(FMA, CARO)
Organ
Function
(FMP, CPR O)
Orga nism -Level Process
(GO)
CELL AND
CELLUL AR
COMP ONENT
Cell
(CL)
Cel lular Compo nent
(FMA ,GO)
Cel lular Function
(GO)
Phenot ypic Quality (PaTO )
Cel lular Process
(GO)
MOL ECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Molecular Process
(GO)
Chris Mungall, PATO
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hasParent(?x, ?y) ^ hasBrother(?y, ?z)
→ hasUncle(?x, ?z)
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Person(Amar) ^ hasSibling(Amar, ?s)
^ Woman(?s)
→ hasSister(Amar, ?s)
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Person(?p) ^ hasAge(?p,?age)
^ swrlb:lessThan(?age,17)
→ Child(?p)
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Figure 1. The representation of data collected through the ADI-2003 autism assessment instrument as part of the autism
ontology.
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Figure 2. The representation of the Status of age of words phentotype group as a OWL class partition by the possible statuses.
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ADI_2003_result(?assessment) ^
acqorlossoflang_aword(?assessment,?wordage) ^
swrlb:greaterThan(?wordage, 24) ^
subject_id(?assessment, ?subjectId) ^
orgtax:Human(?subject) ^
subject_id(?subject, ?subjectId)
→ birn_obo_ubo:bearer_of(?subject, Delayed_word)
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Young, L. IEEE CBMS (2009)
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Develop an ontology of endophenotypes that maps brain connectivity, neural deficits, and genetic markers into a subject domain theory
Develop logic-based methods to encode and classify endophenotypes based on multi-scale measurements
Create tools to acquire new endophenotypes and annotate phenotype-genotype findings in online resources such as published literature
Develop query-elicitation methods that can evaluate hypotheses about the subject domain theory of endophenotypes using deductive inference
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Dat abase
Phenot ype
Def init ions
New
Associat ions
Query
Catalog Analysis
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