Transcript Haendel.uberonx - Buffalo Ontology Site

Uberon – a multi-species ontology for phenomics and
translational science
Melissa Haendel, OHSU
Chris Mungall, LBNL
Carlo Torniai, OHSU
The problem: Data Silos
is_a (SubClassOf)
part_of
develops_from
surrounded_by
GO
FMA
multicellular
organismal process
EHDAA2
pharyngeal region
organ system
solid organ
respiratory
system
parenchymatous
organ
Lower
respiratory
tract
lobular organ
pleural sac
lung
respiratory gaseous
exchange
respiratory
primordium
respiratory system
process
lung bud
lung
MPO
abnormal respiratory
system morphology
MA
thoracic
cavity
organ system
thoracic
cavity organ
respiratory
system
abnormal lung
morphology
lung
abnormal pulmonary
acinus morphology
pulmonary
acinus
abnormal pulmonary
alveolus morphology
lung
alveolus
alveolar sac
Ontologies built for one species will
not work for others
http://ccm.ucdavis.edu/bcancercd/22/mouse_figure.html
http://fme.biostr.washington.edu:8080/FME/index.html
Anatomy Ontology Menagerie
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Mouse:
– MA (adult)
– EMAP / EMAPA (embryonic)
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Human
– FMA (adult)
– EHDAA2 (CS1-CS20)
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Amphibian
Reduced taxonomic scope
=
Reduced complexity
Historically little
coordination
– AAO
– XAO
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Fish
– ZFA
– TAO
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Nematode
– WBbt
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Arthropod
– FBbt (Drosophila)
– HAO
– Arthropod anatomy ontology
Contrast to:
Gene Ontology (GO)
(all kingdoms of life)
Semantic Similarity of Phenotypes
FMA+PATO
MP
ZFA+PATO
FBbt+PATO
"Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation." PLoS Biol 7(11): e1000247.
doi:10.1371/journal.pbio.1000247 Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE
Uberon info
• Size:
– >6500 classes
– >19000 relationships (50 relations)
– >2000 logical definitions
• Scope:
– Metazoa
• vertebrate bias, in particular mammals
• Availability
– many versions, in obo and owl
• http://uberon.org
– Source version is obo, compiled to owl using Oort
• Use
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Washington, Haendel et al, PlosBiology 2009
Mousefinder
Phenomenet
FANTOM5
What does uberon look like?
is_a (SubClassOf)
part_of
develops_from
capable_of
is_a (taxon equivalent)
only_in_taxon
anatomical
structure
endoderm
organ part
foregut
swim bladder
organ
NCBITaxon:
Actinopterygii
respiration organ
endoderm of
forgut
respiratory
primordium
GO: respiratory
gaseous exchange
pulmonary acinus
alveolus
NCBITaxon: Mammalia
lung
alveolus of lung
MA:lung
alveolus
FMA:
pulmonary
alveolus
alveolar sac
lung primordium
lung bud
FMA:lung
MA:lung
EHDAA:
lung bud
Uberon classes generalize species-specific ones, and connect to other ontologies via a
variety of relations
Logical definitions in GO using Uberon
GO:notochord formation: The formation of the notochord from the chordamesoderm. The notochord is composed
of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of
the neural tube. In vertebrates, the notochord contributes to the vertebral column.
Cross-Product Extensions of the Gene Ontology Journal of Biomedical Informatics 2010. Christopher J. Mungall and Michael Bada
and Tanya Z. Berardini and Jennifer Deegan and Amelia Ireland and Midori A. Harris and David P. Hill and Jane Lomax
Conclusions
Anatomy ontologies have been developed independently
and do not integrate well without additional help
•Uberon generalizes over species-specific anatomy classes
• Includes detailed anatomical knowledge via a variety of
relationships
• designed for reasoning
• Highly interconnected with other ontologies
• Homology is largely separated
• Growing number of applications
•For more info:
•http://uberon.org
http://genomebiology.com/2012/13/1/R5
Acknowledgments
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Uberon
Chris Mungall
George Gkoutos
Carlo Torniai
Suzanna Lewis
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Contributions
Alan Ruttenberg
Rob Hoehndorf
Wacek Kusnierczyk
Harry Hochheiser
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Ontologies
Jonathan Bard (EHDAA2)
Terry Meehan (CL)
Alex Diehl (CL)
Terry Hayamizu (MA/CL)
Onard Mejino (FMA)
David Hill (GO)
David Osumi Sutherland (FBbt/CARO)
Paul Schofield (MPATH)
Wasilla Dahdul (TAO/VAO)
Paula Mabee (TAO/VAO)
Erik Segerdell (XAO)
Monte Westerfield (ZFA)
Cynthia Smith (MP)
Maryanne Martone (NIF)
Frederic Bastian (vHOG)
Marc Robinson-Rechavi (vHOG)