the “über-ontology” (uberon) melissa häendel, chris müngall, george gkoütos cell ontology...
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The “über-ontology” (Uberon)
Melissa Häendel, Chris Müngall, George Gkoütos
Cell Ontology Workshop May, 2010
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Uberon consists of species-neutral classes derived from many contributing ontologies
What is Uberon?
UBERON:ear vesicleUBERON:
ear vesicle
D
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Uberon composition
Uberon classes subsume classes in contributing AOs
13629 Xrefs to 4087 classes
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Anatomical ontology domains and Uberon
CARO
TAOAAO
XAO ZFA
UBERON
MAFBbt
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Uberon advantages
• Logical definitions in species-neutral ontologies • Ontology alignment • Mapping validation • Reasoning across species• Homology neutral
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Logical definitions in GO using Uberon
Uberon can make explicit many anatomical definitions already in GO
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.
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Logical definitions in CL using Uberon
UBERON: trachea
UBERON: respiratory airway
CL: tracheal epithelial cell
CL: epithelial cell
is_apart_of
is_a
Vertebrataonly_in_taxon
Uberon trachea: A trachea held open by up to 20 C-shaped rings of cartilage. The trachea is the portion of the airway that attaches to the bronchi as it branches.[GO:0060438, Wikipedia:Vertebrate_trachea]
Uberon can help ensure applicability of definitions in CL that rely on gross anatomical structures.
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Uberon logical definitions represent functional, developmental, spatial, etc., axes of classification
Logical definitions in Uberon using external ontologies
UBERON: trachea
UBERON: respiratory airway
CL: tracheal epithelial cell
CL: epithelial cell
is_apart_of
is_a
Vertebrataonly_in_taxon
UBERON: respiratory system
part_of
GO: respiratory gaseous exchangecapable_of
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Differences in bone and bone tissue representation
Ontology alignment
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Using Uberon for alignment facilitates identification of missing classes
Ontology alignment
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Using Uberon to validate ontology mappings
Class A Class B Biportal Uberon
FMA portion of blood MA blood No Yes
ZFA Macula MA macula Yes No
ZFA aortic arch MA arch of aorta Yes No
ZFA hypophysis MA pitiuitary No Yes
FMA gustatory organ FBbt gustatory sensory organ
No Yes
FMA extensor retinaculum of wrist
MA retina Yes No
FMA tibia FBbt tibia Yes No
Many of these mappings have higher level least-common subsumers
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Developmental Biology, Scott Gilbert, 6th ed.
Using Uberon to validate ontology mappings
Text match mappingFruit fly ‘tibia’ Human ‘tibia’
UBERON: tibia
UBERON: bone
is_a
is_a
is_a
Vertebrata
Drosophila melanogaster
part_of
Homo sapiens
is_a
only_in_taxon
part_of
NOT is_a
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Text matchingStem and synonym
matching
Reasoning• Keep axioms that are
consistent across AOs• automated
consistency checks for disjointeness violations
Uberon iterative development cycle
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Reasoning across species: querying for genes in similar structures
• Genetic mechanisms may be reused in analogous structures• Structures may be homologous in ways that are yet undetermined
Vertebrate chambered heart
Arthropod dorsal vessel
Xavier-Neto et al., Cell Mol Life Sci, 2007
Process Conserved genesSpecification tinman/nkx2.5, wnts
A-P patterning Hox genes, RA
Morphogenesis Seven-up/Couptf-II
Uberon heart: A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GO:0007507]Xrefs to FBbt, ZFA, FMA, etc.
Uberon has a heart.
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Panganiban et al., PNAS, 1997
Distal-less orthologs participate in distal-proximal pattern formation and appendage morphogenesis
Distal-less (Dll) expression
mouse limbsea urchin tube feet
ascidian ampulla polychaete parapodia
Reasoning across species: querying for genes in similar structures
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What about homology? Evolutionary community: Capture multiple homologous_to statements external to Uberon using evidence and attribution. Allows for phylogenetic optimization.
Model organism databases: Use single well-established homologous_to relations between structures in different MODs to create homology links between structures.
ZFIN
Uberon is homology-neutral
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Uberon Conclusions
• Species-neutral ontology that subsumes contributing taxon-specific anatomy ontologies
• Useful for ontology alignment
• Useful for mapping validation
• Can be used for logical definitions in other species-neutral OBO ontologies
• Inferred multiple inheritance to represent non-structural axes of anatomical classification
• Allows query across species for similar structures and separate homology attribution
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http://github.com/cmungall/uberon
Uberon is available at:
http://obofoundry.org/wiki/index.php/UBERON:Main_Page
More information is here:
(open uberon_edit.obo with the reasoner on)