The “über-ontology” (Uberon)

Melissa Häendel, Chris Müngall, George Gkoütos

Cell Ontology Workshop May, 2010

Uberon consists of species-neutral classes derived from many contributing ontologies

What is Uberon?

UBERON:ear vesicleUBERON:

ear vesicle

D

Uberon composition

Uberon classes subsume classes in contributing AOs

13629 Xrefs to 4087 classes

Anatomical ontology domains and Uberon

CARO

TAOAAO

XAO ZFA

UBERON

MAFBbt

Uberon advantages

• Logical definitions in species-neutral ontologies • Ontology alignment • Mapping validation • Reasoning across species• Homology neutral

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.

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.

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

Differences in bone and bone tissue representation

Ontology alignment

Using Uberon for alignment facilitates identification of missing classes

Ontology alignment

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

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

Text matchingStem and synonym

matching

Reasoning• Keep axioms that are

consistent across AOs• automated

consistency checks for disjointeness violations

Uberon iterative development cycle

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.

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

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

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

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)