Uberon – a multi-species ontology for phenomics and translational science

Melissa Haendel, OHSUChris Mungall, LBNLCarlo Torniai, OHSU

lung

lung

respiratory gaseous exchange

lobular organ

parenchymatous organ

solid organ

pleural sac

thoracic cavity organ

thoracic cavity

multicellular organismal process

abnormal lung morphology

abnormal respiratory system morphology

GO

MPO

MA

FMA

abnormal pulmonary acinus morphology

abnormal pulmonary alveolus morphology

lungalveolus

respiratory system process

organ system

respiratory system

Lower respiratory

tract

alveolar sac

pulmonary acinus

organ system

respiratory system

EHDAA2

lung

lung bud

respiratory primordium

pharyngeal region

develops_frompart_of

is_a (SubClassOf)

surrounded_by

The problem: Data Silos

Ontologies built for one species will not work for others

http://fme.biostr.washington.edu:8080/FME/index.html

http://ccm.ucdavis.edu/bcancercd/22/mouse_figure.html

Anatomy Ontology Menagerie• Mouse:

– MA (adult)– EMAP / EMAPA (embryonic)

• Human– FMA (adult)– EHDAA2 (CS1-CS20)

• Amphibian– AAO– XAO

• Fish– ZFA– TAO

• Nematode– WBbt

• Arthropod– FBbt (Drosophila)– HAO– Arthropod anatomy ontology

Reduced taxonomic scope =Reduced complexity

Contrast to: Gene Ontology (GO)(all kingdoms of life)

Historically littlecoordination

Semantic Similarity of Phenotypes

"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

FMA+PATO MP ZFA+PATO FBbt+PATO

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– Washington, Haendel et al, PlosBiology 2009– Mousefinder– Phenomenet– FANTOM5

anatomical structure

endoderm of forgut

lung bud

lung

respiration organ

organ

foregut

alveolus

alveolus of lung

organ part

FMA:lung

MA:lung

endoderm

GO: respiratory gaseous exchange

MA:lung alveolus

FMA: pulmonary

alveolus

is_a (taxon equivalent)

develops_frompart_of

is_a (SubClassOf)

capable_of

NCBITaxon: Mammalia

EHDAA:lung bud

only_in_taxon

pulmonary acinus

alveolar sac

lung primordium

swim bladder

respiratory primordium

NCBITaxon:Actinopterygii

Uberon classes generalize species-specific ones, and connect to other ontologies via a variety of relations

What does uberon look like?

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.orghttp://genomebiology.com/2012/13/1/R5

Acknowledgments• Uberon• Chris Mungall• George Gkoutos• Carlo Torniai• Suzanna Lewis

• 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)

• Contributions• Alan Ruttenberg• Rob Hoehndorf• Wacek Kusnierczyk• Harry Hochheiser