Uberon – a multi-species ontology covering the anatomy of animals

Chris Mungall, Lawrence Berkeley Laboratory

PAG Ontology WorkshopSan Diego 2013

Anatomical ontologies are vital for plant and animal genomics

• High throughput transcriptomic and phenomic data

• Need to analyze within and across species

Most animal anatomy ontologies are species specific

• Mouse:– MA (adult)– EMAP / EMAPA (embryonic)

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

• Amphibian– XAO (Xenopus)

• Fish– ZFA – (Zebrafish)

• Nematode– WBbt – (C elegans)

• Arthropod– FBbt (Drosophila)

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

Uberon: a multi-species anatomy ontology

• Contents:– Over 8,000 classes (terms)– Multiple relationships, including subclass, part-of and

develops-from• Scope: metazoa (animals)

– Current focus is chordates– Federated approach for other taxa

• Uberon classes are generic / species neutral– ‘mammary gland’: you can use this class for any mammal!– ‘lung’: you can use this class for any vertebrate (that has lungs)

Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012). Uberon, an integrative multi-species anatomy ontology. Genome Biology, 13(1), R5. doi:10.1186/gb-2012-13-1-r5 http://genomebiology.com/2012/13/1/R5

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

Bridging anatomy ontologies

ZFA

MA FMA

EHDAA2EMAPA

Uberon

CJ Mungall, C Torniai, GV Gkoutos, SE Lewis, MA Haendel.Uberon, an integrative multi-species anatomy ontology. Genome biology 13 (1), R5

SNOMED

NCIt

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

Inter-ontology links

Uberon PURLs

Permanent URL

Humans see HTML view

Uberon PURLs

Machines see this

Different versions for different purposesontology contents

basic simple relationships

http://purl.obolibrary.org/obo/uberon/basic.owl

uberon main ontology

http://purl.obolibrary.org/obo/uberon.owl

merged main ontology + links to GO, CL, NCBITaxon, NBO

http://purl.obolibrary.org/obo/uberon/merged.owl

Composite-metazoan

Uberon plus species-specific ontology classes merged in http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl

http://uberon.org Formats: • OBO-Format • OWL

Text processingOntology matchingWikipedia extraction

Expert CurationMultiple knowledge

acquisution toolsContent meetingsExpert interviews

Automated Reasoning• Automated QC checks in

Jenkins pipeline[*]• Automated hierarchy building

using OWL reasoners

Efficient Ontology Development

* http://bio-ontologies.knowledgeblog.org/405 http://owltools.googlecode.com/

Applications

• Phenomics: comparing phenotypes across species

• Transcriptomics: gene expression• Systematics and evolutionary biology

Finding disease models

• Washington, N. L., Haendel, M. A., Mungall, C. J., Ashburner, M., Westerfield, M., & Lewis, S. E. (2009). Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation. PLoS Biol, 7(11). Public Library of Science. doi:10.1371/journal.pbio.1000247

• Chen, C.-K., Mungall, C. J., Gkoutos, G. V., Doelken, S. C., Koehler, S., Ruef, B. J., Smith, C., et al. (2012). MouseFinder: Candidate disease genes from mouse phenotype data. Human mutation, 33(5), 858-66. doi:10.1002/humu.22051

Uberon and FANTOM5

Kenneth Baillie, FANTOM5 consortium

Niknejad, A., Comte, A., Parmentier, G., Roux, J., Frederic, B., & Robinson-rechavi, M. (2011). vHOG , a multi-species vertebrate ontology of homologous or- gans groups. Ecology, 1-5.

http://bgee.unil.ch

Evo-devo applications

LAMHDI: Linking across models for human disease initiative

• Integrating multiple data sources– OMIM, OMIA (Online Mendelian Inheritance in

Animals), model organisms, phenotype and trait data, etc

– Annotating using ontology terms• Providing novel semantic linking and

navigation methods

http://lamhdi.org (early prototype)https://neuinfo.org/mynif/ (search)

Beyond the core model organisms

• Phase 1 development: 2009-2011– Core model organism and human anatomy

• Phase 2 development: 2012– Vertebrate skeletal system

• Collaboration with phenoscape• Incorporate TAO (teleost), AAO (amphibian), VSAO (vertebrate

skeleton)

• Phase 3 development: 2013-– Other taxa

• E.g– Ruminants– Aves

Conclusions

• Most animal anatomy ontologies are specialized for core model organisms or humans

• Uberon bridges across species-specific anatomical ontologies and is a complete ontology in its own right

• Uberon is richly connected with other orthogonal ontologies and is being used for annotation in a variety of projects

Get involved

• Tracker– http://purl.obolibrary.org/obo/uberon/tracker

• Mailing list– https://lists.sourceforge.net/lists/listinfo/obo-anatomy

• Website– http://uberon.org

• Data (coming soon)– http://bgee.unil.ch– http://kb.phenoscape.org– http://lamhdi.org

AcknowledgmentsUberon Developers• Alex Dececchi• Nizar Ibrahim• Melissa Haendel

Contributors• Carlo Torniai (eagle i)• George Gkoutos (NBO)• Jonathan Bard (EHDAA2)• Terry Meehan (CL)• Alex Diehl (CL)• Terry Hayamizu (MA/CL)• Yvonne Bradford (ZFA)• Ceri van Slyke (ZFA)• David Hill (GO)• David Osumi Sutherland

(FBbt/CARO)• Paul Schofield (MPATH)• Wasilla Dahdul

(TAO/VAO)

Applications and software development• Frederic Bastian• Heiko Dietze• Jim Balhoff• Paula Mabee• Suzanna Lewis

Contributors• Erik Segerdell (XAO /

Phenotype RCN)• Paul Sereno (Phenoscape)• Monte Westerfield (ZFA)• Cynthia Smith (MP)• Maryanne Martone (NIF)• Bill Bug (NIF)• Aurelie Comte (Bgee)• Anna Niknejad (Bgee)• Marc Robinson-Rechavi (Bgee)• Robert Druzinsky (FEED)• Brian K Hall (neural crest)• Sarah Whitcher Kansa• Ann Maglia (AAO)• Paul Sereno (Phenoscape)• David Blackburn (Phenoscape)