Uberon is a multi-species anatomy ontology covering animal anatomy. It contains over 8,000 classes describing anatomical structures across metazoans in a species-neutral way. Uberon bridges species-specific anatomy ontologies and allows cross-species analysis of high-throughput genomics and phenomics data. It is extensively connected to other biomedical ontologies and has been applied in projects involving phenomics, transcriptomics, systematics and finding disease models.

1. Uberon – a multi-species ontology covering the
anatomy of animals
Chris Mungall, Lawrence Berkeley Laboratory
PAG Ontology Workshop
San Diego 2013

2. Anatomical ontologies are vital for
plant and animal genomics
• High throughput transcriptomic and phenomic
data
• Need to analyze within and across species

3. 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)

4. 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

5. 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

6. is_a (SubClassOf) anatomical
part_of structure
develops_from
capable_of
is_a (taxon equivalent) endoderm
only_in_taxon
organ part
foregut
swim bladder organ endoderm of
forgut
NCBITaxon:
respiration organ
Actinopterygii
respiratory
primordium
GO: respiratory
gaseous exchange
pulmonary acinus
alveolus lung lung primordium
NCBITaxon: Mammalia alveolus of lung alveolar sac lung bud
FMA:
pulmonary FMA:lung
MA:lung alveolus EHDAA:
MA:lung
alveolus lung bud

7. Bridging anatomy ontologies
SNOMED
Uberon
NCIt
ZFA EMAPA EHDAA2
MA FMA
CJ Mungall, C Torniai, GV Gkoutos, SE Lewis, MA Haendel.
Uberon, an integrative multi-species anatomy ontology. Genome biology 13 (1), R5

8. Inter-ontology links
UBERON: respiratory system capable_of GO: respiratory gaseous exchange
part_of
UBERON: respiratory airway
is_a
only_in_taxon
UBERON: trachea Vertebrata
CL: epithelial cell
part_of
is_a
CL: tracheal epithelial cell

9. Uberon PURLs
Permanent URL
Humans see HTML view

10. Uberon PURLs
Machines see this

11. Different versions for different
purposes
ontology 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- Uberon plus species-specific ontology classes merged in
metazoan http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl
Formats:
http://uberon.org • OBO-Format
• OWL

12. Efficient Ontology Development
Text processing
Ontology matching
Wikipedia extraction
Automated Reasoning
Expert Curation • Automated QC checks in
Multiple knowledge Jenkins pipeline[*]
acquisution tools • Automated hierarchy building
Content meetings using OWL reasoners
Expert interviews
* http://bio-ontologies.knowledgeblog.org/405 http://owltools.googlecode.com/

13. Applications
• Phenomics: comparing phenotypes across
species
• Transcriptomics: gene expression
• Systematics and evolutionary biology

14. 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

15. Uberon and FANTOM5
Kenneth Baillie, FANTOM5 consortium

16. http://bgee.unil.ch
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.

17. Evo-devo applications

18. 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)

19. 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

20. 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

21. 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

22. Acknowledgments
Uberon Developers Contributors Contributors
• Carlo Torniai (eagle i) • Erik Segerdell (XAO /
• Alex Dececchi Phenotype RCN)
• Nizar Ibrahim • George Gkoutos (NBO) • Paul Sereno (Phenoscape)
• Melissa Haendel • Jonathan Bard (EHDAA2) • Monte Westerfield (ZFA)
• Terry Meehan (CL) • Cynthia Smith (MP)
• Alex Diehl (CL) • Maryanne Martone (NIF)
Applications and
• Bill Bug (NIF)
software development • Terry Hayamizu (MA/CL)
• Aurelie Comte (Bgee)
• Frederic Bastian • Yvonne Bradford (ZFA)
• Anna Niknejad (Bgee)
• Heiko Dietze • Ceri van Slyke (ZFA) • Marc Robinson-Rechavi
• Jim Balhoff • David Hill (GO) (Bgee)
• Paula Mabee • David Osumi Sutherland • Robert Druzinsky (FEED)
(FBbt/CARO) • Brian K Hall (neural crest)
• Suzanna Lewis
• Paul Schofield (MPATH) • Sarah Whitcher Kansa
• Ann Maglia (AAO)
• Wasilla Dahdul
• Paul Sereno (Phenoscape)
(TAO/VAO)
• David Blackburn
(Phenoscape)