Uberon is an integrative multi-species anatomy ontology that contains over 11,000 classes describing anatomical structures across multiple animal species, with a focus on chordates and mammals. It uses multiple relationship types like subclass, part-of, and develops-from to connect these classes in a structured ontology. Uberon aims to bridge between existing species-specific anatomy ontologies like the Mouse Anatomy ontology and the Foundational Model of Anatomy for human. It allows cross-referencing between these ontologies and helps integrate anatomical knowledge across models and humans.
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Uberon - The Multi-Species Anatomy Ontology
1. Uberon – an integrative multi-species
anatomy ontology
Chris Mungall, Lawrence Berkeley Laboratory
Monarch Initiative
Gene Ontology Consortium
Phenoscape
EBI Industry Workshop 2013
2. What is an anatomical ontology?
brain
skull
located
in
forebrain midbrain
jaw
hippocampus
CA1 CA2
CNS
neuron
dopaminergic
neuron
Part
Part
Part
Part
Part
Part Part
Part
Is-a
cell
Is-a
3. Anatomical data annotation
phenotype
1
drug 2
brain
skull
located
in
forebrain midbrain
jaw
hippocampus
CA1 CA2
CNS
neuron
dopaminergic
neuron
Part
Part
Part
Part
Part
Part Part
Part
Is-a
document 3gene 4
cell
Is-a
4. Uses of anatomical ontologies
• Transcriptome data
– Genes expressed in hippocampal CA1 region
• Describing clinical phenotypes
– Loss of beta cells in the pancreas
• Biospecimen annotation
– Liver-derived sample
• Functional characterization of gene products
– BMP4 involved in bone development
• Describing species diversity
– Extant avians lack teeth but have feathers
• NLP and text processing
5. More than a terminology
• Use of is-a (Sub Class Of)
– Tell me about phenotypes that affect bone
growth
• Answers include femur growth phenotypes
• Use of part-of
– Which genes are expressed in the
hippocampus
• Answers include genes expressed in CA1
region
6. Use of relationships in
anatomical ontologies
• Use of develops-from
– Cancers of neural-crest lineage cells?
• Answers include melanocytomas
• Use of other relationship types
– Structures are made from connective tissue?
– Branches of the trigeminal nerve?
– Brain regions associated with ataxia?
– Neurons that secrete dopamine?
– Brain regions near the striatum?
8. Which ontology?
• Mouse:
– MA (adult)
– EMAP (embryo, staged)
– EMAPA (embryo,
abstract)
• Other models
– XAO - Xenopus
– ZFA – zebrafish
– FBbt – Drosophila
– WBbt – C elegans
– DDAnat - Dictyostelium
• Human
– FMA (adult)
– EHDAA2 (CS1-CS20)
– SNOMED-CT
– NIF GrossAnatomy
– …
Why not just
select one and
adopt it as the
standard?
9. Why not just pick one?
http://fme.biostr.washington.edu:8080/FME/index.html
10. 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_figur
e.html
x
11. 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_figur
e.html
12. 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_figur
e.html
13. Ontologies built for one species
will not work for others
http://en.wikipedia.org/wiki/Pharyngeal_jaw
14. Can we effectively apply model
organism data to human?
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). doi:10.1371/journal.pbio.1000247
15. 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
lung
alveolus
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_from
part_of
is_a (SubClassOf)
surrounded_by
The problem: Data Silos
16. 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
lung
alveolus
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_from
part_of
is_a (SubClassOf)
surrounded_by
Can we map between terms?
17. Automated mapping doesn’t
work
Class A Class B In mapping DB? Useful?
FMA extensor
retinaculum of wrist
MA retina Yes No
FMA portion of blood MA blood No Yes
ZFA Macula MA macula Yes No
ZFA aortic arch MA arch of aorta Yes Misleading
ZFA hypophysis MA pitiuitary No Yes
FMA tibia FBbt tibia Yes No
FMA colon GAZ Colón, Panama Yes No
18. Linking animal models to human
disease through a multi-species
anatomy ontology
• Initial Approach:
– Generalize existing species-specific
anatomy ontology terms
– Use these as a bridge to connect data
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
lung
FMA:lungMA:lung
19. 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_from
part_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
20. Uberon: a multi-species
anatomy ontology
• Contents:
– 11,000 classes (terms)
– Multiple relationship types, including
subclass (is-a), part-of and develops-from
– Detailed OWL axiomatization
• Scope: metazoa (animals)
– Current focus is chordates
• Particularl emphasis on mammalia
– Federated approach for other taxa
21. Text
processing
• Sync with other
ontologies
Manual Curation
Literature
Workshops with domain experts
Tracker
OWL Reasoning
• Auto-classification
• QC pipeline
Uberon iterative development cycle
2009:
Primarily entity-matching based
ontology
2013:
Almost entirely manual curation and
automated reasoning
22. Uberon for NLP and text mining
• Lexical contents
– 11414 primary labels
– 29753 synonyms
• Classified by category (broad, narrow, exact,
related)
• Tagged with source
• Additional synonym types (abbreviations,
formal Latin term, plural, etc)
– 270 adjectival forms
• E.g. “hippocampal”
23. Uberon as a bridge between
anatomy ontologies
• Cross-references to
– FMA (4627)
– Human developmental anatomy [Bard et al] (1463)
– Multiple model organism anatomy ontologies (15256)
• MA, ZFA, etc
– Allen Brain Atlas (273)
– NIF Neuroanatomical Ontology (1013)
– SNOMED-CT (3453)
– UMLS (2189)
– NCI thesaurus (2286)
– Wikipedia/Dbpedia (2966)
– EFO (616)
– …
• Cross-references are curated and validated
– Manually
– Through OWL reasoning
26. MA:blood vessel
UBERON: retinal blood vessel
MP:abnormal retinal blood vessel
morphology
Phenotype of
is_a
MA: retina
HP: Central retinal artery vascular
tortuosity
FMA:central retinal artery
Phenotype of
Connecting phenotype
ontologies through anatomy
27. Uberon on the semantic web
Permanent URL
Humans see HTML view
28. Integrated views in Monarch
http://monarchinitiative.org
Linking model systems to
human diseases
29. Challenge: building the right
view
• An ontology built for multiple purposes
will usually be more complex than one
built for one purpose
– Most people don’t need the whole ontology
• Solution: create subsets or views
– Based on
• Taxonomy (e.g. mouse plus human)
• Organ system (e.g. skeletal)
• Domain (e.g. diabetes)
– See
• http://uberon.org
31. Latest developments
• Evolution of ontology
– Initial goals: primarily a mapping resource
– Now: Data is being annotated to Uberon directly
• Gene expression, transcriptomic, phenotype, functional
• The big roll up
– Community converging around a single solution
– Multiple ontologies being absorbed
• Anatomy subset of EFO
• Neuro-Anatomy subset of NIFSTD
• CALOHA (NextProt)
• vHOG (Bgee gene expression db)
• VSAO (Evolutionary biologists)
32. Availability
• Web page:
– http://uberon.org
– Multiple different OWL and Obo-format views
available
• Browsing:
– http://www.ontobee.org/browser/index.php?o=UBERO
N
– http://amigo2.berkeleybop.org/
– http://ols.wordvis.com/ont=UBERON
• Tracker:
– http://purl.obolibrary.org/obo/uberon/tracker
• Mailing list
– https://lists.sourceforge.net/lists/listinfo/obo-anatomy
33. Summary
• Multiplicity of ontologies causes problems
– Duplication of effort
– Data silos
• Uberon bridges across species-specific
anatomical ontologies
– Can function as a standalone vertebrate anatomy
ontology
• A common multi-species anatomy ontology
can bridge multiple datatypes
– Gene expression
– Phenotype
– …
34. Acknowledgments
Uberon Developers
• Alex Dececchi
• Nizar Ibrahim
• Wasila Dahdul
• 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/VSAO)
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)
35. 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-
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
36. 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
Editor's Notes
UBERON uses GO or other external ontologies for logicaldefinitions (e.g. chemosensory organ, respiration organ, reproductivesystem -- GO; smooth muscle tissue - CL)
UBERON uses GO or other external ontologies for logicaldefinitions (e.g. chemosensory organ, respiration organ, reproductivesystem -- GO; smooth muscle tissue - CL)