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 vesicle
U...
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
• Reasonin...
Logical definitions in GO using Uberon
Uberon can make explicit many anatomical definitions already in GO
GO:notochord for...
Logical definitions in CL using Uberon
UBERON: trachea
UBERON: respiratory airway
CL: tracheal epithelial cell
CL: epithel...
Uberon logical definitions represent functional, developmental,
spatial, etc., axes of classification
Logical definitions ...
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...
Developmental Biology, Scott Gilbert, 6th
ed.
Using Uberon to validate ontology mappings
Text match mappingFruit fly ‘tibi...
Text matching
Stem and synonym
matching
Reasoning
• Keep axioms that are
consistent across AOs
• automated
consistency che...
Reasoning across species: querying for genes in
similar structures
• Genetic mechanisms may be reused in analogous structu...
Panganiban et al., PNAS, 1997
Distal-less orthologs participate in distal-proximal pattern formation and
appendage morphog...
What about homology?
Evolutionary community: Capture multiple homologous_to statements external to
Uberon using evidence a...
Uberon Conclusions
• Species-neutral ontology that subsumes
contributing taxon-specific anatomy ontologies
• Useful for on...
http://github.com/cmungall/uberon
Uberon is available at:
http://obofoundry.org/wiki/index.php/UBERON:Main_Page
More infor...
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Uberon cl workshop_haendel

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Comparing anatomical data across species is unreliable due to
the use of species-specific anatomical ontologies. Existing
approaches include the generation of inter-ontology mappings
using text matching, but these can be error prone and difficult
to maintain.


We have developed an uber-anatomy ontology called Uberon which
consists of classes generic enough to subsume species-specific
classes in existing ontologies. Uberon was seeded using
standard text matching methods, but was iteratively refined
through a combination of manual curation and automated
ontology population and computational reasoning. The resulting
ontology includes groupings that would not have been found
using text matching methods alone, and excludes common
mistakes found in mappings.


Text-based mappings are unreliable, and manual curation can be
time consuming. However if NLP methods are combined with
curation, then we can have the benefits of rapid ontology
construction with expert oversight. Using logic-based
automation techniques the results can be enhanced further.

Uberon has been applied in different domains, including
phenotype comparison and the Gene Ontology.

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  • Uberon classes were created wherever there was a need to generalize across two existing
    species-specific anatomical ontology classes. Everything that is true of an UBERON internal ear must be true of a human and fish internal ear. The converse does not hold - a fish inner ear may have properties not specified in the generic class.
    is a, part of and develops from relations, for subsumption, mereology and ontogeny respectively. Many of these relationships were derived from source ontologies
    (although care was taken in generalizing up from the species level).
    In addition to part of other spatial relations include adjacent to overlaps surrounded by, as well as a
    number of directional relations such as anterior to. Uberon also includes an overlap relation, defined as the
    relation chain of has part and part of T˙ hese relations can be used in spatial reasoning.
    Uberon can even enhance single-species queries - for example, it is possible to ask for genes
    expressed in structures that develop from the foregut using the developmental relationships in Uberon,
    even if the source ontology has only adult structures.
  • Point here is that Uberon can help ensure correct usage of gross anatomical terms in CL. In this example, this means that the tracheal epithelial cell should be defined only for Vertebrata.
    [Term]
    id: CL:0000307 ! tracheal epithelial cell
    intersection_of: CL:0000066 ! epithelial cell
    intersection_of: part_of UBERON:0003126 ! trachea
  • UBERON uses GO or other external ontologies for logicaldefinitions (e.g. chemosensory organ, respiration organ, reproductivesystem -- GO; smooth muscle tissue - CL)
  • Uberon uses the only_in_taxon method to make relationships such as lactifierous gland only in taxon Mammalia and bone
    only in taxon Vertebrata. These relations are useful for human users of the ontology, and can be used for
    consistency checking within the ontology. For example if the FBbt class “tibia” (representing a segment of
    an insect leg) were accidentally placed as a child of UBERON:0000979 tibia, this would be flagged by the
    reasoner because tibia is a bone, bones are found only in vertebrates, and FBbt is a Drosophila ontology
  • Dorsal vessel/vertebrate chambered heart homology is controversial, discuss how homology may not be known and how two homologous structures may not have homologous parts or vice versa.
  • evo biologists need to do their data-set-specific phylogenetic optimization, but the MODs want to be able to link homologous structures to one another without doing such a thing.
  • Uberon cl workshop_haendel

    1. 1. The “über-ontology” (Uberon) Melissa Häendel, Chris Müngall, George Gkoütos Cell Ontology Workshop May, 2010
    2. 2. Uberon consists of species-neutral classes derived from many contributing ontologies What is Uberon? UBERON: ear vesicle UBERON: ear vesicle D
    3. 3. Uberon composition Uberon classes subsume classes in contributing AOs 13629 Xrefs to 4087 classes
    4. 4. Anatomical ontology domains and Uberon CARO TAOAAO XAO ZFA UBERON MAFBbt
    5. 5. Uberon advantages • Logical definitions in species-neutral ontologies • Ontology alignment • Mapping validation • Reasoning across species • Homology neutral
    6. 6. 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.
    7. 7. Logical definitions in CL using Uberon UBERON: trachea UBERON: respiratory airway CL: tracheal epithelial cell CL: epithelial cell is_a part_of is_a Vertebrata only_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.
    8. 8. 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_a part_of is_a Vertebrata only_in_taxon UBERON: respiratory system part_of GO: respiratory gaseous exchangecapable_of
    9. 9. Differences in bone and bone tissue representation Ontology alignment
    10. 10. Using Uberon for alignment facilitates identification of missing classes Ontology alignment
    11. 11. 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
    12. 12. 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
    13. 13. Text matching Stem and synonym matching Reasoning • Keep axioms that are consistent across AOs • automated consistency checks for disjointeness violations Uberon iterative development cycle
    14. 14. 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 Vertebrate chambered heart Arthropod dorsal vessel Xavier-Neto et al., Cell Mol Life Sci, 2007 Process Conserved genes Specification 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.
    15. 15. Panganiban et al., PNAS, 1997 Distal-less orthologs participate in distal-proximal pattern formation and appendage morphogenesis Distal-less (Dll) expression mouse limb sea urchin tube feet ascidian ampulla polychaete parapodia Reasoning across species: querying for genes in similar structures
    16. 16. 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
    17. 17. 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
    18. 18. 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)

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