uberon cl workshop_haendel
DESCRIPTION
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.TRANSCRIPT
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 vesicleUBERON:
ear vesicle
D
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 • Reasoning across species• Homology neutral
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.
Logical definitions in CL using Uberon
UBERON: trachea
UBERON: respiratory airway
CL: tracheal epithelial cell
CL: epithelial cell
is_apart_of
is_a
Vertebrataonly_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.
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_apart_of
is_a
Vertebrataonly_in_taxon
UBERON: respiratory system
part_of
GO: respiratory gaseous exchangecapable_of
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 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
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
Text matchingStem and synonym
matching
Reasoning• Keep axioms that are
consistent across AOs• automated
consistency checks for disjointeness violations
Uberon iterative development cycle
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 undetermined
Vertebrate chambered heart
Arthropod dorsal vessel
Xavier-Neto et al., Cell Mol Life Sci, 2007
Process Conserved genesSpecification 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.
Panganiban et al., PNAS, 1997
Distal-less orthologs participate in distal-proximal pattern formation and appendage morphogenesis
Distal-less (Dll) expression
mouse limbsea urchin tube feet
ascidian ampulla polychaete parapodia
Reasoning across species: querying for genes in similar structures
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
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
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)