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Uberon – a multi-species ontology for phenomics and translational science

Uberon – a multi-species ontology for phenomics and translational science. Melissa Haendel, OHSU Chris Mungall , LBNL Carlo Torniai , OHSU. The problem: Data Silos. is_a ( SubClassOf ). GO. part_of. FMA. develops_from. surrounded_by. multicellular organismal process. EHDAA2.

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Uberon – a multi-species ontology for phenomics and translational science

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  1. Uberon – a multi-species ontology for phenomics and translational science Melissa Haendel, OHSU Chris Mungall, LBNL Carlo Torniai, OHSU

  2. The problem:Data Silos is_a (SubClassOf) GO part_of FMA develops_from surrounded_by multicellularorganismal process EHDAA2 organ system solid organ pharyngeal region respiratory gaseous exchange respiratory primordium respiratory system parenchymatous organ lung bud respiratory system process lung MA Lower respiratory tract lobular organ thoracic cavity organ system MPO abnormal respiratory system morphology thoracic cavity organ respiratory system pleural sac lung abnormal lung morphology lung abnormal pulmonary acinus morphology pulmonary acinus abnormal pulmonary alveolus morphology alveolar sac lung alveolus

  3. 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

  4. Anatomy Ontology Menagerie • Mouse: • MA (adult) • EMAP / EMAPA (embryonic) • Human • FMA (adult) • EHDAA2 (CS1-CS20) • Amphibian • AAO • XAO • Fish • ZFA • TAO • Nematode • WBbt • Arthropod • FBbt (Drosophila) • HAO • Arthropod anatomy ontology Reduced taxonomic scope = Reduced complexity Historically little coordination Contrast to: Gene Ontology (GO) (all kingdoms of life)

  5. Semantic Similarity of Phenotypes MP ZFA+PATO FBbt+PATO FMA+PATO "Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation." PLoSBiol 7(11): e1000247. doi:10.1371/journal.pbio.1000247 Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE

  6. Uberon info • Size: • >6500 classes • >19000 relationships (50 relations) • >2000 logical definitions • Scope: • Metazoa • vertebrate bias, in particular mammals • Availability • many versions, in obo and owl • http://uberon.org • Source version is obo, compiled to owl using Oort • Use • Washington, Haendel et al, PlosBiology2009 • Mousefinder • Phenomenet • FANTOM5

  7. What does uberon look like? is_a (SubClassOf) anatomical structure part_of develops_from capable_of endoderm is_a (taxon equivalent) only_in_taxon organ part foregut swim bladder organ endoderm of forgut NCBITaxon: Actinopterygii respiration organ respiratory primordium GO: respiratory gaseous exchange pulmonary acinus alveolus lung lung primordium NCBITaxon: Mammalia alveolus of lung alveolar sac lung bud FMA: pulmonary alveolus FMA:lung MA:lung alveolus MA:lung EHDAA: lung bud Uberon classes generalize species-specific ones, and connect to other ontologies via a variety of relations

  8. Logical definitions in GO using Uberon 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. Cross-Product Extensions of the Gene Ontology Journal of Biomedical Informatics 2010. Christopher J. Mungall and Michael Bada and Tanya Z. Berardini and Jennifer Deegan and Amelia Ireland and Midori A. Harris and David P. Hill and Jane Lomax

  9. Conclusions • Anatomy ontologies have been developed independently and do not integrate well without additional help • Uberon generalizes over species-specific anatomy classes • Includes detailed anatomical knowledge via a variety of relationships • designed for reasoning • Highly interconnected with other ontologies • Homology is largely separated • Growing number of applications • For more info: • http://uberon.org http://genomebiology.com/2012/13/1/R5

  10. Acknowledgments • Uberon • Chris Mungall • George Gkoutos • Carlo Torniai • Suzanna Lewis • Ontologies • Jonathan Bard (EHDAA2) • Terry Meehan (CL) • Alex Diehl (CL) • Terry Hayamizu (MA/CL) • OnardMejino (FMA) • David Hill (GO) • David Osumi Sutherland (FBbt/CARO) • Paul Schofield (MPATH) • Wasilla Dahdul (TAO/VAO) • Paula Mabee (TAO/VAO) • Erik Segerdell (XAO) • Monte Westerfield (ZFA) • Cynthia Smith (MP) • Maryanne Martone (NIF) • Frederic Bastian (vHOG) • Marc Robinson-Rechavi (vHOG) • Contributions • AlanRuttenberg • RobHoehndorf • WacekKusnierczyk • Harry Hochheiser

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