Uberon – a multi-species ontology covering the            anatomy of animalsChris Mungall, Lawrence Berkeley LaboratoryPAG...
Anatomical ontologies are vital for     plant and animal genomics• High throughput transcriptomic and phenomic  data• Need...
Most animal anatomy ontologies are          species specific• Mouse:   – MA (adult)   – EMAP / EMAPA (embryonic)• Human   ...
Ontologies built for one species will                   not work for others                                               ...
Uberon: a multi-species anatomy                       ontology     • Contents:          – Over 8,000 classes (terms)      ...
is_a (SubClassOf)                                           anatomical                      part_of                       ...
Bridging anatomy ontologies                                                                                              S...
Inter-ontology links                 UBERON: respiratory system   capable_of      GO: respiratory gaseous exchange        ...
Uberon PURLs                       Permanent URLHumans see HTML view
Uberon PURLsMachines see this
Different versions for different                      purposesontology       contentsbasic          simple relationships  ...
Efficient Ontology Development                                    Text processing                                    Ontol...
Applications• Phenomics: comparing phenotypes across  species• Transcriptomics: gene expression• Systematics and evolution...
Finding disease models•   Washington, N. L., Haendel, M. A., Mungall, C. J., Ashburner, M., Westerfield, M., & Lewis, S. E...
Uberon and FANTOM5Kenneth Baillie, FANTOM5 consortium
http://bgee.unil.chNiknejad, A., Comte, A., Parmentier, G., Roux, J., Frederic, B., & Robinson-rechavi, M. (2011).vHOG , a...
Evo-devo applications
LAMHDI: Linking across models for      human disease initiative• Integrating multiple data sources   – OMIM, OMIA (Online ...
Beyond the core model organisms• Phase 1 development: 2009-2011  – Core model organism and human anatomy• Phase 2 developm...
Conclusions• Most animal anatomy ontologies are  specialized for core model organisms or  humans• Uberon bridges across sp...
Get involved• Tracker   – http://purl.obolibrary.org/obo/uberon/tracker• Mailing list   – https://lists.sourceforge.net/li...
AcknowledgmentsUberon Developers     Contributors                Contributors                      • Carlo Torniai (eagle ...
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Uberon PAG 2013

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Brief overview of Uberon presented at PAG ontologies workshop. See http://uberon.org for more details

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Uberon PAG 2013

  1. 1. Uberon – a multi-species ontology covering the anatomy of animalsChris Mungall, Lawrence Berkeley LaboratoryPAG Ontology WorkshopSan Diego 2013
  2. 2. Anatomical ontologies are vital for plant and animal genomics• High throughput transcriptomic and phenomic data• Need to analyze within and across species
  3. 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. 4. Ontologies built for one species will not work for others http://ccm.ucdavis.edu/bcancercd/22/mouse_figure.htmlhttp://fme.biostr.washington.edu:8080/FME/index.html
  5. 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, anintegrative 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. 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 primordiumNCBITaxon: Mammalia alveolus of lung alveolar sac lung bud FMA: pulmonary FMA:lung MA:lung alveolus EHDAA: MA:lung alveolus lung bud
  7. 7. Bridging anatomy ontologies SNOMED Uberon NCIt ZFA EMAPA EHDAA2 MA FMACJ Mungall, C Torniai, GV Gkoutos, SE Lewis, MA Haendel.Uberon, an integrative multi-species anatomy ontology. Genome biology 13 (1), R5
  8. 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 VertebrataCL: epithelial cell part_of is_aCL: tracheal epithelial cell
  9. 9. Uberon PURLs Permanent URLHumans see HTML view
  10. 10. Uberon PURLsMachines see this
  11. 11. Different versions for different purposesontology contentsbasic simple relationships http://purl.obolibrary.org/obo/uberon/basic.owluberon main ontology http://purl.obolibrary.org/obo/uberon.owlmerged main ontology + links to GO, CL, NCBITaxon, NBO http://purl.obolibrary.org/obo/uberon/merged.owlComposite- Uberon plus species-specific ontology classes merged inmetazoan http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl Formats:http://uberon.org • OBO-Format • OWL
  12. 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. 13. Applications• Phenomics: comparing phenotypes across species• Transcriptomics: gene expression• Systematics and evolutionary biology
  14. 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. 15. Uberon and FANTOM5Kenneth Baillie, FANTOM5 consortium
  16. 16. http://bgee.unil.chNiknejad, 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. 17. Evo-devo applications
  18. 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 methodshttp://lamhdi.org (early prototype)https://neuinfo.org/mynif/ (search)
  19. 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. 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. 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. 22. AcknowledgmentsUberon 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)

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