Uberon PAG 2013
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Transcript of Uberon PAG 2013
Uberon – a multi-species ontology covering the anatomy of animals
Chris Mungall, Lawrence Berkeley Laboratory
PAG Ontology WorkshopSan Diego 2013
Anatomical ontologies are vital for plant and animal genomics
• High throughput transcriptomic and phenomic data
• Need to analyze within and across species
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)
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_figure.html
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, 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
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_frompart_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
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
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
Inter-ontology links
Uberon PURLs
Permanent URL
Humans see HTML view
Uberon PURLs
Machines see this
Different versions for different purposesontology 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
Text processingOntology matchingWikipedia extraction
Expert CurationMultiple knowledge
acquisution toolsContent meetingsExpert interviews
Automated Reasoning• Automated QC checks in
Jenkins pipeline[*]• Automated hierarchy building
using OWL reasoners
Efficient Ontology Development
* http://bio-ontologies.knowledgeblog.org/405 http://owltools.googlecode.com/
Applications
• Phenomics: comparing phenotypes across species
• Transcriptomics: gene expression• Systematics and evolutionary biology
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
Uberon and FANTOM5
Kenneth Baillie, FANTOM5 consortium
Niknejad, 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.
http://bgee.unil.ch
Evo-devo applications
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 methods
http://lamhdi.org (early prototype)https://neuinfo.org/mynif/ (search)
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
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
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
AcknowledgmentsUberon Developers• Alex Dececchi• Nizar Ibrahim• 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/VAO)
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)