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Uberon – an integrative multi-speciesanatomy ontologyChris Mungall, Lawrence Berkeley LaboratoryMonarch InitiativeGene Ont...
What is an anatomical ontology?brainskulllocatedinforebrain midbrainjawhippocampusCA1 CA2CNSneurondopaminergicneuronPartPa...
Anatomical data annotationphenotype1drug 2brainskulllocatedinforebrain midbrainjawhippocampusCA1 CA2CNSneurondopaminergicn...
Uses of anatomical ontologies• Transcriptome data– Genes expressed in hippocampal CA1 region• Describing clinical phenotyp...
More than a terminology• Use of is-a (Sub Class Of)– Tell me about phenotypes that affect bonegrowth• Answers include femu...
Use of relationships inanatomical ontologies• Use of develops-from– Cancers of neural-crest lineage cells?• Answers includ...
Which ontology?• Mouse:– MA (adult)– EMAP (embryo, staged)– EMAPA (embryo,abstract)• Other models– XAO - Xenopus– ZFA – ze...
Which ontology?• Mouse:– MA (adult)– EMAP (embryo, staged)– EMAPA (embryo,abstract)• Other models– XAO - Xenopus– ZFA – ze...
Why not just pick one?http://fme.biostr.washington.edu:8080/FME/index.html
Ontologies built for one specieswill not work for othershttp://fme.biostr.washington.edu:8080/FME/index.htmlhttp://ccm.ucd...
Ontologies built for one specieswill not work for othershttp://fme.biostr.washington.edu:8080/FME/index.htmlhttp://ccm.ucd...
Ontologies built for one specieswill not work for othershttp://fme.biostr.washington.edu:8080/FME/index.htmlhttp://ccm.ucd...
Ontologies built for one specieswill not work for othershttp://en.wikipedia.org/wiki/Pharyngeal_jaw
Can we effectively apply modelorganism data to human?Washington, N. L., Haendel, M. A., Mungall, C. J., Ashburner, M., Wes...
lunglungrespiratory gaseousexchangelobular organparenchymatousorgansolid organpleural sacthoraciccavity organthoraciccavit...
lunglungrespiratory gaseousexchangelobular organparenchymatousorgansolid organpleural sacthoraciccavity organthoraciccavit...
Automated mapping doesn’tworkClass A Class B In mapping DB? Useful?FMA extensorretinaculum of wristMA retina Yes NoFMA por...
Linking animal models to humandisease through a multi-speciesanatomy ontology• Initial Approach:– Generalize existing spec...
anatomicalstructureendoderm offorgutlung budlungrespirationorganorganforegutalveolusalveolus of lungorgan partFMA:lungMA:l...
Uberon: a multi-speciesanatomy ontology• Contents:– 11,000 classes (terms)– Multiple relationship types, includingsubclass...
Textprocessing• Sync with otherontologiesManual CurationLiteratureWorkshops with domain expertsTrackerOWL Reasoning• Auto-...
Uberon for NLP and text mining• Lexical contents– 11414 primary labels– 29753 synonyms• Classified by category (broad, nar...
Uberon as a bridge betweenanatomy ontologies• Cross-references to– FMA (4627)– Human developmental anatomy [Bard et al] (1...
Bridging orthogonal resources• Validated logical relationshipsconnecting– Cell types (OBO Cell Ontology, CL)– Taxonomy (NC...
UBERON: tracheaUBERON:respiratory airwayCL: tracheal epithelial cellCL: epithelial cellis_apart_ofis_aNCBITaxon:Vertebrata...
MA:blood vesselUBERON: retinal blood vesselMP:abnormal retinal blood vesselmorphologyPhenotype ofis_aMA: retinaHP: Central...
Uberon on the semantic webPermanent URLHumans see HTML view
Integrated views in Monarchhttp://monarchinitiative.orgLinking model systems tohuman diseases
Challenge: building the rightview• An ontology built for multiple purposeswill usually be more complex than onebuilt for o...
Challenge: visualizationhttp://ols.wordvis.com/q=UBERON:0002107
Latest developments• Evolution of ontology– Initial goals: primarily a mapping resource– Now: Data is being annotated to U...
Availability• Web page:– http://uberon.org– Multiple different OWL and Obo-format viewsavailable• Browsing:– http://www.on...
Summary• Multiplicity of ontologies causes problems– Duplication of effort– Data silos• Uberon bridges across species-spec...
AcknowledgmentsUberon Developers• Alex Dececchi• Nizar Ibrahim• Wasila Dahdul• MelissaHaendelContributors• Carlo Torniai (...
Different versions for differentpurposesontology contentsbasic simple relationshipshttp://purl.obolibrary.org/obo/uberon/b...
Bridging anatomy ontologiesZFAMA FMAEHDAA2EMAPAUberonCJ Mungall, C Torniai, GV Gkoutos, SE Lewis, MA Haendel.Uberon, an in...
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Uberon EBI industry workshop

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  • UBERON uses GO or other external ontologies for logicaldefinitions (e.g. chemosensory organ, respiration organ, reproductivesystem -- GO; smooth muscle tissue - CL)
  • UBERON uses GO or other external ontologies for logicaldefinitions (e.g. chemosensory organ, respiration organ, reproductivesystem -- GO; smooth muscle tissue - CL)
  • Images: Seth Ruffins
  • Transcript of "Uberon EBI industry workshop"

    1. 1. Uberon – an integrative multi-speciesanatomy ontologyChris Mungall, Lawrence Berkeley LaboratoryMonarch InitiativeGene Ontology ConsortiumPhenoscapeEBI Industry Workshop 2013
    2. 2. What is an anatomical ontology?brainskulllocatedinforebrain midbrainjawhippocampusCA1 CA2CNSneurondopaminergicneuronPartPartPartPartPartPart PartPartIs-acellIs-a
    3. 3. Anatomical data annotationphenotype1drug 2brainskulllocatedinforebrain midbrainjawhippocampusCA1 CA2CNSneurondopaminergicneuronPartPartPartPartPartPart PartPartIs-adocument 3gene 4cellIs-a
    4. 4. Uses of anatomical ontologies• Transcriptome data– Genes expressed in hippocampal CA1 region• Describing clinical phenotypes– Loss of beta cells in the pancreas• Biospecimen annotation– Liver-derived sample• Functional characterization of gene products– BMP4 involved in bone development• Describing species diversity– Extant avians lack teeth but have feathers• NLP and text processing
    5. 5. More than a terminology• Use of is-a (Sub Class Of)– Tell me about phenotypes that affect bonegrowth• Answers include femur growth phenotypes• Use of part-of– Which genes are expressed in thehippocampus• Answers include genes expressed in CA1region
    6. 6. Use of relationships inanatomical ontologies• Use of develops-from– Cancers of neural-crest lineage cells?• Answers include melanocytomas• Use of other relationship types– Structures are made from connective tissue?– Branches of the trigeminal nerve?– Brain regions associated with ataxia?– Neurons that secrete dopamine?– Brain regions near the striatum?
    7. 7. Which ontology?• Mouse:– MA (adult)– EMAP (embryo, staged)– EMAPA (embryo,abstract)• Other models– XAO - Xenopus– ZFA – zebrafish– FBbt – Drosophila– WBbt – C elegans– DDAnat – Dictyostelium– …• Human– FMA (adult)– EHDAA2 (CS1-CS20)– SNOMED-CT– NIF GrossAnatomy(mammal brain)– …
    8. 8. Which ontology?• Mouse:– MA (adult)– EMAP (embryo, staged)– EMAPA (embryo,abstract)• Other models– XAO - Xenopus– ZFA – zebrafish– FBbt – Drosophila– WBbt – C elegans– DDAnat - Dictyostelium• Human– FMA (adult)– EHDAA2 (CS1-CS20)– SNOMED-CT– NIF GrossAnatomy– …Why not justselect one andadopt it as thestandard?
    9. 9. Why not just pick one?http://fme.biostr.washington.edu:8080/FME/index.html
    10. 10. Ontologies built for one specieswill not work for othershttp://fme.biostr.washington.edu:8080/FME/index.htmlhttp://ccm.ucdavis.edu/bcancercd/22/mouse_figure.htmlx
    11. 11. Ontologies built for one specieswill not work for othershttp://fme.biostr.washington.edu:8080/FME/index.htmlhttp://ccm.ucdavis.edu/bcancercd/22/mouse_figure.html
    12. 12. Ontologies built for one specieswill not work for othershttp://fme.biostr.washington.edu:8080/FME/index.htmlhttp://ccm.ucdavis.edu/bcancercd/22/mouse_figure.html
    13. 13. Ontologies built for one specieswill not work for othershttp://en.wikipedia.org/wiki/Pharyngeal_jaw
    14. 14. Can we effectively apply modelorganism data to human?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). doi:10.1371/journal.pbio.1000247
    15. 15. lunglungrespiratory gaseousexchangelobular organparenchymatousorgansolid organpleural sacthoraciccavity organthoraciccavitymulticellularorganismal processabnormal lungmorphologyabnormal respiratorysystem morphologyGOMPOMAFMAabnormal pulmonaryacinus morphologyabnormal pulmonaryalveolus morphologylungalveolusrespiratory systemprocessorgan systemrespiratorysystemLowerrespiratorytractalveolar sacpulmonaryacinusorgan systemrespiratorysystemEHDAA2lunglung budrespiratoryprimordiumpharyngeal regiondevelops_frompart_ofis_a (SubClassOf)surrounded_byThe problem: Data Silos
    16. 16. lunglungrespiratory gaseousexchangelobular organparenchymatousorgansolid organpleural sacthoraciccavity organthoraciccavitymulticellularorganismal processabnormal lungmorphologyabnormal respiratorysystem morphologyGOMPOMAFMAabnormal pulmonaryacinus morphologyabnormal pulmonaryalveolus morphologylungalveolusrespiratory systemprocessorgan systemrespiratorysystemLowerrespiratorytractalveolar sacpulmonaryacinusorgan systemrespiratorysystemEHDAA2lunglung budrespiratoryprimordiumpharyngeal regiondevelops_frompart_ofis_a (SubClassOf)surrounded_byCan we map between terms?
    17. 17. Automated mapping doesn’tworkClass A Class B In mapping DB? Useful?FMA extensorretinaculum of wristMA retina Yes NoFMA portion of blood MA blood No YesZFA Macula MA macula Yes NoZFA aortic arch MA arch of aorta Yes MisleadingZFA hypophysis MA pitiuitary No YesFMA tibia FBbt tibia Yes NoFMA colon GAZ Colón, Panama Yes No
    18. 18. Linking animal models to humandisease through a multi-speciesanatomy ontology• Initial Approach:– Generalize existing species-specificanatomy ontology terms– Use these as a bridge to connect dataMungall, 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/R5lungFMA:lungMA:lung
    19. 19. anatomicalstructureendoderm offorgutlung budlungrespirationorganorganforegutalveolusalveolus of lungorgan partFMA:lungMA:lungendodermGO: respiratorygaseous exchangeMA:lungalveolusFMA:pulmonaryalveolusis_a (taxon equivalent)develops_frompart_ofis_a (SubClassOf)capable_ofNCBITaxon:MammaliaEHDAA:lung budonly_in_taxonpulmonaryacinusalveolar saclungprimordiumswim bladderrespiratoryprimordiumNCBITaxon:Actinopterygii
    20. 20. Uberon: a multi-speciesanatomy ontology• Contents:– 11,000 classes (terms)– Multiple relationship types, includingsubclass (is-a), part-of and develops-from– Detailed OWL axiomatization• Scope: metazoa (animals)– Current focus is chordates• Particularl emphasis on mammalia– Federated approach for other taxa
    21. 21. Textprocessing• Sync with otherontologiesManual CurationLiteratureWorkshops with domain expertsTrackerOWL Reasoning• Auto-classification• QC pipelineUberon iterative development cycle2009:Primarily entity-matching basedontology2013:Almost entirely manual curation andautomated reasoning
    22. 22. Uberon for NLP and text mining• Lexical contents– 11414 primary labels– 29753 synonyms• Classified by category (broad, narrow, exact,related)• Tagged with source• Additional synonym types (abbreviations,formal Latin term, plural, etc)– 270 adjectival forms• E.g. “hippocampal”
    23. 23. Uberon as a bridge betweenanatomy ontologies• Cross-references to– FMA (4627)– Human developmental anatomy [Bard et al] (1463)– Multiple model organism anatomy ontologies (15256)• MA, ZFA, etc– Allen Brain Atlas (273)– NIF Neuroanatomical Ontology (1013)– SNOMED-CT (3453)– UMLS (2189)– NCI thesaurus (2286)– Wikipedia/Dbpedia (2966)– EFO (616)– …• Cross-references are curated and validated– Manually– Through OWL reasoning
    24. 24. Bridging orthogonal resources• Validated logical relationshipsconnecting– Cell types (OBO Cell Ontology, CL)– Taxonomy (NCBI)– Functional and developmental knowledge(GO)– Behaviors (NBO)– Proteins (PRO)– Chemical entities (CHEBI)
    25. 25. UBERON: tracheaUBERON:respiratory airwayCL: tracheal epithelial cellCL: epithelial cellis_apart_ofis_aNCBITaxon:Vertebrataonly_in_taxonUBERON:respiratory systempart_ofGO:respiratory gaseousexchangecapable_ofMulti-ontology knowledge graph
    26. 26. MA:blood vesselUBERON: retinal blood vesselMP:abnormal retinal blood vesselmorphologyPhenotype ofis_aMA: retinaHP: Central retinal artery vasculartortuosityFMA:central retinal arteryPhenotype ofConnecting phenotypeontologies through anatomy
    27. 27. Uberon on the semantic webPermanent URLHumans see HTML view
    28. 28. Integrated views in Monarchhttp://monarchinitiative.orgLinking model systems tohuman diseases
    29. 29. Challenge: building the rightview• An ontology built for multiple purposeswill usually be more complex than onebuilt for one purpose– Most people don’t need the whole ontology• Solution: create subsets or views– Based on• Taxonomy (e.g. mouse plus human)• Organ system (e.g. skeletal)• Domain (e.g. diabetes)– See• http://uberon.org
    30. 30. Challenge: visualizationhttp://ols.wordvis.com/q=UBERON:0002107
    31. 31. Latest developments• Evolution of ontology– Initial goals: primarily a mapping resource– Now: Data is being annotated to Uberon directly• Gene expression, transcriptomic, phenotype, functional• The big roll up– Community converging around a single solution– Multiple ontologies being absorbed• Anatomy subset of EFO• Neuro-Anatomy subset of NIFSTD• CALOHA (NextProt)• vHOG (Bgee gene expression db)• VSAO (Evolutionary biologists)
    32. 32. Availability• Web page:– http://uberon.org– Multiple different OWL and Obo-format viewsavailable• Browsing:– http://www.ontobee.org/browser/index.php?o=UBERON– http://amigo2.berkeleybop.org/– http://ols.wordvis.com/ont=UBERON• Tracker:– http://purl.obolibrary.org/obo/uberon/tracker• Mailing list– https://lists.sourceforge.net/lists/listinfo/obo-anatomy
    33. 33. Summary• Multiplicity of ontologies causes problems– Duplication of effort– Data silos• Uberon bridges across species-specificanatomical ontologies– Can function as a standalone vertebrate anatomyontology• A common multi-species anatomy ontologycan bridge multiple datatypes– Gene expression– Phenotype– …
    34. 34. AcknowledgmentsUberon Developers• Alex Dececchi• Nizar Ibrahim• Wasila Dahdul• MelissaHaendelContributors• 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/VSAO)Applications andsoftwaredevelopment• Frederic Bastian• Heiko Dietze• Jim Balhoff• Paula Mabee• Suzanna LewisContributors• 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)
    35. 35. Different versions for differentpurposesontology contentsbasic simple relationshipshttp://purl.obolibrary.org/obo/uberon/basic.owluberon main ontologyhttp://purl.obolibrary.org/obo/uberon.owlmerged main ontology + links to GO, CL, NCBITaxon, NBOhttp://purl.obolibrary.org/obo/uberon/merged.owlComposite-metazoanUberon plus species-specific ontology classes merged inhttp://purl.obolibrary.org/obo/uberon/composite-metazoan.owlhttp://uberon.orgFormats:• OBO-Format• OWL
    36. 36. Bridging anatomy ontologiesZFAMA FMAEHDAA2EMAPAUberonCJ Mungall, C Torniai, GV Gkoutos, SE Lewis, MA Haendel.Uberon, an integrative multi-species anatomy ontology. Genome biology 13 (1), R5SNOMEDNCIt
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