Uberon EBI industry workshop
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Uberon is an integrative multi-species anatomy ontology that contains over 11,000 classes describing anatomical structures across multiple animal species, with a focus on chordates and mammals. It uses multiple relationship types like subclass, part-of, and develops-from to connect these classes in a structured ontology. Uberon aims to bridge between existing species-specific anatomy ontologies like the Mouse Anatomy ontology and the Foundational Model of Anatomy for human. It allows cross-referencing between these ontologies and helps integrate anatomical knowledge across models and humans.
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Uberon EBI industry workshop
- 1. Uberon – an integrative multi-species anatomy ontology Chris Mungall, Lawrence Berkeley Laboratory Monarch Initiative Gene Ontology Consortium Phenoscape EBI Industry Workshop 2013
- 2. What is an anatomical ontology? brain skull located in forebrain midbrain jaw hippocampus CA1 CA2 CNS neuron dopaminergic neuron Part Part Part Part Part Part Part Part Is-a cell Is-a
- 3. Anatomical data annotation phenotype 1 drug 2 brain skull located in forebrain midbrain jaw hippocampus CA1 CA2 CNS neuron dopaminergic neuron Part Part Part Part Part Part Part Part Is-a document 3gene 4 cell Is-a
- 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. More than a terminology • Use of is-a (Sub Class Of) – Tell me about phenotypes that affect bone growth • Answers include femur growth phenotypes • Use of part-of – Which genes are expressed in the hippocampus • Answers include genes expressed in CA1 region
- 6. Use of relationships in anatomical 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. 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. 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 just select one and adopt it as the standard?
- 9. Why not just pick one? http://fme.biostr.washington.edu:8080/FME/index.html
- 10. 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_figur e.html x
- 11. 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_figur e.html
- 12. 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_figur e.html
- 13. Ontologies built for one species will not work for others http://en.wikipedia.org/wiki/Pharyngeal_jaw
- 14. Can we effectively apply model organism 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. lung lung respiratory gaseous exchange lobular organ parenchymatous organ solid organ pleural sac thoracic cavity organ thoracic cavity multicellular organismal process abnormal lung morphology abnormal respiratory system morphology GO MPO MA FMA abnormal pulmonary acinus morphology abnormal pulmonary alveolus morphology lung alveolus respiratory system process organ system respiratory system Lower respiratory tract alveolar sac pulmonary acinus organ system respiratory system EHDAA2 lung lung bud respiratory primordium pharyngeal region develops_from part_of is_a (SubClassOf) surrounded_by The problem: Data Silos
- 16. lung lung respiratory gaseous exchange lobular organ parenchymatous organ solid organ pleural sac thoracic cavity organ thoracic cavity multicellular organismal process abnormal lung morphology abnormal respiratory system morphology GO MPO MA FMA abnormal pulmonary acinus morphology abnormal pulmonary alveolus morphology lung alveolus respiratory system process organ system respiratory system Lower respiratory tract alveolar sac pulmonary acinus organ system respiratory system EHDAA2 lung lung bud respiratory primordium pharyngeal region develops_from part_of is_a (SubClassOf) surrounded_by Can we map between terms?
- 17. Automated mapping doesn’t work Class A Class B In mapping DB? Useful? FMA extensor retinaculum of wrist MA retina Yes No FMA portion of blood MA blood No Yes ZFA Macula MA macula Yes No ZFA aortic arch MA arch of aorta Yes Misleading ZFA hypophysis MA pitiuitary No Yes FMA tibia FBbt tibia Yes No FMA colon GAZ Colón, Panama Yes No
- 18. Linking animal models to human disease through a multi-species anatomy ontology • Initial Approach: – Generalize existing species-specific anatomy ontology terms – Use these as a bridge to connect data 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 lung FMA:lungMA:lung
- 19. 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_from part_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
- 20. Uberon: a multi-species anatomy ontology • Contents: – 11,000 classes (terms) – Multiple relationship types, including subclass (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. Text processing • Sync with other ontologies Manual Curation Literature Workshops with domain experts Tracker OWL Reasoning • Auto-classification • QC pipeline Uberon iterative development cycle 2009: Primarily entity-matching based ontology 2013: Almost entirely manual curation and automated reasoning
- 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. Uberon as a bridge between anatomy 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. Bridging orthogonal resources • Validated logical relationships connecting – Cell types (OBO Cell Ontology, CL) – Taxonomy (NCBI) – Functional and developmental knowledge (GO) – Behaviors (NBO) – Proteins (PRO) – Chemical entities (CHEBI)
- 25. UBERON: trachea UBERON: respiratory airway CL: tracheal epithelial cell CL: epithelial cell is_ a part_of is_a NCBITaxon: Vertebrata only_in_taxon UBERON: respiratory system part_of GO: respiratory gaseous exchange capable_of Multi-ontology knowledge graph
- 26. MA:blood vessel UBERON: retinal blood vessel MP:abnormal retinal blood vessel morphology Phenotype of is_a MA: retina HP: Central retinal artery vascular tortuosity FMA:central retinal artery Phenotype of Connecting phenotype ontologies through anatomy
- 27. Uberon on the semantic web Permanent URL Humans see HTML view
- 28. Integrated views in Monarch http://monarchinitiative.org Linking model systems to human diseases
- 29. Challenge: building the right view • An ontology built for multiple purposes will usually be more complex than one built 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
- 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. Availability • Web page: – http://uberon.org – Multiple different OWL and Obo-format views available • Browsing: – http://www.ontobee.org/browser/index.php?o=UBERO N – 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. Summary • Multiplicity of ontologies causes problems – Duplication of effort – Data silos • Uberon bridges across species-specific anatomical ontologies – Can function as a standalone vertebrate anatomy ontology • A common multi-species anatomy ontology can bridge multiple datatypes – Gene expression – Phenotype – …
- 34. Acknowledgments Uberon Developers • Alex Dececchi • Nizar Ibrahim • Wasila Dahdul • 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/VSAO) 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)
- 35. Different versions for different purposes ontology 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
- 36. 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
Notes de l'éditeur
- 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