Uberon: opening up to community contributions
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The document discusses Uberon, an integrative multi-species anatomy ontology. It describes Uberon's taxonomic scope covering metazoans with a focus on vertebrates. It outlines how Uberon is edited on GitHub and maintained with cross-references to other species-specific anatomy ontologies. It also discusses how phenotypes from the Phenotype and Human Phenotype Ontology are directly mapped to Uberon and species-specific anatomies, as well as considerations for which anatomy ontology a phenotype ontology should use.
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Uberon: opening up to community contributions
- 1. Uberon: the phenotype ontology editors guide Chris Mungall POTATO II workshop
- 2. 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 original problem: OntoSilos
- 3. 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?
- 4. 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 Also: N^2 mapping problem
- 5. 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 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
- 6. 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
- 7. UBERON: pancreas CL: pancreatic epithelial cell CL: epithelial cell is_a part_of NCBITaxon: Vertebrata only_in_taxon Uberon and CL ZFA: epithelial cell of pancreas ZFA: epithelial cell ZFA: pancreas Zebrafiash equiv Zebrafiash equiv Zebrafiash equiv
- 8. MA:blood vessel UBERON: retinal blood vessel MP:abnormal retinal blood vessel morphology Inheres in is_a MA: retina HP: Central retinal artery vascular tortuosity FMA:central retinal artery Inheres in Original phenotype logical definitions
- 11. Taxonomic Scope • Covers metazoan – (applies to both CL and Uberon) • Focus on vertebrates – Overlap between Uberon and WBbt or PLANA is very small • Brain, circulatory organ, epithelium, … • But we now have an insecta module in Uberon
- 12. Editing Uberon • GitHub repo layout predates ODK – Some oddities! • All content is in uberon_edit.obo – [caveat: phenoscape and insecta extensions still to be incorporated] – Can be opened and edited in Protégé • Anyone can make Pull Requests – Travis-CI will check the PR • Release cycle is semi-regular
- 13. Maintenance of xrefs in Uberon • Xrefs to multiple other AOs maintained within uberon_edit.obo – All manually curated – Use entity-matching for assistance – E.g. ZFA, FMA, EMAPA, MA, … • Some AOs also maintain reciprocal mappings back ‘up’ to Uberon – E.g. XAO – No official sync pipeline as yet • Is this how people want to maintain this moving forward?
- 14. Translation of xrefs to axioms in Release • Each ssAO xref is treated as a taxon- equivalence axiom – E.g. ZFA:heart EquivalentTo Uberon:heart and part-of some Danio rerio – See ontology metadata for mappings to taxa • Should we change any of these? E.g. species vs genus – These go in inter-ontology bridge files – Reasoner checks performed pre-release
- 17. Uberon and Design Patterns • Uberon pre-dated DOSDPs • Some high-level DPs are specified as narrative documents – E.g. modeling endochondral elements document • DOSDP templates are in progress • Lots of New Term Requests are for things like left + right subclasses of existing classes
- 18. How people have contributed so far • Issue Tracker • External Ontology Alignment – Other AOs – GO – Phenotype Ontologies • Extension modules – Phenoscape – Insecta • All direct edits by yours truly
- 19. Contribution model moving forward • PRs open to anyone (with basic training) – On uberon_edit.obo – On TSVs (TODO) • Core of editors will merge PRs – Core TBD • Make release pipeline easier to run – Help from ssAOs appreciated (e.g. standardize on relations) – Run more frequently, possibly as Jenkins job
- 20. Which AO should a phenotype ontology use? • MP and HP use Uberon (and CL) directly • Non-mammalian use their own – Species-specific phenotypes inferred to be under generic ones • Advantages of Uberon (and CL) – Work has been done up-front to try and ensure consistency with other ssAOs, GO, phenotype ontologies – Reasonably complete is-a, part-of, develops-from • Disadvantages – Generalizing across species may lose information – Low coverage for invertebrates (intentional) • Discussion – Should we have mechanism for ‘pushing down’ suggestions to ssAOs?