A new major release is available for Uberon. For download details for the different modules and subsets, see http://uberon.org The stable url prefix for this release is: * http://purl.obolibrary.org/obo/uberon/releases/2012-05-30/ E.g http://purl.obolibrary.org/obo/uberon/releases/2012-05-30/uberon.owl for the main ontology == Summary == Uberon releases are incremental, occurring a couple of times a week. However, this seemed like a good time to announce a major release and describe some progress since the Genome Biology paper (http://genomebiology.com/2012/13/1/R5). This version of the ontology contains * 7318 non-obsolete classes in the 'uberon' ID space * 3204 logical definitions * 43667 logical axioms It contains up-to-date logically verified relationships to multiple other ontologies, and has a number of new relationship types (primarily for representing development and topology), improved definitions and features more in-depth coverage of selected systems. Some highlights are listed below. == Anatomy ontology interoperation == Uberon includes bridge modules for interoperating with other AOs. See http://uberon.org#Individual_Bridge_Modules for details. Taxonomic equivalence axioms are up to date with respect to the latest releaed versions of the following ontologies: * FMA 4192 * MA 2718 * ZFA 929 * TAO 901 * AAO 734 * XAO 570 * FBbt 155 * HAO 79 * TGMA 58 * TADS 26 * WBbt 44 Direct equivalence axioms: * CARO (40) (still using v1 so largely unchanged) * VSAO (124) (see notes below) * NIF_GrossAnatomy (967) (will be updated to latest NIFSTD in next major release) Subclass axioms are up to date for: * EMAPA 2419 (last publicly available release) * EHDAA2 1400 * ncithesaurus 2108 * VHOG 1017 We also have 995 cross-references for EHDAA, but these may not be up to date (these are retained to allow people to migrate to EHDAA2 from the obsolete EHDAA). In future releases, EHDAA2 classes will be treated as taxonomic equivalents rather than subclasses. Note that with this version of Uberon, the semantics of the VHOG mappings have changed, such that the VHOG class becomes the parent class. For example: * VHOG:lung-swim bladder * Uberon:lung * MA:lung * FMA:lung * Uberon:swim bladder * ZFA:swim bladder We are working with the VHOG developers to closely coordinate resources. The ontology formerly known as VAO is now VSAO (Vertebrate Skeletal Anatomy Ontology). In this release, the "VAO" namespace is replaced by "VSAO". VSAO and Uberon developers are working together on an optimal unified representation. This release includes many improvements in the representation of skeletal tissue types and the skeletal system as a result of the VSAO editors' efforts. In addition to the above, there are semantics-free cross-references to the anatomy subsets of: * SNOMED-CT (2783) * Wikipedia/Dbpedia (2530) * BTO (1277) * MESH (884) * EFO (561) * ABA [Allan Brain Atlas] (263) === Non-gross anatomy ontologies === The uberon/merged ontology also bundles the latest cell ontology (CL), together with part_of and has_part relationships connecting cells to tissues. This bundle also includes a subset of GO, PRO, PATO and CHEBI. For relationships originating from classes in other ontologies (GO, Phenotype ontologies) and referencing Uberon classes, see the respective project pages. E.g. * http://wiki.geneontology.org/index.php/Ontology_extensions * http://code.google.com/p/phenotype-ontologies/ == Developmental Relationships == * Introduction of a new has_developmental_contribution_from ( http://purl.obolibrary.org/obo/RO_0002254 ) relationship type * Addition of new developmental relationships connecting various structures to the neural crest. This is the start of a project to improve representation of NC across multiple ontologies, based on a Phenotype RCN content expert meeting hosted at NESCENT. Details here: http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop The uberon class for NC is http://purl.obolibrary.org/obo/UBERON_0002342 * Classification of endochondral bones is performed automatically based on develeopmental relationships. Cartilage precursors should be asserted for most endochondral bones, following the same schema as EHDAA2. == Organism Subdivisions and the Muscoloskeletal System == * Skeleton subdivisions have been updated and should be consistent with this working document: https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit (comments on this design document most welcome) * Many parts of the skeletal system have connected_to relationships as proposed in the following working document: https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit These relations do _not_ yet have RO IDs and may change in the future based on community feedback. * Many muscles now have logical definitions or relationships specified using attachment relations. These also lack RO IDs at this time, same comments apply. As a starting point, try exploring under forelimb zeugopod muscle: http://purl.obolibrary.org/obo/UBERON_0004254 == Terminology and definitions == * Many wikipedia-sourced definitions have been replaced by more formal ontology-style definitions, cross-checked against relationships and logical definitions * We are working to neutralize some of the human-centric primary labels and term descriptions. There are some cases where a human or medical term is used in the primary label, particular with respect to autopods. == Ontology Coordination == * Sponge terms have been pruned and ceded to the new Porifera ontology, PORO http://code.google.com/p/porifera-ontology/ We're interested in pruning off other tips. Planaria is a high priority. We expect to be able to prune off arthropods in a future release, as the arthropod AO matures. == New Ontology Subsets == In addition to taxonomic subsets, we are experimenting with exporting system-specific subsets (immune, musculoskeletal, reproductive). These subsets are 'minimal' in that they do not MIREOT in any classes outside the subset, and as a result may not be isa-complete. * http://purl.obolibrary.org/obo/uberon/subsets/circulatory-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/digestive-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/excretory-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/immune-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/musculoskeletal-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/nervous-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/reproductive-minimal.obo * http://purl.obolibrary.org/obo/uberon/subsets/sensory-minimal.obo == New Applications == In addition to the applications listed in the Genome Biology paper, Uberon is also being used by GOA annotators for post-composition of developmental process classes in gene product annotations. http://www.geneontology.org/GO.downloads.annotations.shtml#filter download: "UniProt [multispecies]" Uberon is being applied to new applications - watch this space for details in the near future!