Downloads

Releases

Uberon is released roughly every month, depending on stakeholder needs. A release generates a number of different files, described below. Each release version of each file is stored permanently, and these are always available via Permanent URLs of the form:

http://purl.obolibrary.org/obo/uberon/releases/YYYY-MM-DD

A description of each release, with a complete change log is available on front page of the uberon site.

Core Ontology

Extended Version

uberon/ext is the recommended version. It imports subsets of other ontologies such as GO, and includes all of the cell ontology (CL). This is the version available for browsing on OntoBee.

Download: uberon/ext.owl
OBO Format: uberon/ext.obo

No extensions

This excludes any relationships to other ontologies - it is a self-contained unit

Download: uberon.owl
OBO Format: uberon.obo

Subsets

Different kinds of subsets are available.

  • Taxon subsets exclude any classes not relevant for a particular taxon
  • System subsets exclude any classes not relevant for a particular anatomical system
  • Logic subsets exclude some relationships or certain patterns of relationships

Taxon Subsets

These are constructed using Uberon taxon constraints

Developmental stages are included, and species-specific stages start and end ranges are encoded as Taxon GCIs

System Subsets

Logic Subsets

Currently the main logic subset available is uberon/basic. This excludes all relationship types other than is_a, part_of and develops_from. Such an ontology always forms a Directed Ayclic Graph (DAG), which is a desirable property for some systems.

The basic subset is only available in obo format (use of OWL reasoners means that this is not necessary for OWL).

Anatomical Bridging Ontologies

Anatomical Bridging ontologies consist of OWL axioms that connect Uberon to another anatomical ontology. See Wiki documentation for more details.

Gross Anatomy

Cell Types

Combined Multispecies Ontologies

Composite (merged) Multispecies Ontologies

See the wiki for more details. See also the old wiki.

Composite ontologies merge species ontologies into the structure of Uberon, merging in taxonomic equivalents, and relabeling species-specific classes. Note the composite ontologies also merge in all of the cell ontology (CL).

name obo owl includes
composite-vertebrate .obo .owl MA, EHDAA2, ZFA, XAO, CL
composite-metazoan .obo
.owl MA, EHDAA2, ZFA, XAO, CL, FBbt, WBbt, PORO, CTENO, CEPH
composite-metazoan-basic .obo n/a MA, EHDAA2, ZFA, XAO, CL, FBbt, WBbt, PORO, CTENO, CEPH

Importer (collector) Multispecies Ontologies

See the wiki for more details. See also Fig 3 from the Uberon paper:

The ontology collected-eukaryote.owl imports uberon plus bridging axioms plus individual species anatomy ontologies. The ontology is constructed recursively, and it is possible to obtain an importer ontology for a variety of taxa.

The uberon/bridge folder contains all collected-X ontologies.

Data annotated using Uberon

Uberon is currently being used for diverse types of data annotation, from evolutionary phenotype data to description of samples in next-gen sequencing projects. We currently do not provide an aggregated download of all this data. Please visit the adopters page for details on how to download individual datasets.

Uberon can also be used to integrate data provided by groups that do not explicitly adope Uberon. For example, data from annotated using the MGI adult mouse ontology can be integrated with data from the Allen Brain Atlas by using the two corresponding bridge ontologies.

logo Uberon is an integrated cross-species ontology covering anatomical structures in animals. See the about page for more info.

github.com/obophenotype/uberon
 

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