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Repository structure

The main kinds of files in the repository:

  1. Release files
  2. Imports
  3. Components

Release files

Release file are the file that are considered part of the official ontology release and to be used by the community. A detailed descripts of the release artefacts can be found here.

Imports

Imports are subsets of external ontologies that contain terms and axioms you would like to re-use in your ontology. These are considered "external", like dependencies in software development, and are not included in your "base" product, which is the release artefact which contains only those axioms that you personally maintain.

These are the current imports in UBERON

Import URL Type
pr https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl None
cl http://purl.obolibrary.org/obo/cl.owl None
go http://purl.obolibrary.org/obo/go.owl None
envo http://purl.obolibrary.org/obo/envo.owl None
ro http://purl.obolibrary.org/obo/ro.owl None
bspo http://purl.obolibrary.org/obo/bspo.owl None
chebi http://purl.obolibrary.org/obo/chebi.owl None
pato http://purl.obolibrary.org/obo/pato.owl None
bfo http://purl.obolibrary.org/obo/bfo.owl None
ncbitaxon http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl None
nbo http://purl.obolibrary.org/obo/nbo.owl None
ceph http://purl.obolibrary.org/obo/ceph.owl None
cteno http://purl.obolibrary.org/obo/cteno.owl None
ehdaa2 https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo None
emapa http://purl.obolibrary.org/obo/emapa.owl None
fbbt http://purl.obolibrary.org/obo/fbbt.owl None
fbdv http://purl.obolibrary.org/obo/fbdv.owl None
ma http://purl.obolibrary.org/obo/ma.owl None
poro http://purl.obolibrary.org/obo/poro.owl None
wbbt http://purl.obolibrary.org/obo/wbbt.owl None
wbls http://purl.obolibrary.org/obo/wbls.owl None
xao http://purl.obolibrary.org/obo/xao.owl None
zfa http://purl.obolibrary.org/obo/zfa.owl None
caro http://purl.obolibrary.org/obo/caro.owl None

Components

Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered native to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

  1. There is an automated process that generates and re-generates a part of the ontology
  2. A part of the ontology is managed in ROBOT templates
  3. The expressivity of the component is higher than the format of the edit file. For example, people still choose to manage their ontology in OBO format (they should not) missing out on a lot of owl features. They may chose to manage logic that is beyond OBO in a specific OWL component.

These are the components in UBERON

Filename URL
mappings.owl None
in-subset.owl None
hra_subset.owl None
vasculature_class.owl None