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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 description of the release artefacts can be found here.


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 UPHENO

Import URL Type
go None
nbo None
uberon None
cl None
pato None
mpath None
ro None
omo None
chebi None
oba None
ncbitaxon None
pr None
bspo None
ncit None
fbbt None
fbdv None
hsapdv None
wbls None
wbbt None
plana None
zfa None
xao None
hsapdv-uberon custom
zfa-uberon custom
zfs-uberon custom
xao-uberon custom
wbbt-uberon custom
wbls-uberon custom
fbbt-uberon custom
xao-cl custom
wbbt-cl custom
fbbt-cl custom


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 choose to manage logic that is beyond OBO in a specific OWL component.

These are the components in UPHENO

Filename URL
phenotypes_manual.owl None
upheno-mappings.owl None
cross-species-mappings.owl None