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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

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 PHENIO

Import URL Type
chebi http://purl.obolibrary.org/obo/chebi.owl None
eco http://purl.obolibrary.org/obo/eco.owl None
ncbitaxon-taxslim http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl None
oba http://purl.obolibrary.org/obo/oba.owl None
pato http://purl.obolibrary.org/obo/pato.owl None
uberon-bridge-to-emapa http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl None
uberon-bridge-to-zfa http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl None
uberon-bridge-to-ma http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl None
uberon-bridge-to-wbbt http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl None
uberon-bridge-to-fbbt http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl None
uberon-bridge-to-fma http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl None
cl-bridge-to-emapa http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl None
cl-bridge-to-ma http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl None
cl-bridge-to-fma http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl None
cl-bridge-to-wbbt http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl None
cl-bridge-to-fbbt http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl None
cl-bridge-to-zfa http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.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 choose to manage logic that is beyond OBO in a specific OWL component.

These are the components in PHENIO

Filename URL
bfo.owl http://purl.obolibrary.org/obo/bfo.owl
emapa.owl http://purl.obolibrary.org/obo/emapa.owl
fbbt.owl http://purl.obolibrary.org/obo/fbbt.owl
go.owl http://purl.obolibrary.org/obo/go.owl
hsapdv.owl http://purl.obolibrary.org/obo/hsapdv.owl
mondo.owl http://purl.obolibrary.org/obo/mondo.owl
mpath.owl http://purl.obolibrary.org/obo/mpath.owl
nbo.owl http://purl.obolibrary.org/obo/nbo.owl
ro.owl http://purl.obolibrary.org/obo/ro.owl
uberon.owl http://purl.obolibrary.org/obo/uberon.owl
upheno.owl http://purl.obolibrary.org/obo/upheno/v2/upheno.owl
wbbt.owl http://purl.obolibrary.org/obo/wbbt.owl
zfa.owl http://purl.obolibrary.org/obo/zfa.owl