Cellular Component Ontology Guidelines

The cellular component ontology describes locations, at the levels of subcellular structures and macromolecular complexes. Examples of cellular components include nuclear inner membrane, with the synonym inner envelope, and the ubiquitin ligase complex, with several subtypes of these complexes represented.

Generally, a gene product is located in or is a subcomponent of a particular cellular component. The cellular component ontology includes multi-subunit enzymes and other protein complexes, but not individual proteins or nucleic acids. Cellular component also does not include multicellular anatomical terms.

Maintaining complete is a and part of trees in cellular component

The cellular component ontology is is a complete, meaning that every term has a path to the root node which passes solely through is a relationships. This should be preserved; the following guidelines should help maintain this structure.

  • Make sure the term has an is a path to the root, i.e. there are is a parent terms by at least one path all the way to cellular component.
  • Make sure the term has at least one part of relation in its ancestry, to ensure that there are no part of orphans. It does not need to be an immediate part of parent, but every term has to be part of something. So, for complex Y, this would be okay for example:

    cell
    [p] complex X
    ---[i] complex Y

    because complex Y is transitively part of cell.
  • Ensure that all logical is a parents are added. So, for example, if your term is a protein complex, make sure it has the parent protein complex. Or if your term, or one of its parents, is part of cell, it will need to be is a cell part, or have cell part in its ancestry.
  • Check none of the relations you create are redundant. You can check for this in OBO-Edit by using the reasoner, and then using the link filter [self] [self] [is redundant].

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Last modified on 24/09/2012