Folding and Unfolding

From GO Wiki
Jump to navigation Jump to search

Back to Annotation usage examples for each annotation extension relation

Extended annotations can be ‘folded’ to create a logical equivalent of a GO term, regardless of whether the term is included in the ontology. GO terms that are included in the ontology are said to be ‘pre-composed’, whereas the combination of terms and annotation extensions effectively ‘post-compose’ a term. It is also possible to perform the inverse and ‘unfoldpre-composed GO terms into the equivalent extended annotation expression.

Whether terms are pre- or post-composed during the annotation process is thus not critical because it is possible to interconvert seamlessly between the two. Identical information can thus be captured by either of two routes, creation of a new pre-composed term or during the recording of an annotation.

The folding operation creates a new application ontology on the fly, with each extended annotation materializing a new GO term. An OWL reasoner is used to automatically construct the graph in this new ontology. Application of this method can be seen as a stopgap to allow continued use of existing tools – the resulting application ontology, whilst logically complete, may be unwieldy for querying and browsing.

The unfolding method takes annotations to existing highly specific GO terms, and replaces them with an annotation to a more basic GO term, with the equivalent additional information now expressed as extensions.

When a new GO term is created, rather than using the annotation extension field

If a curator knows that they will be creating many annotations using a specific GO term and annotation extension then they will create a new GO term rather than using the annotation extension field.

The curator will also consider the placement of the new GO term, that will be 'created' by the use of the annotation extension field, within the ontology and will request a new GO term if the ontology created does not accurately represent the intention of the use of the annotation extension field. ie when there is not an appropriate annotation extension relationship available.

Examples of when a new GO term was created rather than using the annotation extension field [1] :

  • negative regulation of neuron death in response to H2O2 [2]

Examples of the folding of annotation extension relationships:

  • acts_on_a_population_of [3] OWL class required for example
  • activated_by [4] OWL class required for example
  • causally_upstream_of [5] OWL class required for example
  • happens_during [6] OWL class required for examples
  • has_input [7] OWL class required for transcription example only
    • has_direct_input [8] OWL class required for example
  • has_output [9] OWL class required for example
  • occurs_in [10] OWL class required for 2 of the 4 examples
  • part_of [11] OWL class required for 1 of the 3 examples
  • results_in_morphogenesis_of [12] OWL class required for example
  • results_in_development_of [13] OWL class required for example