PO Annotation Extensions (column 16)

The use of annotation extensions in the PO is based on the usage developed by the GO. A discussion of GO's annotation extension column can be found on the GO wiki.

Each PO annotation pairs a single gene product to a single term from the ontology. This restricts annotators in what they can say - there must be a pre-existing term in the ontology, or one must be requested. It would be far less restrictive if the annotator could combine additional terms in a single annotation. These terms could even come from other OBO ontologies, or they could be gene products.

This page describes column 16 in the gene annotation file (see GAF 2.0 format), which allows additional terms to be specified to extend the meaning of an annotation. If and when an annotator chooses to do this, they are effectively creating an "on-the-fly" [cross product] term. We say "on-the-fly" because the combinatorial term is not added to the ontology (although it could be at a later stage, if the ontology editors choose to do do).

There are many possible cases where one might with to create annotation extensions.

Column 16 should be used when the appropriated relation is not specified or cannot be inferred within the PO, for example, for creating specific part_of relations when only a general part_of relation exists (see example 1), for linking a structure to a specific growth or developmental stage, when that link does not already exist or cannot be inferred (example 2), for specifying spacial relations that may be present in the experiment being annotated, but that are not specified in the PO (example 3).

See the documentation on using the annotation extension column for details of practical usage;

Link to Annotation_Association_File_Format PO wiki page.