General Gene Ontology Principles
For in depth background on principles of the Gene Ontology, see the following publication:
- Paul's chapter in the GO handbook
- Every term in the ontology must have at least one _is a_ parent and can have as many relationships to other terms as necessary.
- These represent a special set of relationships that define a term with both necessary and sufficient conditions. For example the equivalence axiom for
GO:0055085 transmembrane transportis
transport and ('results in transport across' some membrane). This means that if a process is transmembrane transport, it result in transport across a membrane (necessary condition). It also means that any process that transports across a membrane _is a_ transmembrane transport (sufficient).
- Whenever possible, equivalence axioms should be created for every term.
- Terms are made
disjointwhen they have no children in common.
- Disjoint relationships can be very useful in that they can be used to identify inconsistencies in the ontology. For example,
GO:0003690 double-stranded DNA bindingis
GO:0003697 single-stranded DNA binding.
Importance of reasoning
Reasoning is critical to the keeping the GO maintainable. Any term in GO may have many parents. In an ontology as large and complex as the GO, maintaining classifications of this type by hand in is very error-prone as placing a class correctly in the hierarchy requires editors to know what parents are available. It is much more sustainable to record just one asserted classification along with a set of conditions for class membership and then to rely on automated classification for the rest.
- Classes: terms
- Relations: OWL object Properties