General Gene Ontology Principles
Jump to navigation
Jump to search
In progress
Background reading
To write:
- democratization of expert knowledge (see also http://geneontology.org/docs/ontology-documentation/) - shared conceptualization
- domain: concepts pertinent to the description of gene and gene product function under normal physiological conditions (= evolved functions)
- built around the principle of genus-differentia
- describes functions, not specific gene products (enablers or targets)
- mf specificity usually corresponds to the set of substrates a reaction; some activities can use a wide range of substrates
- bp: specificity usually corresponds to a particular biological program; general programs such as transcription and translation would not have children for specific outputs, as these outputs would be the result of the same biological program
Signaling >> transcription >> translation >> secretion >> signaling in next cell
ie
Process 1 - x signaling pathway ; last step is activation of dbTF activity >> dbTF activity positively regulates transcription of input I >> transcription process (not specific, so no transcription of I GO term) >> translation >> secretion (not specific, so no secretion of I GO term) >> input I involved in signaling in next cell (y signaling pathway)
Term relationships
Parents
- Every term in the ontology must have at least one _is a_ parent and can have as many relationships to other terms as necessary.
Equivalence axioms
- 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 transportistransport 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.
Disjoint axioms
- 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 bindingisdisjoint withGO:0003697 single-stranded DNA binding.
Logical 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.
Glossary
IN PROGRESS
- Classes: terms
- Relations: OWL object Properties
Review Status
Last reviewed: