Often when terms are created, there are several words or phrases that could be used as the term name. In such cases, one form will be chosen as term name whilst the other possible names are added as synonyms. Despite the name, GO synonyms are not always 'synonymous' in the strictest sense of the word, as they do not always mean exactly the same as the term they are attached to. Instead, a GO synonym may be broader or narrower than the term string; it may be a related phrase; it may be alternative wording, spelling or use a different system of nomenclature; or it may be a true synonym. This flexibility allows GO synonyms to serve as valuable search aids, as well as being useful for applications such as text mining and semantic matching.
Having a single, broad relationship between a GO term and its synonyms is adequate for most search purposes, but for other applications such as semantic matching, the inclusion of a more formal relationship set is valuable. For this reason, GO records a relationship type for each synonym. These relationships are stored in the OBO format GO file.
The synonym relationship scopes are:
- the term is an exact synonym
ornithine cycle is an exact synonym of urea cycle
- the synonym is broader than the term name
cell division is a broad synonym of cytokinesis
- the synonym is narrower or more precise than the term name
pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair
- the terms are related
cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis
The synonym scope related should be used where the relationship between a term and its synonym is NOT exact, narrower or broader.
In some cases, broader and narrower synonyms are created in the place of new parent or child terms because some synonym strings may not be valid GO terms but may still be useful for search purposes. For example, the string "respiration" is synonymous with both cellular respiration, the energy-generating metabolic processes of a cell, and respiratory gaseous exchange, or breathing; as its meaning is ambiguous, it is unsuitable for use as a GO term string, but we can add it as a broad synonym to both terms.
When you add a synonym using OBO-Edit, choose a scope from the pull-down selector (see the OBO-Edit user guide for more information). OBO-Edit will incorporate the synonym scope into the OBO format flat file when you save. The default synonym scope is 'related synonym', but this should be changed to a different scope if appropriate.
The number of synonyms for a term is not limited, and the same text string can be used as a synonym for more than one GO term.
Add synonyms if you edit a term name but the old name is still a valid synonym; for example, if you change "respiration" to "cellular respiration", keep "respiration" as a synonym. This helps other users to find familiar terms.
Add synonyms if the term has (or contains) a commonly used abbreviation. For example, FGF binding could be used as a synonym for fibroblast growth factor binding.
Do not add a synonym if the only difference is case (e.g. start vs. START). Synonyms, like term names, are all lower case except where demanded by context (e.g. DNA, not dna).
Rules For Synonyms
- acronyms are exactly synonymous with the full name, as long as the acronym is not used in any other sense elsewhere
- include implicit information when making a decision and take into account which ontology the term is in; e.g. an entry that ends in 'factor' is not synonymous with a molecular function
- jargon type phrases are exactly synonymous with the full name, as long as the phrase is not used in any other sense elsewhere
- proton is exactly synonymous with hydrogen where hydrogen refers to H+ (hydrogen ion); proton is not synonymous with H2 (hydrogen gas)
- ligand is not exactly synonymous with binding (ligand is an entity, binding is an action)
- x receptor ligand is not exactly synonymous with x (x is only one of the potential ligands so XXX receptor ligand is broader than x)
- x complex is not exactly synonymous with x (x is ambiguous - could be describing the activity of x)
- x transporter is broader than x porter, x symporter or x antiporter