Guide to GO Synonyms

Synonyms in GO

GO synonyms are useful for many purposes, primarily for searching, but also for applications such as text mining and semantic matching. Despite their name, they are not always exactly synonymous to the term they are attached to. This is because it is often useful to search on a string related to the term of interest, for example, if I search GO for 'respiration' I retrieve two terms, 'respiratory gaseous exchange ; GO:0007585' and 'cellular respiration ; GO:0045333' which I can choose between, although respiration is not directly synonymous with either term. Equally, it is also useful to include exactly synonymous terms and very loosely related terms such as individual gene products, so there is actually a spectrum of relationships between GO terms and their 'synonyms'.

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 currently stored in a flat file but in the future will be included in the structure of GO itself.

Synonym types

=   the term is an exact synonym
~   the terms are related (eg. XXX complex and XXX)
<   the synonym is broader than the term name
>   the synonym is more precise than the term name
!=   the term is not the same as the synonym (no precise relationship assigned)

The synonyms file

You will find the synonyms file in go/doc/synonyms. It is maintained by Amelia Ireland (aji@ebi.ac.uk) and Jane Lomax (jane@ebi.ac.uk). Please email them if you have any questions or if you spot an error.

Updating the synonyms file

When GO curators add new synonyms to the ontologies, they should add them to the synonyms file and then commit it to CVS.

Adding your synonym to the synonyms file

The format of the synonyms file is as follows:

GO id[tab] GO term name[tab] relationship type[tab] synonym

for example: GO:0007631 feeding behavior > eating

To add your synonym, insert a line in the file in the format shown, choosing one of the synonym types from the list above. If you are not sure what type the synonym should have, use ~ .

Some terms have additional data at the end clarifying the relationship between the terms. If you wish to append such data, add it after the synonym separated by a tab.

The synonyms file is in tab-delimited plain text format so it can be easily edited in spreadsheet applications such as Excel. If you edit the file using Excel, please save the file in text (tab-delimited) format. This adds speech marks around any term with a comma in it; these can be left in the file.

The synonyms file will be checked regularly for missing synonyms so please attempt to keep it up to date. If you have problems altering the file, send your synonyms, along with the relationship type, to Amelia Ireland (aji@ebi.ac.uk), who will add them with a rather convenient perl script.

Rules For Synonyms

1. porter and transporter are NOT synonymous (transporter is broader)
   
2. symporter/antiporter and transporter are NOT synonymous (transporter is broader)
   
3. ligand is NOT synonymous with binding (ligand is an entity, binding an action)
   
4. symport(er) is NOT symonymous with co-transport(er) (symport is ion co-transport > co-tranport is broader than symport)
   
5. carrier is NOT synonymous with transporter (transporter is broader)
   
6. XXX receptor ligand is NOT synonymous with XXX (XXX is only one of the potential ligands so XXX receptor ligand is broader than XXX)
   
7. Acronyms are SYNONYMOUS with the full name (as long as the acronym is not used in any other sense elsewhere)
   
8. 'Jargon' type phrases are SYNONYMOUS with the full name (as long as the phrase is not used in any other sense elsewhere)
   
9. proton is SYNONYMOUS with hydrogen in most senses
   
10. include implicit information when making decision; take into account which ontology the term is in - e.g. an entry term that ends in 'factor' is not synonymous with a molecular function.
    
11. XXX complex is NOT synonymous with XXX (XXX is ambiguous - could be describing the activity of XXX)