GO SYNONYMS FILE READ ME
========================

The GO synonyms files are 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 in the files.


Synonym types
=============

~	the terms are related (e.g. XXX complex and XXX)
=	the term is an exact synonym
<	the synonym is broader than the term name
>	the synonym is more precise than the term name
!=	the term is related, but the exact relationship is not specified
(i.e. not exact, broader or narrower, e.g. pathogenesis and virulence)

These types form a loose hierarchy:

related (~)
  %exact (=)
  %broader (<)
  %narrower (>)
  %other related (!=)

The default relationship is related to (~), as all synonyms are in some
way related to the term name, but it is preferable to assign one of the
more specific relationships where possible. Other related (!=) should be
used where the relationship between a term and its synonym is NOT exact,
narrower or broader.


Adding your synonym
===================

When you add a synonym using DAG-Edit, choose a type from the
pull-down selector (see the DAG-Edit user guide for more
information). DAG-Edit will incorporate the synonym type into the OBO
format flat file when you save. The default is "synonym," equivalent
to "~" in this 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

The Synonyms.txt file is generated by a script from the OBO format
file (gene_ontology.obo).


Rules For Synonyms
==================

porter and transporter are NOT synonymous (transporter is broader)

symporter/antiporter and transporter are NOT synonymous (transporter is broader)

ligand is NOT synonymous with binding (ligand is an entity, binding an action)

symport(er) is NOT symonymous with co-transport(er) (symport is ion co-transport
==> co-tranport is broader than symport)

carrier is NOT synonymous with transporter (transporter is broader)

XXX receptor ligand is NOT synonymous with XXX (XXX is only one of the potential
ligands so XXX receptor ligand is broader than XXX)

Acronyms are SYNONYMOUS with the full name (as long as the acronym is not used
in any other sense elsewhere)

'Jargon' type phrases are SYNONYMOUS with the full name (as long as the phrase
is not used in any other sense elsewhere)

proton is SYNONYMOUS with hydrogen in most senses

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.
 
XXX complex is NOT synonymous with XXX (XXX is ambiguous - could be describing
the activity of XXX)

Complexes with a sedimentation coefficient are always NARROWER than the complex i.e. 16S xxx complex is NARROWER than xxx complex.