README for gene_association.wb
Submitted by WormBase (http://www.wormbase.org)
March 31, 2005.
Last_updated: March 11, 2014

Description of file: 
Consists of annotations of Caenorhabditis elegans (C. elegans) genes and  gene products (RNA and proteins) 
to gene ontology (GO) terms.

Note: 
The current gene association file is in the gaf 2.0 format, please see documentation at 
http://www.geneontology.org/GO.format.gaf-2_0.shtml.

Annotations:
The gene_association.wb contains three types of annotations:

1. Manual annotations:
This type of annotation is based on the published literature.  Please note that this file also uses 
abstracts from C. elegans meetings as references.  Since these are unpublished information, they
are to be cited only as personal communications, with author permission.

2. Annotations based on Phenotype2GO mappings:
These annotations are obtained by a semi-automated method wherein phenotypes are mapped to a 
GO term/s by WormBase curators.  These mappings are then used by a script to attach GO_terms to genes. 
These annotations all have the evidence code 'IMP'. Currently, allele phenotypes or phenotypes obtained by 
large scale RNA interference screens have been used for the mapping. For example, the phenotype 'STErile' (Ste) 
which is a specialization of 'post-embryonic defect' and 'reproductive defect' is mapped to the GO term 
'reproduction' (GO:0000003).


3. Electronic annotations:
These annotations are annotations of C. elegans proteins to GO terms based on electronic matching 
of protein motifs/domains to those documented in the Interpro database (http://www.ebi.ac.uk/interpro/), and their 
mapping to GO terms provided by the Interpro2go file generated by the EBI (PMID:12654719, PMID:12520011). Note that 
the 'IEA' annotations are not reviewed for accuracy by human curators. As such, all of these annotations use the 
evidence code 'IEA'.  


4. External Annotations (from the GOA project at the EBI)
This version of the gene_association.wb incorporates non-redundant and non-IEA annotations to 
C. elegans proteins made by the GOA project at the EBI (http://www.ebi.ac.uk/GOA/).  These annotations can be 
recognised as those having the contributing database in column 15 as either 'IntAct' or 'UniProt'. 

Use of references in the gene_association.wb:
As indicated in the GO annotation guide, the source for a reference attached to an annotation may 
be a literature reference, another database or a computational analysis.  WormBase curators refer 
to the paper that describes BLAST analysis (PMID:2231712) when they assign a GO term with the 
evidence code 'ISS' to a gene product based on their use of the BLAST analysis.

Contact information:
Questions about the gene_association.wb maybe addressed to WormBase curators by writing to: 
wormbase-help@wormbase.org.