Rattus norvegicus annotations provided by the Rat Genome Database (RGD) project at the Medical College of Wisconsin, Milwaukee, Wisconsin  (https://rgd.mcw.edu/)

The gene_association.rgd file follows the gaf-version 2.1 specification available at http://www.geneontology.org/page/go-annotation-file-gaf-format-21.

The GAF is a tab-delimited text file.  Columns in the GAF are as follows:

Column  Content
1	DB
2	DB Object ID
3	DB Object Symbol
4	Qualifier
5	GO ID
6	DB:Reference (|DB:Reference)
7	Evidence Code
8	With (or) From
9	Aspect (P, F or C)
10	DB Object Name
11	DB Object Synonym (|Synonym)
12	DB Object Type
13	Taxon ID (NCBI:txid10116, Rattus norvegicus)
14	Date
15	Assigned By (database or annotation group abbreviation)
16	Annotation Extension   (not currently used at RGD)
17	Gene Product Form ID  (not currently used at RGD)


Recent changes to the data contained in RGD's GAF include:

=====December 2016=====
The gene_association.rgd file now contains only 'RGD' in column 1 and RGD gene identifiers in column 2.  Previously, that file contained annotations for genes from RGD and annotations for gene products, specifically proteins, from UniProtKB.  The file containing annotations assigned to both RGD gene and UniProt protein IDs ("gene_protein_association.rgd") is still available on the RGD ftp site at ftp://ftp.rgd.mcw.edu/pub/data_release/gene_protein_association.rgd.gz.


=====March 2018=====
At the request of the GOC, and to comply with the GOC specifications for GAFs, information about the original references for ISO annotations were removed from the gene_association.rgd file's reference field (column 6).  "Original references" refers to (e.g.) PubMed or other reference IDs of publications used to make experimental annotations for orthologous human or mouse genes, from which ISO annotations were inferred to the corresponding rat genes.  Original references for ISO annotations can still be found on the RGD website (https://rgd.mcw.edu) and in files on the RGD ftp site (ftp://ftp.rgd.mcw.edu/pub/data_release/gene_protein_association.rgd.gz, as well as the ...go files in the ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/ directory and the ...bp, ...mf and ...cc files in the 'with terms' subdirectory).




For questions with regard to the gene_association.rgd file or its annotations, please contact RGD at https://rgd.mcw.edu/contact/index.shtml