GOslim_gene_association.cgd.gz Contains all CGD GO slim annotations (protein and RNA) The GOslim_gene_association.cgd file contains GO Slim annotations for Candida genes, using the Candida GO Slim instead of the entire Gene Ontology. The file listing all Candida GO Slim terms can be downloaded at: http://www.candidagenome.org/download/go/go_slim/goslim_candida.obo A GO Slim is a small subset of terms from the Gene Ontology, which is intended to provide a general overview without all the fine-grained detail contained in the GO itself. Further explanation on GO slim can be found at: http://www.geneontology.org/GO.slims.shtml For the actual CGD GO curation, please use the gene_association.cgd file at: http://www.candidagenome.org/download/go/gene_association.cgd.gz The GOslim_gene_association.cgd.gz file is updated weekly and uses the standard file format for gene_association files of the Gene Ontology (GO) Consortium. A more complete description of the file format is found here: http://www.geneontology.org/doc/GO.annotation.html#file Columns are: Contents: 1) DB - database contributing the file (always "CGD" for this file) 2) DB_Object_ID - CGDID 3) DB_Object_Symbol - see below 4) NOT (optional) - 'NOT' qualifier for a GO annotation, when needed 5) GO ID - unique numeric identifier for the GO term 6) DB:Reference(|DB:Reference) - the reference associated with the GO annotation 7) Evidence - the evidence code for the GO annotation 8) With (or) From (optional) - any With or From qualifier for the GO annotation 9) Aspect - which ontology the GO term belongs in 10) DB_Object_Name(|Name) (optional) - a name for the gene product in words, e.g. 'acid phosphatase' 11) DB_Object_Synonym(|Synonym) (optional) - see below 12) DB_Object_Type - type of object annotated, e.g. gene, protein, etc. 13) taxon(|taxon) - taxonomic identifier of species encoding gene product 14) Date - date GO annotation was made 15) Assigned_by - source of the annotation (CGD; see below) Note on use of Candida slim terms: Column 5 - GO IDs in this column refer to the GO ID for the closest Candida GO slim term, instead of the GO term that each gene is annotated to. Column 15 - GO annotations in CGD are either assigned by CGD curators or predicted computationally. For more information, please see http://www.candidagenome.org/download/go/gene_association_README.txt Note on CGD nomenclature (pertaining to columns 3 and 11): Column 3 - When a Standard Gene Name (e.g. CDC28, COX2) has been conferred, it will be present in Column 3. When no Gene Name has been conferred, the ORF Name (e.g., C. albicans orf19.6632, C. glabrata CAGL0K12694g) will be present in column 3. Column 11 - The ORF Name (e.g., C. albicans orf19.6632, C. glabrata CAGL0K12694g) will be the first name present in Column 11. Any other names (except the Standard Name, which will be in Column 3 if one exists), including Aliases used for the gene will also be present in this column. Note: The files are gzip compressed tab-delimited text files. There are several freely available software options for decompressing gzipped files using Windows. The software and other useful information is available on these web sites: - WinZip (http://www.winzip.com/) - Stuffit (http://www.stuffit.com/) - Gzip (http://www.gzip.org/ and the gzip user's manual: http://www.math.utah.edu/docs/info/gzip_toc.html