49 lines
2.3 KiB
Plaintext
49 lines
2.3 KiB
Plaintext
gene_association.sgd.gz This file is TAB delimited and contains all GO annotations for yeast genes (protein and RNA)
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The gene_association.sgd.gz file uses the standard file format for
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gene_association files of the Gene Ontology (GO) Consortium. A more
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complete description of the file format is found here:
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http://www.geneontology.org/GO.format.annotation.shtml
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Columns are: Contents:
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1) DB - database contributing the file (always "SGD" for this file)
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2) DB_Object_ID - SGDID
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3) DB_Object_Symbol - see below
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4) NOT (optional) - 'NOT', 'contributes_to', or 'colocalizes_with' qualifier for a GO annotation, when needed
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5) GO ID - unique numeric identifier for the GO term
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6) DB:Reference(|DB:Reference) - the reference associated with the GO annotation
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7) Evidence - the evidence code for the GO annotation
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8) With (or) From (optional) - any With or From qualifier for the GO annotation
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9) Aspect - which ontology the GO term belongs in
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10) DB_Object_Name(|Name) (optional) - a name for the gene product in words, e.g. 'acid phosphatase'
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11) DB_Object_Synonym(|Synonym) (optional) - see below
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12) DB_Object_Type - type of object annotated, e.g. gene, protein, etc.
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13) taxon(|taxon) - taxonomic identifier of species encoding gene product
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14) Date - date GO annotation was made
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15) Assigned_by - source of the annotation (e.g. SGD, UniProtKB, YeastFunc, bioPIXIE_MEFIT)
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Note on SGD nomenclature (pertaining to columns 3 and 11):
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Column 3 - When a Standard Gene Name (e.g. CDC28, COX2) has been
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conferred, it will be present in Column 3. When no Gene Name
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has been conferred, the Systematic Name (e.g. YAL001C,
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YGR116W, YAL034W-A) will be present in column 3.
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Column 11 - The Systematic Name (e.g. YAL001C, YGR116W, YAL034W-A,
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Q0010) will be the first name present in Column 11. Any other
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names (except the Standard Name, which will be in Column 3 if
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one exists), including Aliases used for the gene will also be
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present in this column.
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Please note that ORFs classified as 'Dubious' are not included in this file, as there is currently
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no experimental evidence that a gene product is produced in S. cerevisiae.
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This file is updated weekly.
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For more information on the Gene Ontology (GO) project, see:
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http://www.geneontology.org/
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