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First attempt at script-run-workflow

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Bryan Roessler
2024-07-21 23:50:24 -04:00
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workflow/templates/qhtcp/Code/Updating files/SGD readme files/gene_association.README Normal file
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gene_association.sgd.gz This file is TAB delimited and contains all GO annotations for yeast genes (protein and RNA)
The gene_association.sgd.gz file 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/GO.format.annotation.shtml
Columns are: Contents:
1) DB - database contributing the file (always "SGD" for this file)
2) DB_Object_ID - SGDID
3) DB_Object_Symbol - see below
4) NOT (optional) - 'NOT', 'contributes_to', or 'colocalizes_with' 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 (e.g. SGD, UniProtKB, YeastFunc, bioPIXIE_MEFIT)
Note on SGD 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 Systematic Name (e.g. YAL001C,
YGR116W, YAL034W-A) will be present in column 3.
Column 11 - The Systematic Name (e.g. YAL001C, YGR116W, YAL034W-A,
Q0010) 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.
Please note that ORFs classified as 'Dubious' are not included in this file, as there is currently
no experimental evidence that a gene product is produced in S. cerevisiae.
This file is updated weekly.
For more information on the Gene Ontology (GO) project, see:
http://www.geneontology.org/

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workflow/templates/qhtcp/Code/Updating files/SGD readme files/go_terms.README Normal file
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go_terms.tab This file is TAB delimited and contains the GO terms and their definitions.
NOTE: This file is NO LONGER periodically updated. Please see the Last Modified date on the Web display to find the file creation date on which the file was created.
** For the most recent data, please use YeastMine. The YeastMine template at https://yeastmine.yeastgenome.org/yeastmine/template.do?name=GO_Terms_Tab&scope=allwill retrieve the most recent data. **
Columns the go_terms.tab is shown below.
Columns are: Contents:
1) GOID (mandatory) - the unique numerical identifer of the GO term
2) GO_Term (mandatory) - the name of the GO term
3) GO_Aspect (mandatory) - which ontology: P=Process, F=Function, C=Component
4) GO_Term_Definition - the full definition of the GO term
(optional)
For more information on the Gene Ontology (GO) project, see:
http://www.geneontology.org/
go_terms.README last updated Sept 14, 2023