Difference between revisions of "Specifications for a GAF for gene-disease data"

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Line 16: Line 16:
 
|5 || GO ID || '''required''' || 1 ||DOID:0060041
 
|5 || GO ID || '''required''' || 1 ||DOID:0060041
 
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|6 ||DB:Reference (<nowiki>|</nowiki>DB:Reference)||'''required'''||1 or greater||WBPaper00041363
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|6 ||DB:Reference (<nowiki>|</nowiki>DB:Reference)||'''required'''||1 or greater||WBPaper00041363<nowiki>|</nowiki>WBPaperXXXXXXXX
 
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|-
 
|7 ||Evidence code||'''required'''||1|| IMP or ISS (use 'IMP' for Experimental_model <br/>genes and ISS for Potential_model genes)
 
|7 ||Evidence code||'''required'''||1|| IMP or ISS (use 'IMP' for Experimental_model <br/>genes and ISS for Potential_model genes)
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|13||Taxon||'''required'''||1 or 2||taxon:6239
 
|13||Taxon||'''required'''||1 or 2||taxon:6239
 
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|14||Date||required||1||20130422 (this is the date of annotation<br/>dumped under Date_last_updated<br/>for potential_model genes use the date on which the OMIM homology script is run)
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|14||Date||required||1||20130422 (this is the date of annotation dumped under Date_last_updated;<br/>for potential_model genes, use the date on which the OMIM homology script is run)
 
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|15|| Assigned By||'''required'''||1||WB
 
|15|| Assigned By||'''required'''||1||WB

Revision as of 00:39, 7 February 2014

GAF 2.0 for gene-disease data includes all genes with the Experimental_model and/or Potential_model tags.

Mapping of GAF column to gene-disease data
Column Content Required? Cardinality Example
1 DB required 1 WB
2 DB Object ID required 1 WBGene00007799
3 DB Object Symbol required 1 nrx-1
4 Qualifier optional 0 or greater (no value, leave empty)
5 GO ID required 1 DOID:0060041
6 DB:Reference (|DB:Reference) required 1 or greater WBPaper00041363|WBPaperXXXXXXXX
7 Evidence code required 1 IMP or ISS (use 'IMP' for Experimental_model
genes and ISS for Potential_model genes)
8 With (or) From optional 0 or greater
(separate values with pipes)
OMIM:600565|OMIM:600566
9 Aspect required 1 D (D for disease ontology, all annotations
have this value)
10 DB Object Name optional 0 or 1 (no value, leave empty)
11 DB Object Synonym (|Synonym) optional 0 or greater (no value, leave empty)
12 DB Object Type required 1 gene (all annotations have this value)
13 Taxon required 1 or 2 taxon:6239
14 Date required 1 20130422 (this is the date of annotation dumped under Date_last_updated;
for potential_model genes, use the date on which the OMIM homology script is run)
15 Assigned By required 1 WB
16 Annotation Extension optional 0 or greater (no value, leave empty)
17 Gene Product Form ID optional 0 or greater (no value, leave empty)