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

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!Column !! Content !! Required? !! Cardinality !! Example
 
!Column !! Content !! Required? !! Cardinality !! Example
 
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|1 ||DB||required||1||WB
+
|1 ||DB||'''required'''||1||WB
 
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|2 ||DB Object ID||'''required'''|| 1||WBGene00007799
 
|2 ||DB Object ID||'''required'''|| 1||WBGene00007799
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|4 || Qualifier || ''optional'' || 0 or greater ||(no value, leave empty)
 
|4 || Qualifier || ''optional'' || 0 or greater ||(no value, leave empty)
 
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|-
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|5 || GO ID || required || 1 ||DOID:0060041
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|5 || GO ID || '''required''' || 1 ||DOID:0060041
 
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|6 ||DB:Reference (|DB:Reference)||required'''Bold text'''||1 or greater||WBPaper00041363
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|6 ||DB:Reference (|DB:Reference)||'''required'''||1 or greater||WBPaper00041363
 
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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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|12||DB Object Type||'''required'''||1||gene (all annotations have this value)
 
|12||DB Object Type||'''required'''||1||gene (all annotations have this value)
 
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|-
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|13||Taxon(|taxon)||'''required'''||1 or 2||taxon:6239
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|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)
 
|14||Date||required||1||20130422 (this is the date of annotation<br/>dumped under Date_last_updated)
 
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|15|| Assigned By||required'''Bold text'''||1||WB
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|15|| Assigned By||'''required'''||1||WB
 
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|16||Annotation Extension||''optional''||0 or greater||(no value, leave empty)
 
|16||Annotation Extension||''optional''||0 or greater||(no value, leave empty)
 
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|17||Gene Product Form ID||''optional''||0 or greater||(no value, leave empty)
 
|17||Gene Product Form ID||''optional''||0 or greater||(no value, leave empty)

Revision as of 21:09, 6 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) required 1 or greater WBPaper00041363
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 (no value, leave empty)
9 Aspect required 1 D (D for disease ontology, all annotations
have this value)
10 DB Object Name optional 0 or 1
11 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)
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)
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