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

From WormBaseWiki
Jump to navigationJump to search
Line 8: Line 8:
 
|1 ||DB||required||1||WB
 
|1 ||DB||required||1||WB
 
|-
 
|-
−
|2 ||DB Object ID||required|| 1||WBGene00007799
+
|2 ||DB Object ID||'''required'''|| 1||WBGene00007799
 
|-
 
|-
−
|3 || DB Object Symbol || required || 1 ||nrx-1
+
|3 || DB Object Symbol || '''required''' || 1 ||nrx-1
 
|-
 
|-
 
|4 || Qualifier || ''optional'' || 0 or greater ||(no value, leave empty)
 
|4 || Qualifier || ''optional'' || 0 or greater ||(no value, leave empty)
Line 16: Line 16:
 
|5 || GO ID || required || 1 ||DOID:0060041
 
|5 || GO ID || required || 1 ||DOID:0060041
 
|-
 
|-
−
|6 ||DB:Reference (|DB:Reference)||required||1 or greater||WBPaper00041363
+
|6 ||DB:Reference (|DB:Reference)||required'''Bold text'''||1 or greater||WBPaper00041363
 
|-
 
|-
−
|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)
 
|-
 
|-
 
|8 ||With (or) From||''optional''||0 or greater||(no value, leave empty)
 
|8 ||With (or) From||''optional''||0 or greater||(no value, leave empty)
 
|-
 
|-
−
|9 || Aspect|| required||1||D (D for disease ontology, all annotations<br/> have this value)
+
|9 || Aspect|| '''required'''||1||D (D for disease ontology, all annotations<br/> have this value)
 
|-
 
|-
 
|10||DB Object Name||''optional''||0 or 1||
 
|10||DB Object Name||''optional''||0 or 1||
Line 28: Line 28:
 
|11||DB Object Synonym (|Synonym)||''optional''||0 or greater||(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)
+
|12||DB Object Type||'''required'''||1||gene (all annotations have this value)
 
|-
 
|-
−
|13||Taxon(|taxon)||required||1 or 2||taxon:6239
+
|13||Taxon(|taxon)||'''required'''||1 or 2||taxon:6239
 
|-
 
|-
 
|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)
 
|-
 
|-
−
|15|| Assigned By||required||1||WB
+
|15|| Assigned By||required'''Bold text'''||1||WB
 
|-
 
|-
 
|16||Annotation Extension||''optional''||0 or greater||(no value, leave empty)
 
|16||Annotation Extension||''optional''||0 or greater||(no value, leave empty)
 
|-
 
|-
 
|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 21:07, 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) requiredBold text 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 requiredBold text 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)
Retrieved from "https://wiki.wormbase.org/index.php?title=Specifications_for_a_GAF_for_gene-disease_data&oldid=22292"