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

Revision as of 09:33, 28 March 2014

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

Format: The gene association file is a 17 column tab-delimited file, where 11 columns have to have data and 6 are optional.

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	Life_stage ID	required	1	WBls:00000xx
6	DB:Reference (\|DB:Reference)	required	1 or greater (separate values with pipes)	WBPaper00041363\|WBPaperXXXXXXXX
7	Evidence code	required	1	IDA
8	With (or) From	optional	0 or greater (separate values with pipes)	(no value, leave empty)
9	Aspect	required	1	L (for Life_stage 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	not sure about the date
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)

@@ Line 18: / Line 18: @@
 |4 || Qualifier || ''optional'' || 0 or greater ||(no value, leave empty)
 |-
-|5 || GO ID || '''required''' || 1 ||DOID:0060041
+|5 || Life_stage ID || '''required''' || 1 ||WBls:00000xx
 |-
 |6 ||DB:Reference (<nowiki>|</nowiki>DB:Reference)||'''required'''||1 or greater<br/> (separate values with pipes)||WBPaper00041363<nowiki>|</nowiki>WBPaperXXXXXXXX
 |-
-|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|| IDA
 |-
-|8 ||With (or) From||''optional''||0 or greater<br/> (separate values with pipes)||OMIM:600565<nowiki>|</nowiki>OMIM:600566
+|8 ||With (or) From||''optional''||0 or greater<br/> (separate values with pipes)||(no value, leave empty)
 |-
-|9 || Aspect|| '''required'''||1||D (D for disease ontology, all annotations<br/> have this value)
+|9 || Aspect|| '''required'''||1||L (for Life_stage ontology, all annotations<br/> have this value)
 |-
 |10||DB Object Name||''optional''||0 or 1||(no value, leave empty)
@@ Line 36: / Line 36: @@
 |13||Taxon||'''required'''||1 or 2||taxon:6239
 |-
-|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)
+|14||Date||required||1||not sure about the date
 |-
 |15|| Assigned By||'''required'''||1||WB