Difference between revisions of "Specifications for a GAF for gene-disease data"
From WormBaseWiki
Jump to navigationJump to search| Line 4: | Line 4: | ||
|+Mapping of GAF column to gene-disease data | |+Mapping of GAF column to gene-disease data | ||
|- | |- | ||
| − | !Column !! Content !! Required? !! Cardinality | + | !Column !! Content !! Required? !! Cardinality !! Example |
|- | |- | ||
| − | |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 || | + | |3 || DB Object Symbol || required || 1 ||nrx-1 |
|- | |- | ||
| − | |4 || Qualifier || ''optional'' || 0 or greater || | + | |4 || Qualifier || ''optional'' || 0 or greater ||(no value, leave empty) |
|- | |- | ||
| − | |5 || GO ID || required || 1 || | + | |5 || GO ID || required || 1 ||DOID:0060041 |
|- | |- | ||
| − | |6 ||DB:Reference (|DB:Reference)||required||1 or greater|| | + | |6 ||DB:Reference (|DB:Reference)||required||1 or greater||WBPaper00041363 |
|- | |- | ||
| − | |7 ||Evidence code||required||1|| | + | |7 ||Evidence code||required||1|| IMP (use 'IMP' for Experimental_model <br/>genes and ISS for Potential_model genes) |
|- | |- | ||
| − | |8 ||With (or) From||''optional''||0 or greater|| | + | |8 ||With (or) From||''optional''||0 or greater||(no value, leave empty) |
|- | |- | ||
| − | |9 || Aspect|| required||1|| | + | |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|| | ||
|- | |- | ||
| − | |11||DB Object Synonym (|Synonym)||''optional''||0 or greater|| | + | |11||DB Object Synonym (|Synonym)||''optional''||0 or greater||(no value, leave empty) |
|- | |- | ||
| − | |12||DB Object Type||required||1|| | + | |12||DB Object Type||required||1||gene (all annotations have this value) |
|- | |- | ||
| − | |13||Taxon(|taxon)||required||1 or 2|| | + | |13||Taxon(|taxon)||required||1 or 2||taxon:6239 |
|- | |- | ||
| − | |14||Date||required||1|| | + | |14||Date||required||1||20130422 (this is the date of annotation<br/>dumped under |
|- | |- | ||
|15|| Assigned By||required||1|| | |15|| Assigned By||required||1|| | ||
Revision as of 20:56, 6 February 2014
GAF 2.0 for gene-disease data includes all genes with the Experimental_model and Potential_model tags.
| 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 (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 |
| 15 | Assigned By | required | 1 | |
| 16 | Annotation Extension | optional | 0 or greater | |
| 17 | Gene Product Form ID | optional | 0 or greater |
