Difference between revisions of "Specifications for a GAF for gene-disease data"
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Jump to navigationJump to search| 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 (<nowiki>|</nowiki>DB:Reference)||'''required'''||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<br/> (separate values with pipes)||OMIM:600565|OMIM:600566 | + | |8 ||With (or) From||''optional''||0 or greater<br/> (separate values with pipes)||OMIM:600565<nowiki>|</nowiki>OMIM:600566 |
|- | |- | ||
|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) | ||
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|10||DB Object Name||''optional''||0 or 1||(no value, leave empty) | |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) | + | |11||DB Object Synonym (<nowiki>|</nowiki>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) | ||
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|13||Taxon||'''required'''||1 or 2||taxon:6239 | |13||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'''||1||WB | ||
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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) | ||
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Revision as of 00:32, 7 February 2014
GAF 2.0 for gene-disease data includes all genes with the Experimental_model and/or 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 (|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 (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) |
| 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) |
