Difference between revisions of "Specifications for a DAF for gene-disease data"
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|5 ||DB Object Symbol|| '''R''' || 1 ||DOID:0060041 | |5 ||DB Object Symbol|| '''R''' || 1 ||DOID:0060041 | ||
|- | |- | ||
− | |6 || | + | |6 ||Inferred Gene Association||'''O'''||1 or greater<br/> (separate values with pipes)||WBPaper00041363<nowiki>|</nowiki>WBPaperXXXXXXXX |
|- | |- | ||
− | |7 || | + | |7 ||Gene Product Form ID||'''O'''||1|| IMP or ISS (use 'IMP' for Experimental_model <br/>genes and ISS for Potential_model genes) |
|- | |- | ||
− | |8 || | + | |8 ||Experimental Conditions <br/> (to create the model)||''O''||0 or greater<br/> (separate values with pipes)||OMIM:600565<nowiki>|</nowiki>OMIM:600566 |
|- | |- | ||
− | |9 || | + | |9 || Association Type|| '''R'''||1||D (D for disease ontology, all annotations<br/> have this value) |
|- | |- | ||
− | |10|| | + | |10||Qualifier||''O''||0 or 1||(no value, leave empty) |
|- | |- | ||
− | |11|| | + | |11||DO ID||''R''||0 or greater||(no value, leave empty) |
|- | |- | ||
− | |12|| | + | |12||With||'''O'''||1||gene (all annotations have this value) |
|- | |- | ||
− | |13|| | + | |13||Modifier Association Type||'''O'''||1 or 2||taxon:6239 |
|- | |- | ||
− | |14|| | + | |14||Modifier - qualifier||O||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) |
|- | |- | ||
− | |15|| | + | |15||Modifier (genetic)||'''O'''||1||WB |
|- | |- | ||
− | |16|| | + | |16||Modifier - experimental conditions||''O''||0 or greater||(no value, leave empty) |
|- | |- | ||
− | |17|| | + | |17||Evidence Code||''R''||0 or greater||(no value, leave empty) |
+ | |- | ||
+ | |18||Genetic sex||O|| | ||
+ | |- | ||
+ | |19||DB:Reference||R|| | ||
+ | |- | ||
+ | |20||Date||R|| | ||
+ | |- | ||
+ | |21||Assigned By||R|| | ||
+ | |||
|} | |} | ||
Revision as of 23:36, 27 January 2017
New AGR Disease Working Group specified DAF
- These specifications have been discussed and specified by the Disease Working Group of the AGR
- Annotations from the computational pipeline that WB currently has for assigning 'Potential models' will not be included in the MOD-specific DAFs. The plan is to have a separate AGR orthology pipeline to link human genes, orthologs from model organisms and disease.
- Note that all models are not in place yet in WB, though some of the data is already being curated in the Caltech Ontology Annotator curation tool for disease.
Column | Column Name | Required(R)/Optional(O) | Cardinality | Example | Model tag | New/Exists | Comment | |
---|---|---|---|---|---|---|---|---|
1 | Taxon | R | 1 | WB | ||||
2 | DB Object Type | R | 1 | WBGene00007799 | ||||
3 | DB | R | 1 | nrx-1 | ||||
4 | DB Object ID | R | 0 or greater | (no value, leave empty) | ||||
5 | DB Object Symbol | R | 1 | DOID:0060041 | ||||
6 | Inferred Gene Association | O | 1 or greater (separate values with pipes) |
WBPaper00041363|WBPaperXXXXXXXX | ||||
7 | Gene Product Form ID | O | 1 | IMP or ISS (use 'IMP' for Experimental_model genes and ISS for Potential_model genes) | ||||
8 | Experimental Conditions (to create the model) |
O | 0 or greater (separate values with pipes) |
OMIM:600565|OMIM:600566 | ||||
9 | Association Type | R | 1 | D (D for disease ontology, all annotations have this value) | ||||
10 | Qualifier | O | 0 or 1 | (no value, leave empty) | ||||
11 | DO ID | R | 0 or greater | (no value, leave empty) | ||||
12 | With | O | 1 | gene (all annotations have this value) | ||||
13 | Modifier Association Type | O | 1 or 2 | taxon:6239 | ||||
14 | Modifier - qualifier | O | 1 | 20130422 (this is the date of annotation dumped under Date_last_updated; for potential_model genes, use the date on which the OMIM homology script is run) | ||||
15 | Modifier (genetic) | O | 1 | WB | ||||
16 | Modifier - experimental conditions | O | 0 or greater | (no value, leave empty) | ||||
17 | Evidence Code | R | 0 or greater | (no value, leave empty) | ||||
18 | Genetic sex | O | ||||||
19 | DB:Reference | R | ||||||
20 | Date | R | ||||||
21 | Assigned By | R |
Current WormBase DAF (pre-AGR)
DAF 2.0 for gene-disease data includes all genes with the Experimental_model and/or Potential_model tags.
Format: The gene-disease association file is a 17 column tab-delimited file, where 11 columns have to have data and 6 are optional.
Column | Column Name | 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 (separate values with pipes) |
WBPaper00041363|WBPaperXXXXXXXX |
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; for potential_model genes, use the date on which the OMIM homology script is run) |
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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