Specifications for a DAF for gene-disease data
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- 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 model data.
Column | Column Name | Required/Optional | Cardinality | Example | Model tag | New/Exists |
---|---|---|---|---|---|---|
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) |
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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