Difference between revisions of "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 | *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. | *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 | + | *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. |
{|Class="wikitable" | {|Class="wikitable" | ||
− | |+ | + | |+DAF columns and mapping of gene-disease data to columns |
|- | |- | ||
− | !Column !!Column Name!!Required/Optional!!Cardinality!!Example!!Model tag!!New/Exists | + | !Column !!Column Name!!Required(R)/Optional(O)!!Cardinality!!Example!!Model tag!!New/Exists!!Comment!! |
|- | |- | ||
− | |1 ||DB||''' | + | |1 ||DB||'''R'''||1||WB |
|- | |- | ||
− | |2 ||DB Object ID||''' | + | |2 ||DB Object ID||'''R'''|| 1||WBGene00007799 |
|- | |- | ||
− | |3 || DB Object Symbol || ''' | + | |3 || DB Object Symbol || '''R''' || 1 ||nrx-1 |
|- | |- | ||
− | |4 || Qualifier || '' | + | |4 || Qualifier || ''O'' || 0 or greater ||(no value, leave empty) |
|- | |- | ||
− | |5 || GO ID || ''' | + | |5 || GO ID || '''R''' || 1 ||DOID:0060041 |
|- | |- | ||
|6 ||DB:Reference (<nowiki>|</nowiki>DB:Reference)||'''required'''||1 or greater<br/> (separate values with pipes)||WBPaper00041363<nowiki>|</nowiki>WBPaperXXXXXXXX | |6 ||DB:Reference (<nowiki>|</nowiki>DB:Reference)||'''required'''||1 or greater<br/> (separate values with pipes)||WBPaper00041363<nowiki>|</nowiki>WBPaperXXXXXXXX | ||
|- | |- | ||
− | |7 ||Evidence code||''' | + | |7 ||Evidence code||'''R'''||1|| IMP or ISS (use 'IMP' for Experimental_model <br/>genes and ISS for Potential_model genes) |
|- | |- | ||
− | |8 ||With (or) From||'' | + | |8 ||With (or) From||''O''||0 or greater<br/> (separate values with pipes)||OMIM:600565<nowiki>|</nowiki>OMIM:600566 |
|- | |- | ||
− | |9 || Aspect|| ''' | + | |9 || Aspect|| '''R'''||1||D (D for disease ontology, all annotations<br/> have this value) |
|- | |- | ||
− | |10||DB Object Name||'' | + | |10||DB Object Name||''O''||0 or 1||(no value, leave empty) |
|- | |- | ||
− | |11||DB Object Synonym (<nowiki>|</nowiki>Synonym)||'' | + | |11||DB Object Synonym (<nowiki>|</nowiki>Synonym)||''O''||0 or greater||(no value, leave empty) |
|- | |- | ||
− | |12||DB Object Type||''' | + | |12||DB Object Type||'''R'''||1||gene (all annotations have this value) |
|- | |- | ||
− | |13||Taxon||''' | + | |13||Taxon||'''R'''||1 or 2||taxon:6239 |
|- | |- | ||
− | |14||Date|| | + | |14||Date||R||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|| Assigned By||''' | + | |15|| Assigned By||'''R'''||1||WB |
|- | |- | ||
− | |16||Annotation Extension||'' | + | |16||Annotation Extension||''O''||0 or greater||(no value, leave empty) |
|- | |- | ||
− | |17||Gene Product Form ID||'' | + | |17||Gene Product Form ID||''O''||0 or greater||(no value, leave empty) |
|} | |} | ||
− | |||
− | |||
==Current WormBase DAF (pre-AGR)== | ==Current WormBase DAF (pre-AGR)== |
Revision as of 23:57, 25 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 | DB | R | 1 | WB | ||||
2 | DB Object ID | R | 1 | WBGene00007799 | ||||
3 | DB Object Symbol | R | 1 | nrx-1 | ||||
4 | Qualifier | O | 0 or greater | (no value, leave empty) | ||||
5 | GO ID | R | 1 | DOID:0060041 | ||||
6 | DB:Reference (|DB:Reference) | required | 1 or greater (separate values with pipes) |
WBPaper00041363|WBPaperXXXXXXXX | ||||
7 | Evidence code | R | 1 | IMP or ISS (use 'IMP' for Experimental_model genes and ISS for Potential_model genes) | ||||
8 | With (or) From | O | 0 or greater (separate values with pipes) |
OMIM:600565|OMIM:600566 | ||||
9 | Aspect | R | 1 | D (D for disease ontology, all annotations have this value) | ||||
10 | DB Object Name | O | 0 or 1 | (no value, leave empty) | ||||
11 | DB Object Synonym (|Synonym) | O | 0 or greater | (no value, leave empty) | ||||
12 | DB Object Type | R | 1 | gene (all annotations have this value) | ||||
13 | Taxon | R | 1 or 2 | taxon:6239 | ||||
14 | Date | R | 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 | R | 1 | WB | ||||
16 | Annotation Extension | O | 0 or greater | (no value, leave empty) | ||||
17 | Gene Product Form ID | O | 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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