Difference between revisions of "Specifications for a DAF for gene-disease data"

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!Column !!Column Name!!Required(R)/Optional(O)!!Cardinality!!Example!!Model tag!!New/Exists!!Comment!!
 
!Column !!Column Name!!Required(R)/Optional(O)!!Cardinality!!Example!!Model tag!!New/Exists!!Comment!!
 
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|-
|1 ||DB||'''R'''||1||WB
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|1 ||Taxon||'''R'''||1||WB
 
|-
 
|-
|2 ||DB Object ID||'''R'''|| 1||WBGene00007799
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|2 ||DB Object Type||'''R'''|| 1||WBGene00007799
 
|-
 
|-
|3 || DB Object Symbol || '''R''' || 1 ||nrx-1
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|3 ||DB|| '''R''' || 1 ||nrx-1
 
|-
 
|-
|4 || Qualifier || ''O'' || 0 or greater ||(no value, leave empty)
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|4 ||DB Object ID|| ''R'' || 0 or greater ||(no value, leave empty)
 
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|5 || GO ID || '''R''' || 1 ||DOID:0060041
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|5 ||DB Object Symbol|| '''R''' || 1 ||DOID:0060041
 
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|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

Revision as of 23:14, 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.


DAF columns and mapping of gene-disease data to columns
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 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.


Mapping of GAF column to gene-disease data
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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