Specifications for a DAF for gene-disease data

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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 Content Required(R)
Optional(O)
Cardinality Example Definition Model tag New/Exists Comment
1 Taxon R 1 taxon:6239 NCBI taxonomic identifier for the organism
2 DB Object Type R 1 gene, allele, transgene, genotype, fish The type of object being annotated
3 DB R 1 WB The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn.
4 DB Object ID R WB:WBGene00004887 A unique identifier from the database in DB for the entity being annotated
5 DB Object Symbol R 1 smn-1 A (unique and valid) symbol to which DB object ID is matched
6 Inferred Gene Association O 0 or greater WB:WBGene00004887 Database ID for inferred gene/marker association that can be made based on the DB object ID
7 Gene Product Form ID O 0 or 1 UniProtKB id or PRO ID this field allows the annotation
of specific variants of that gene or gene product.
8 Experimental Conditions
(to create the model)
O 0 or greater standard conditions
chemical/drug treatments (ChEBI ID, ZECO)
dietary manipulations (specifiy entity)
surgery/amputation
bacterial/virus exposure (taxon ID)
Experimental/environmental (i.e. non-genetic) conditions
required for the model, used particularly for induced models
9 Association Type R 1 is_model_of
causes_or_contributes_to_condition

causes_condition
contributes_to_condition
is_marker_for||Relationship between the DB object and the disease

10 Qualifier O 0 or 1 NOT Used to indicate that the DB object is not
associated with the DO term/association type
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.


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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