Specifications for data submission to the Alliance

From WormBaseWiki
Jump to navigationJump to search

Data that needs to be submitted (March 2020)

We need to explicitly submit annotations to all entities—meaning the directly annotated entity and the inferred entities. Otherwise they will not show on the relevant page/table in the Alliance.

Strains, Alleles, Transgenes and Genes associated with disease need to be included.

Disease data submission for Alliance JSON

Mapping of acedb tags to objects in JSON
Acedb Tags in Annotation
(From ?Disease_model_annotation class)
Primary Object Number of Objects
with annotations
JSON Objects
1 Modeled_by Disease_relevant_gene Gene 1 objectID: GeneID
2 Modeled_by Variation
Modeled_by Disease_relevant_gene
Variation 2 objectID: GeneID
primaryGeneticEntityIDs: AlleleID
3 Modeled_by Strain Strain 1 objectID: strainID
4 Modeled_by Strain
Modeled_by Disease_relevant_gene
Strain 2 objectID: strainID

objectID: GeneID
primaryGeneticEntityIDs: strainID

5 Modeled_by Transgene Transgene 1 objectID: TransgeneID
6 Modeled_by Transgene
Modeled_by Disease_relevant_gene
Transgene 2 objectID: Transgene ID

objectID: GeneID
primaryGeneticEntityIDs: TransgeneID

7 Modeled_by Strain
Modeled_by Variation
Modeled_by Disease_relevant_gene
Strain 3 objectID: strainID

objectID: GeneID
primaryGeneticEntityIDs: strainID

objectID: AlleleID
primaryGeneticEntityIDs: strainID


  • ‘InferredGeneAssociation’ is not needed anymore because Alliance is not using this in the pipeline.
  • The old style ‘Experimental model’ annotations not be submitted to the Alliance at all. In our curation database at Caltech, the new style ‘Disease_model_annotation’ and the old style ‘Experimental model’ annotations are the same data, we just take the genes and dump them as ‘Experimental models’ for display sake in WormBase.

Data that should be excluded from Alliance submissions (March 2020)

  • Exclude entire annotation if it has data for any one of the below tags (from the ?Disease_model_annotation class)
    • Interacting_variation
    • Interacting_transgene
    • Interacting_gene
    • RNAi_experiment
    • Qualifier_not
    • Inducing_chemical
    • Inducing_agent
    • Modifier_transgene
    • Modifier_variation
    • Modifier_strain
    • Modifier_gene
    • Modifier_molecule
    • Other_modifier