Specifications for data submission to the Alliance
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
(From ?Disease_model_annotation class)
|Primary Object||JSON Objects|
|1||Modeled_by Disease_relevant_gene||Gene||objectID: GeneID|
|Variation||objectID: GeneID |
|Transgene||objectID: Transgene ID |
|4||Modeled_by Transgene||Transgene||objectID: TransgeneID|
|5||Modeled_by Strain||Strain||objectID: strainID|
|Strain||objectID: GeneID |
- ‘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 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)