Specifications for data submission to the Alliance
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Revision as of 03:45, 9 March 2020 by Rkishore (talk | contribs) (→Data excluded from Alliance submissions (March 2020))
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
Acedb Tag (From ?Disease_model_annotation class) |
Primary Object | JSON Objects | |
---|---|---|---|
1 | Modeled_by Disease_relevant_gene | Gene | objectID: GeneID |
2 | Modeled_by Variation Modeled_by Disease_relevant_gene |
Variation | objectID: GeneID primaryGeneticEntityIDs: AlleleID |
3 | Modeled_by Transgene Modeled_by Disease_relevant_gene |
Transgene | objectID: Transgene ID objectID: GeneID |
4 | Modeled_by Transgene | Transgene | objectID: TransgeneID |
5 | Modeled_by Strain | Strain | objectID: strainID |
6 | Modeled_by Strain Modeled_by Variation Modeled_by Disease_relevant_gene |
Strain | objectID: GeneID primaryGeneticEntityIDs: strain objectID: AlleleID objectID: strainID |
Note:
- ‘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