Difference between revisions of "Specifications for data submission to the Alliance"
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|5||Modeled_by Strain||Strain||objectID: strainID | |5||Modeled_by Strain||Strain||objectID: strainID | ||
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− | |6||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||objectID: GeneID <br/> | + | |6||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||objectID: GeneID <br/>primaryGeneticEntityIDs: strain <br/> |
objectID: AlleleID <br/>primaryGeneticEntityIDs: strain <br/> | objectID: AlleleID <br/>primaryGeneticEntityIDs: strain <br/> |
Revision as of 06:10, 8 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 | 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 |
1. When an annotation has data for acedb tags (from the ?Disease_model_annotation class): *Modeled_by Strain --> primary object *Modeled_by Variation *Modeled_by Disease_relevant_gene there should be 3 submitted annotations for the JSON: objectID: GeneID primaryGeneticEntityIDs: strain objectID: AlleleID primaryGeneticEntityIDs: strain objectID: strainID 2. When annotation has data for the acedb tags: *Modeled_by Strain -->primary object there should be 1 submitted annotation for the JSON: objectID: strainID 3. When the annotation has data for the acedb tag: Modeled_by Disease_relevant_gene -->primary object there should be 1 submitted annotation for the JSON: objectID: GeneID 4. When the annotation has data for the acedb tags: Modeled_by Variation -->primary object Modeled_by Disease_relevant_gene there should be 2 submitted annotations for the JSON: objectID: AlleleID objectID: GeneID primaryGeneticEntityIDs: AlleleID 5. When the annotation has data for the acedb tag: Modeled_by Transgene -->primary object there should be one annotation in the JSON: objectID: TransgeneID 6. When the annotation has data for the acedb tags: Modeled_by Transgene -->primary object Modeled_by Disease_relevant_gene there should be two annotations in our JSON: objectID: Transgene ID objectID: GeneID primaryGeneticEntityIDs: TransgeneID
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 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