Difference between revisions of "Specifications for data submission to the Alliance"
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− | ==Data that needs to be submitted (March 2020)== | + | ==Old stuff--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. | 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. | ||
Line 8: | Line 8: | ||
|+Mapping of acedb tags to objects in JSON | |+Mapping of acedb tags to objects in JSON | ||
|- | |- | ||
− | ! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Object!!JSON Objects | + | ! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Object!!Number of Objects<br/>with annotations!!JSON Objects |
|- | |- | ||
− | |1||Modeled_by Disease_relevant_gene||Gene||objectID: GeneID | + | |1||Modeled_by Disease_relevant_gene||Gene||1||objectID: GeneID |
|- | |- | ||
− | |2||Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Variation||objectID: GeneID <br/> primaryGeneticEntityIDs: AlleleID | + | |2||Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Variation||2||objectID: GeneID <br/> primaryGeneticEntityIDs: AlleleID |
|- | |- | ||
− | |3||Modeled_by Strain||Strain||objectID: strainID | + | |3||Modeled_by Strain||Strain||1||objectID: strainID |
|- | |- | ||
− | |4||Modeled_by Strain<br/>Modeled_by Disease_relevant_gene||Strain||objectID: strainID<br/> | + | |4||Modeled_by Strain<br/>Modeled_by Disease_relevant_gene||Strain||2||objectID: strainID<br/> |
− | objectID: GeneID <br/>primaryGeneticEntityIDs: | + | objectID: GeneID <br/>primaryGeneticEntityIDs: strainID |
|- | |- | ||
− | |5||Modeled_by Transgene<br/> Modeled_by Disease_relevant_gene||Transgene||objectID: Transgene ID <br/> | + | |5||Modeled_by Transgene||Transgene||1||objectID: TransgeneID |
+ | |- | ||
+ | |6||Modeled_by Transgene<br/> Modeled_by Disease_relevant_gene||Transgene||2||objectID: Transgene ID <br/> | ||
objectID: GeneID <br/>primaryGeneticEntityIDs: TransgeneID | objectID: GeneID <br/>primaryGeneticEntityIDs: TransgeneID | ||
|- | |- | ||
− | + | |7||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||3||objectID: strainID | |
− | + | objectID: GeneID <br/>primaryGeneticEntityIDs: strainID <br/> | |
− | |7||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||objectID: strainID | ||
− | objectID: GeneID <br/>primaryGeneticEntityIDs: | ||
− | objectID: AlleleID <br/>primaryGeneticEntityIDs: | + | objectID: AlleleID <br/>primaryGeneticEntityIDs: strainID <br/> |
|} | |} |
Latest revision as of 17:43, 26 October 2023
Old stuff--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 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 |
5 | Modeled_by Transgene | Transgene | 1 | objectID: TransgeneID |
6 | Modeled_by Transgene Modeled_by Disease_relevant_gene |
Transgene | 2 | objectID: Transgene ID objectID: GeneID |
7 | Modeled_by Strain Modeled_by Variation Modeled_by Disease_relevant_gene |
Strain | 3 | objectID: strainID
objectID: GeneID objectID: AlleleID |
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