Difference between revisions of "Specifications for data submission to the Alliance"

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==Data excluded from Alliance submissions (March 2020)==
 
==Data excluded from Alliance submissions (March 2020)==
*Exclude the annotation if any one of the below tags is present (from the ?Disease_model_annotation class)
+
*Exclude the annotation if it has data for any one of the below tags (from the ?Disease_model_annotation class)
 
**Interacting_variation
 
**Interacting_variation
 
**Interacting_transgene
 
**Interacting_transgene

Revision as of 00:16, 7 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.


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 the 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