Specifications for data submission to the Alliance

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Revision as of 23:53, 8 January 2020 by Rkishore (talk | contribs)
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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.

All Strains, Alleles, Transgenes and Genes associated with disease need to be included in the JSON as long as the Alliance is ready to take them in. (At this point, only transgenes are not ready to go into the Alliance. Also additional data such as modifiers are not ready to go into Alliance; so any disease annotation with modifiers needs to be withheld from the JSON.

1. When AGM/strain is the object of the primary annotation, this is when you find all three --gene, strain and allele in a single annotation WB annotation (note that we always choose Strain as the primary object annotated to over allele, though you can’t tell by just the acedb tag names; acedb tags: Modeled_by Strain, Modeled_by Variation, and Modeled_by Disease_relevant_gene) there should be 3 submitted annotations for the JSON as follows:

objectID: Gene ID
primaryGeneticEntityIDs: strain ID

objectID: Allele ID
primaryGeneticEntityIDs: Strain ID

objectID: Strain ID


2. When AGM/strain is the object of the primary annotation, this is when there is only strain in a single WB annotation (acedb tag: Modeled_by Strain), there should be 1 submitted annotation for the JSON as follows:

objectID: Strain ID


3. When gene is the object of the primary annotation, this is when you find only gene in a single WB annotation (acedb tag: Modeled_by Disease_relevant_gene) there should be 1 submitted annotation for the JSON:

objectID: Gene ID


4. When allele is the object of the primary annotation, this is when you find allele and gene in a single WB annotation ((acedb tags: Modeled_by Variation, and Modeled_by Disease_relevant_gene), there should be 2 submitted annotations for the JSON:

objectID: Allele ID


objectID: GeneID
primaryGeneticEntityIDs: Allele ID


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.