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

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==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.  
  
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.
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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.   
  
 
1. When you find all three --gene, strain and allele in a single annotation WB annotation, note that we always choose Strain/AGM as the primary object annotated to, 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, as we want to explicitly submit annotations to the allele and gene as well:
 
1. When you find all three --gene, strain and allele in a single annotation WB annotation, note that we always choose Strain/AGM as the primary object annotated to, 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, as we want to explicitly submit annotations to the allele and gene as well:
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*‘InferredGeneAssociation’ is not needed anymore because Alliance is not using this in the pipeline.
 
*‘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.
 
*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.
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==Data excluded from Alliance submissions==
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*Annotations with data for tags (from the ?Disease_model_annotation class)
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**Interacting_variation
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**Interacting_transgene
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**Interacting_gene
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**RNAi_experiment
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**Modifier_transgene
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**Modifier_variation
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**Modifier_strain
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**Modifier_gene
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**Modifier_molecule
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**Other_modifier

Revision as of 23:44, 6 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.

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.

1. When you find all three --gene, strain and allele in a single annotation WB annotation, note that we always choose Strain/AGM as the primary object annotated to, 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, as we want to explicitly submit annotations to the allele and gene as well:

objectID: GeneID primaryGeneticEntityIDs: strain

objectID: AlleleID primaryGeneticEntityIDs: strain

objectID: strainID


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

objectID: strainID


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: GeneID


4. When you find allele and gene in a single WB annotation ((acedb tags: Modeled_by Variation, and Modeled_by Disease_relevant_gene), allele is the object of the primary annotation, there should be 2 submitted annotations for the JSON, because we want to submit explicitly to the gene as well:

objectID: AlleleID

objectID: GeneID primaryGeneticEntityIDs: AlleleID


5. When Transgene is the object of the primary annotation, this is when you only find Transgene in a single WB annotation (aced tag: Modeled_by Transgene) there should be one annotation in the JSON:

objectID: TransgeneID


6. When you find Transgene and gene in a single WB annotation (aced tags: Modeled_by Transgene, Modeled_by Disease_relevant_gene), Transgene is the object of the primary annotation, so there should be two annotations in our JSON, again because we want to submit the primary annotation to the Transgene but we also want to explicitly submit the gene connection as well.

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

  • Annotations with data for tags (from the ?Disease_model_annotation class)
    • Interacting_variation
    • Interacting_transgene
    • Interacting_gene
    • RNAi_experiment
    • Modifier_transgene
    • Modifier_variation
    • Modifier_strain
    • Modifier_gene
    • Modifier_molecule
    • Other_modifier