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

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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.  
 
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.
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Strains, Alleles, Transgenes and Genes associated with disease need to be included.
  
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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1. When an annotation has data for acedb tags (from the ?Disease_model_annotation class):  
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*Modeled_by  Strain --> primary object
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*Modeled_by  Variation
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*Modeled_by  Disease_relevant_gene
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there should be 3 submitted annotations for the JSON:
  
 
objectID: GeneID
 
objectID: GeneID
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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:
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2. When annotation has data for the acedb tags:  
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*Modeled_by Strain -->primary object
  
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there should be 1 submitted annotation for the JSON:
 
objectID: strainID
 
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:
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3. When the annotation has data for the acedb tag:  
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Modeled_by  Disease_relevant_gene -->primary object
  
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there should be 1 submitted annotation for the JSON:
 
objectID: GeneID
 
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:
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4. When the annotation has data for the acedb tags:  
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Modeled_by  Variation -->primary object
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Modeled_by  Disease_relevant_gene
  
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there should be 2 submitted annotations for the JSON:
 
objectID: AlleleID
 
objectID: AlleleID
  
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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:
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5. When the annotation has data for the acedb tag:  
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Modeled_by Transgene -->primary object
  
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there should be one annotation in the JSON:
 
objectID: TransgeneID
 
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.
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6. When the annotation has data for the acedb tags:  
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Modeled_by Transgene -->primary object
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Modeled_by  Disease_relevant_gene
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there should be two annotations in our JSON:
  
 
objectID: Transgene ID
 
objectID: Transgene ID
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primaryGeneticEntityIDs: TransgeneID
 
primaryGeneticEntityIDs: TransgeneID
  
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Note:  
 
Note:  

Revision as of 00:14, 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 any one of the below tags is present (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