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

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(Created page with "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/...")
 
 
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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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Strains, Alleles, Transgenes and Genes associated with disease need to be included.
  
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:
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====Disease data submission for Alliance JSON====
 
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{|Class="wikitable"
objectID: GeneID <br/>
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|+Mapping of acedb tags to objects in JSON
primaryGeneticEntityIDs: strain
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|-
 
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! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Object!!Number of Objects<br/>with annotations!!JSON Objects
objectID: AlleleID . <br/>
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|-
primaryGeneticEntityIDs: strain
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|1||Modeled_by  Disease_relevant_gene||Gene||1||objectID: GeneID
 
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|-
objectID: strainID
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|2||Modeled_by  Variation<br/>Modeled_by  Disease_relevant_gene||Variation||2||objectID: GeneID <br/> primaryGeneticEntityIDs: AlleleID
 
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|-
 
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|3||Modeled_by Strain||Strain||1||objectID: strainID
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:
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|-
 
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|4||Modeled_by Strain<br/>Modeled_by Disease_relevant_gene||Strain||2||objectID: strainID<br/>
objectID: strainID
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objectID: GeneID <br/>primaryGeneticEntityIDs: strainID
 
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|-
 
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|5||Modeled_by Transgene||Transgene||1||objectID: TransgeneID
 
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|-
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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|6||Modeled_by  Transgene<br/> Modeled_by  Disease_relevant_gene||Transgene||2||objectID: Transgene ID <br/>
 
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objectID: GeneID <br/>primaryGeneticEntityIDs: TransgeneID
objectID: GeneID
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|-
 
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|7||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||3||objectID: strainID
 
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objectID: GeneID <br/>primaryGeneticEntityIDs: strainID <br/>
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:
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objectID: AlleleID <br/>primaryGeneticEntityIDs: strainID <br/>
objectID: AlleleID
 
 
 
 
 
objectID: GeneID .  <br/>
 
primaryGeneticEntityIDs: AlleleID
 
  
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|}
  
 
Note:  
 
Note:  
 
*‘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 that should be excluded from Alliance submissions (March 2020)==
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*Exclude entire annotation if it has data for any one of the below 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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**Qualifier_not
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**Inducing_chemical
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**Inducing_agent
 +
**Modifier_transgene
 +
**Modifier_variation
 +
**Modifier_strain
 +
**Modifier_gene
 +
**Modifier_molecule
 +
**Other_modifier

Latest revision as of 23:02, 9 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.

Disease data submission for Alliance JSON

Mapping of acedb tags to objects in 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
primaryGeneticEntityIDs: strainID

5 Modeled_by Transgene Transgene 1 objectID: TransgeneID
6 Modeled_by Transgene
Modeled_by Disease_relevant_gene
Transgene 2 objectID: Transgene ID

objectID: GeneID
primaryGeneticEntityIDs: TransgeneID

7 Modeled_by Strain
Modeled_by Variation
Modeled_by Disease_relevant_gene
Strain 3 objectID: strainID

objectID: GeneID
primaryGeneticEntityIDs: strainID

objectID: AlleleID
primaryGeneticEntityIDs: strainID

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