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

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|+Mapping of acedb tags to objects in JSON
 
|+Mapping of acedb tags to objects in JSON
 
|-
 
|-
! !!Acedb Tag!!Primary Object!!JSON Objects
+
! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Object!!Number of Objects<br/>with annotations!!JSON Objects
 
|-
 
|-
|1||Modeled_by  Disease_relevant_gene||Gene||objectID: GeneID
+
|1||Modeled_by  Disease_relevant_gene||Gene||1||objectID: GeneID
 
|-
 
|-
|2||Modeled_by  Variation<br/>Modeled_by  Disease_relevant_gene||Variation||objectID: GeneID <br/> primaryGeneticEntityIDs: AlleleID
+
|2||Modeled_by  Variation<br/>Modeled_by  Disease_relevant_gene||Variation||2||objectID: GeneID <br/> primaryGeneticEntityIDs: AlleleID
 
|-
 
|-
|3||Modeled_by Transgene<br/> Modeled_by Disease_relevant_gene||Transgene||objectID: Transgene ID <br/>
+
|3||Modeled_by Strain||Strain||1||objectID: strainID
 
+
|-
objectID: GeneID <br/>primaryGeneticEntityIDs: TransgeneID
+
|4||Modeled_by Strain<br/>Modeled_by Disease_relevant_gene||Strain||2||objectID: strainID<br/>
 +
objectID: GeneID <br/>primaryGeneticEntityIDs: strainID
 
|-
 
|-
|4||Modeled_by Transgene||Transgene||objectID: TransgeneID
+
|5||Modeled_by Transgene||Transgene||1||objectID: TransgeneID
 
|-
 
|-
|5||Modeled_by Strain||Strain||objectID: strainID
+
|6||Modeled_by Transgene<br/> Modeled_by  Disease_relevant_gene||Transgene||2||objectID: Transgene ID <br/>
 +
objectID: GeneID <br/>primaryGeneticEntityIDs: TransgeneID
 
|-
 
|-
|6||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||objectID: GeneID <br/>primaryGeneticEntityIDs: strain <br/>
+
|7||Modeled_by Strain<br/>Modeled_by Variation<br/>Modeled_by Disease_relevant_gene||Strain||3||objectID: strainID
 +
objectID: GeneID <br/>primaryGeneticEntityIDs: strainID <br/>
 
   
 
   
objectID: AlleleID <br/>primaryGeneticEntityIDs: strain <br/>  
+
objectID: AlleleID <br/>primaryGeneticEntityIDs: strainID <br/>  
  
objectID: strainID
 
 
|}
 
|}
 
 
<pre style="white-space: pre-wrap;
 
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
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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
 
 
</pre>
 
  
 
Note:  
 
Note:  
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*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.
  
==Data excluded from Alliance submissions (March 2020)==
+
==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)
 
*Exclude entire annotation if it has data for any one of the below tags (from the ?Disease_model_annotation class)
 
**Interacting_variation
 
**Interacting_variation

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