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Update CSpec Registry API authored by Neethu Shah's avatar Neethu Shah
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CSpec-Registry-API.md
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<span dir="">`"ld": \[ { "CriteriaCode": \[ … \] }, {"RuleSet": \[ … \] }, { "Gene": \[ … \] } \],`</span>
<span dir="">`"ld": \\\[ { "CriteriaCode": \\\[ … \\\] }, {"RuleSet": \\\[ … \\\] }, { "Gene": \\\[ … \\\] } \\\],`</span>
<span dir="">Here, "CriteriaCode", "RuleSet" and "Gene" are the linked data entities for the variant "CA000176"</span>
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......@@ -335,7 +335,7 @@ The table below lists the key fields returned in the API response.
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<span dir="">`"ldFor": \[ { "Gene": \[ … \] } \]`</span>
<span dir="">`"ldFor": \\\[ { "Gene": \\\[ … \\\] } \\\]`</span>
<span dir="">SequenceVariantInterpretation “CA000176” is linked data FOR the Gene “TP53”</span>
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......@@ -465,18 +465,19 @@ The table below lists the key fields returned in the API response.
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### Legacy specification documents.
As per the ClinGen Variant Curation Working Group recommendation a VCEP should be able to maintain and version specifications for a single gene separately. All specifications that are applicable for multiple genes are to be re-released into separate SVI documents.
A legacy document with multiple gene specifications will be fully archived when the attribute `legacyReplaced` is set to `true`. This property will be true only AFTER all the linked specification documents are re-released.
For example API to access a legacy document is given here. - `https://genboree.org/cspec/SequenceVariantInterpretation/id/GN023?fields=entContent.legacyReplaced`. All the corresponding individual, single gene specific documents can be accessed via - `https://genboree.org/cspec/SequenceVariantInterpretation/id/GN023?fields=ld.SequenceVariantInterpretation`. A superseded document fully replaces its legacy document only when the property `entContent.legacyFullySuperseded` is set to true. Identifiers for all the legacy documents in the Registry include - `GN014,GN016,GN004,GN005,GN011,GN018,GN023`
A legacy document with multiple gene specifications will be fully archived when the attribute `legacyReplaced` is set to `true`. This property will be true only AFTER all the linked specification documents are re-released. For example API to access a legacy document is given here. - `https://genboree.org/cspec/SequenceVariantInterpretation/id/GN023?fields=entContent.legacyReplaced`. All the corresponding individual, single gene specific documents can be accessed via - `https://genboree.org/cspec/SequenceVariantInterpretation/id/GN023?fields=ld.SequenceVariantInterpretation`. A superseded document fully replaces its legacy document only when the property `entContent.legacyFullySuperseded` is set to true. Identifiers for all the legacy documents in the Registry include - `GN014,GN016,GN004,GN005,GN011,GN018,GN023`
#### Current versions
#### Current versions
A specification document is valid and has the current version if it meets the following criteria in this order
A specification document is valid and has the current version if it meets the following criteria in this order
a) `entContent.states` object has an item where name === 'Released' AND `entContent.legacyFullySuperseded` === true
a) `entContent.states` object has an item where name === 'Released' AND `entContent.legacyFullySuperseded` === true. Example - https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN037
b) `entContent.states` object has an item where name ==='Released' AND `entContent.legacyReplaced` === false
b) `entContent.states` object has an item where name ==='Released' AND `entContent.legacyReplaced` === false. Example - https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016
c) `entContent.states` object has an item where name ==='Released'
c) `entContent.states` object has an item where name ==='Released'. Example - https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN002
### [Markdown support for Criteria Code Specifications](Markdown-and-Citations)
### [Markdown support for Criteria Code Specifications](Markdown-and-Citations)
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