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[[_TOC_]]
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#### Markdown
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CSpec Registry Version 1.2.3 onwards will support [GitHub Flavored Markdown](https://github.github.com/gfm/) for a criteria code specification. This will include the following in a specification text.
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- bold
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- italics
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- indentation
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- super and subscripts
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- headings, etc.
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Example of a criteria code specification text is given below:
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`For synonymous[<sup>6</sup>](#url_97eb6585-3fe3-5b06-af5d-731078ed9b67), intronic positions (except canonical splice sites) and non-coding variants in the UTRs, if the nucleotide[<sup>1</sup>](#pmid_30771507) is non-conserved award this[<sup>2</sup>](#pmid_31418850) point (PhyloP score \\<0.1).`
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#### References and inline citations
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Three namespaces are currently supported, which includes:
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1. pmid
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2. footnote
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3. url
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A citation id within a specification text is defined as `#{namespace}_{id}`. For example an inline citation with the following identifier `#url_97eb6585-3fe3-5b06-af5d-731078ed9b67` has a corresponding reference item with the same `namespace` and `id` in the `ruleSet.entContent.references` subdocument.
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For instance the following API request returns a reference item that corresponds to the citation id `#url_97eb6585-3fe3-5b06-af5d-731078ed9b67`.
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GET - `https://genboree.org/cspec/RuleSet/id/1499617376?fields=entContent.references[5]`. Note: this API points to the test server.
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PAYLOAD - `{
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"data": {
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"entContent": {
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"references": [
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{
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"id": "97eb6585-3fe3-5b06-af5d-731078ed9b67",
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"namespace": "url",
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"value": "https://gnomad.broadinstitute.org/gene/ENSG00000075043?dataset=gnomad_r3"
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}
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]
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}
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},
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"metadata": {
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"rendered": {
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"by": "https://genboree.org/cspec/srvc",
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"when": "2022-08-09T00:38:02.237Z"
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}
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},
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"status": {
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"code": 200,
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"name": "OK"
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}
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}`
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#### Legacy specification documents.
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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.
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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.
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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` |
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\ No newline at end of file |
