| ... | ... | @@ -8,7 +8,7 @@ CSpec Registry Version 1.2.3 onwards will support [GitHub Flavored Markdown](htt |
|
|
|
- super and subscripts
|
|
|
|
- headings, etc.
|
|
|
|
|
|
|
|
Example of a criteria code specification text is given below:
|
|
|
|
Example of a criteria code specification text is given below with inline citations:
|
|
|
|
|
|
|
|
`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).`
|
|
|
|
|
| ... | ... | @@ -47,6 +47,75 @@ PAYLOAD - `{ |
|
|
|
}
|
|
|
|
}`
|
|
|
|
|
|
|
|
### Additional examples
|
|
|
|
Given below is an example of a criteria code specification text that has all the three namespaces - pmid, url and footnote
|
|
|
|
|
|
|
|
**GET** - `https://genboree.org/cspec/CriteriaCode/id/1526042290?fields=entContent.strengthDescriptor[4].text`
|
|
|
|
|
|
|
|
**PAYLOAD** - `{
|
|
|
|
"data": {
|
|
|
|
"entContent": {
|
|
|
|
"strengthDescriptor": [
|
|
|
|
null,
|
|
|
|
null,
|
|
|
|
null,
|
|
|
|
null,
|
|
|
|
{
|
|
|
|
"text": "Award BP4 for a synonymous, intronic positions[<sup>4</sup>](#url_0b4709d0-66ed-5c02-b471-e65cb61cc189) (except canonical splice sites) or non-coding variants in the UTRs, if two out of three of the splicing prediction tools[<sup>1</sup>](#pmid_28825729) predicted no impact on splicing[<sup>5</sup>](#footnote_29e729be-5b0f-5d41-aee6-519557b48868) function."
|
|
|
|
}
|
|
|
|
]
|
|
|
|
}
|
|
|
|
},
|
|
|
|
"metadata": {
|
|
|
|
"rendered": {
|
|
|
|
"by": "https://genboree.org/cspec/srvc",
|
|
|
|
"when": "2022-08-30T21:13:26.179Z"
|
|
|
|
}
|
|
|
|
},
|
|
|
|
"status": {
|
|
|
|
"code": 200,
|
|
|
|
"name": "OK"
|
|
|
|
}
|
|
|
|
}`
|
|
|
|
1. `[<sup>4</sup>](#url_0b4709d0-66ed-5c02-b471-e65cb61cc189)`
|
|
|
|
|
|
|
|
> uses the `url` namespace with the `id` 0b4709d0-66ed-5c02-b471-e65cb61cc189. This citation value can be obtained from the fourth(third index) reference in the list `entContent.references`
|
|
|
|
|
|
|
|
> GET - `https://genboree.org/cspec/CriteriaCode/id/1526042290?fields=ldFor.RuleSet[0].entContent.references[3]`
|
|
|
|
>
|
|
|
|
> PAYLOAD - `{
|
|
|
|
> "data": {
|
|
|
|
> "ldFor": {
|
|
|
|
> "RuleSet": [
|
|
|
|
> {
|
|
|
|
> "entContent": {
|
|
|
|
> "references": [
|
|
|
|
> null,
|
|
|
|
> null,
|
|
|
|
> null,
|
|
|
|
> {
|
|
|
|
> "id": "0b4709d0-66ed-5c02-b471-e65cb61cc189",
|
|
|
|
> "namespace": "url",
|
|
|
|
> "value": "https://clinicalgenome.org"
|
|
|
|
> }
|
|
|
|
> ]
|
|
|
|
> }
|
|
|
|
> }
|
|
|
|
> ]
|
|
|
|
> }
|
|
|
|
> },
|
|
|
|
> "metadata": {
|
|
|
|
> "rendered": {
|
|
|
|
> "by": "https://genboree.org/cspec/srvc",
|
|
|
|
> "when": "2022-08-30T21:18:53.812Z"
|
|
|
|
> }
|
|
|
|
> },
|
|
|
|
> "status": {
|
|
|
|
> "code": 200,
|
|
|
|
> "name": "OK"
|
|
|
|
> }
|
|
|
|
> }`
|
|
|
|
|
|
|
|
#### 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.
|
|
|
|
|
| ... | ... | |
