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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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...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
The Criteria Specifiication Registry provides RESTful-APIs to browse and search content. Responses are returned in JSON format. The Criteria Specifiication Registry provides RESTful-APIs to browse and search content. Responses are returned in JSON format.
##### <span dir="">Service URL:</span> <https://cspec.genome.network> ##### <span dir="">Service URL:</span> https://cspec.genome.network
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...@@ -41,12 +41,21 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -41,12 +41,21 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/srvc</span>](https://cspec.genome.network/cspec/srvc)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/srvc</span><span dir=""> </span>
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<td>/api/{entType}/id/{entId}</td>
<td>Non-specific id based look up (JSON LD)</td>
<td> <td>
https://cspec.genome.network/cspec/api/SequenceVariantInterpretation/id/GN099<br>https://cspec.genome.network/cspec/api/RuleSet/id/1535826201
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**/id/{val}** **/id/{val}**
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...@@ -55,7 +64,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -55,7 +64,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/id/GN016</span>](https://cspec.genome.network/cspec/id/GN016)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/id/GN016</span><span dir=""> </span>
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...@@ -69,7 +78,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -69,7 +78,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation</span><span dir=""> </span>
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...@@ -83,7 +92,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -83,7 +92,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id</span><span dir=""> </span>
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...@@ -97,7 +106,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -97,7 +106,7 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016</span><span dir=""> </span>
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...@@ -111,9 +120,9 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -111,9 +120,9 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ld</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ld)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ld</span><span dir=""> </span>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ldFor</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ldFor)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/ldFor</span><span dir=""> </span>
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...@@ -127,11 +136,11 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search ...@@ -127,11 +136,11 @@ The Criteria Specifiication Registry provides RESTful-APIs to browse and search
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types</span>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ld</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ld) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ld</span>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ldFor</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ldFor) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016/types/ldFor</span>
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</table> </table>
...@@ -174,7 +183,7 @@ Response from the API endpoints can be filtered or restricted using the followin ...@@ -174,7 +183,7 @@ Response from the API endpoints can be filtered or restricted using the followin
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?ids=GN014,GN016,GN015</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?ids=GN014,GN016,GN015)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?ids=GN014,GN016,GN015</span><span dir=""> </span>
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...@@ -192,7 +201,7 @@ Response from the API endpoints can be filtered or restricted using the followin ...@@ -192,7 +201,7 @@ Response from the API endpoints can be filtered or restricted using the followin
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016?types=Gene,RuleSet</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016?types=Gene,RuleSet)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016?types=Gene,RuleSet</span><span dir=""> </span>
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...@@ -214,11 +223,11 @@ Response from the API endpoints can be filtered or restricted using the followin ...@@ -214,11 +223,11 @@ Response from the API endpoints can be filtered or restricted using the followin
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low</span>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=med</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=med) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=med</span>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high</span>
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...@@ -236,9 +245,9 @@ Response from the API endpoints can be filtered or restricted using the followin ...@@ -236,9 +245,9 @@ Response from the API endpoints can be filtered or restricted using the followin
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low&fields=entId,ldhId</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low&fields=entId,ldhId) <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low&fields=entId,ldhId</span>
[<span dir="">https://cspec.genome.network/cspec/CriteriaCode/id?detail=high&fields=entId,ldhId,entContent.label,entContent.strengthDescriptor</span>](https://cspec.genome.network/cspec/CriteriaCode/id?detail=high&fields=entId,ldhId,entContent.label,entContent.strengthDescriptor) <span dir="">https://cspec.genome.network/cspec/CriteriaCode/id?detail=high&fields=entId,ldhId,entContent.label,entContent.strengthDescriptor</span>
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...@@ -260,7 +269,7 @@ Response from the API endpoints can be filtered or restricted using the followin ...@@ -260,7 +269,7 @@ Response from the API endpoints can be filtered or restricted using the followin
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=1&pgSize=250&detail=low&fields=entId,ldhId</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=1&pgSize=250&detail=low&fields=entId,ldhId)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=1&pgSize=250&detail=low&fields=entId,ldhId</span><span dir=""> </span>
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...@@ -282,7 +291,7 @@ Response from the API endpoints can be filtered or restricted using the followin ...@@ -282,7 +291,7 @@ Response from the API endpoints can be filtered or restricted using the followin
</td> </td>
<td> <td>
[<span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=6&pgSize=250&detail=low&fields=entId</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=6&pgSize=250&detail=low&fields=entId)<span dir=""> </span> <span dir="">https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?pg=6&pgSize=250&detail=low&fields=entId</span><span dir=""> </span>
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...@@ -367,7 +376,7 @@ The table below lists the key fields returned in the API response. ...@@ -367,7 +376,7 @@ The table below lists the key fields returned in the API response.
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<td> <td>
<span dir="">`"entIri": "`</span>[<span dir="">`https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1097`</span>](https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1097)<span dir="">`"`,</span> <span dir="">`"entIri": "`</span><span dir="">`https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1097`</span><span dir="">`"`,</span>
<span dir="">where the IRI is the “link” to this entity in the external data source</span> <span dir="">where the IRI is the “link” to this entity in the external data source</span>
</td> </td>
...@@ -415,7 +424,7 @@ The table below lists the key fields returned in the API response. ...@@ -415,7 +424,7 @@ The table below lists the key fields returned in the API response.
</td> </td>
<td> <td>
<span dir="">`"ldhIri": "`</span>[<span dir="">`https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/41889804`</span>](https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/41889804)<span dir="">"</span> <span dir="">`"ldhIri": "`</span><span dir="">`https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/41889804`</span><span dir="">"</span>
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...@@ -471,35 +480,16 @@ As per the ClinGen Variant Curation Working Group recommendation a VCEP should b ...@@ -471,35 +480,16 @@ As per the ClinGen Variant Curation Working Group recommendation a VCEP should b
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 Approved Versions #### Current Approved Versions
- Cspec Registry API on SequenceVariantInterpretation will return all the specifications that are both approved and under review.To get the current "Released" (SVI approved) versions do the following: - Cspec Registry API on SequenceVariantInterpretation will return all the specifications that are both approved and under review.To get the current "Released" (SVI approved) versions do the following:
> 1. Get the SequenceVariantInterpretation documents, say for instance from the following endpoint - _https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high&fields=entContent.states,entContent.legacyFullySuperseded,entContent.legacyReplaced,entId,ldhId,entContent.title_ > 1. Get the SequenceVariantInterpretation documents, say for instance from the following endpoint - _https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high&fields=entContent.states,entContent.legacyFullySuperseded,entContent.legacyReplaced,entId,ldhId,entContent.title_
> 2. Now drop the ones that > 2. Now drop the ones that
>> 1. have never been approved, that is _entContent.states_ has NO item where name === 'Released' >
>> 2. is a legacy document which have been replaced, that is, _entContent.legacyReplaced_ is true > > 1. have never been approved, that is _entContent.states_ has NO item where name === 'Released'
>> 3. is a document that has not yet superseded the legacy doc, that is _entContent.legacyFullySuperseded_ is false > > 2. is a legacy document which have been replaced, that is, _entContent.legacyReplaced_ is true
> > 3. is a document that has not yet superseded the legacy doc, that is _entContent.legacyFullySuperseded_ is false
For instance, given below is an example where the above logic is applied to the end point mentioned in step(1). For instance, given below is an example where the above logic is applied to the end point mentioned in step(1).
<pre>
let currentVersions = [] <pre>let currentVersions = \[\] if( respObj && respObj.status && respObj.status === 200 ) { const sviObj = respObj.data.data for(const svi of sviObj){ if(svi.entContent.states) { const stateNames = svi.entContent.states.map((x) => x.name); if(stateNames.includes("Released")) { // has been approved if(svi.entContent.legacyFullySuperseded === false || svi.entContent.legacyReplaced === true) { // drop the doc that has not superseded the legacy yet or the ones that have been fully replaced. continue } else { currentVersions.push(svi.entId) } } } } }</pre>### [Markdown support for Criteria Code Specifications](Markdown-and-Citations)
if( respObj && respObj.status && respObj.status === 200 ) { \ No newline at end of file
const sviObj = respObj.data.data
for(const svi of sviObj){
if(svi.entContent.states) {
const stateNames = svi.entContent.states.map((x) => x.name);
if(stateNames.includes("Released")) { // has been approved
if(svi.entContent.legacyFullySuperseded === false || svi.entContent.legacyReplaced === true) {
// drop the doc that has not superseded the legacy yet or the ones that have been fully replaced.
continue
}
else {
currentVersions.push(svi.entId)
}
}
}
}
}
</pre>
### [Markdown support for Criteria Code Specifications](Markdown-and-Citations)
\ No newline at end of file