Criteria Specification (CSpec) Registry is intended to provide access to the Criteria Specifications used and applied by ClinGen Variant Curation Expert Panels and biocurators in the classification of variants.
For general information about the ClinGen Expert Panels and Variant Curation please visit: Clinical Domain Working Groups. For specific inquiries regarding content correction or adding a new criteria specification refer to the Help page.
Should you encounter any issues regarding the data displayed, lack of functionality or other problems, please let us know by contacting us via email.
Help
To add a new criteria specification or change the content of a specification in the CSpec Registry:
- Log in to CSpec Editor.
- Through the CSpec Editor, VCEP members can a) create new specification b) reopen a previously approved specification and make edits to the document c) submit completed specification documents for SVI approval.
- For comments, feedback and questions email us at brl-cspec at bcm dot edu
- Refer to the documentation for CSpec Registry API and other resources
The Criteria Specifiication Registry provides RESTful-APIs to browse and search content. Responses are returned in JSON format.
Service URL: https://genboree.org/cspec/
Refer to additional documentation for CSpec Registry API and other resources.
Several REST API endpoints are available to GET links and excerpts from CSpec. Detailed API documentation will be released soon.
Endpoints | Description | Example |
/srvc | CSpec Service; lists all entity types and counts | |
/id/{val} | Non-specific identity-based lookup | |
| /{type} | Get info about an CSpec entity type | |
| /{type}/id | Paged list; Batch entity retrieval | |
/{type}/id/{val} | Specific identity-based lookup for an entity type | https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016 |
| /{type}/id/{val}/ld /{type}/id/{val}/ldFor | Get LD for an entity or get entities for which this one IS LD | https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016/ld https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016/ldFor |
| /{type}/id/{val}/types /{type}/id/{val}/types/ld /{type}/id/{val}/types/ldFor | Get the list of types for an entity or get types of LD an entity has or types it is LD for; includes entity counts | https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016/types https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016/types/ld https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016/types/ldFor |
Response from the API endpoints can be filtered or restricted using the following modifiers:
Modifiers | Possible values | Description | Example |
ids | Comma separated list of identifiers | Allows batch search of a list of identifiers | https://genboree.org/cspec/SequenceVariantInterpretation/id?ids=GN014,GN016,GN015 |
types | Comma separated list of entity types | Allows filtering the results to show certain entity types only | https://genboree.org/cspec/SequenceVariantInterpretation/id/GN016?types=Gene,RuleSet |
detail | low, med, high | low - Only identifier level info for the entity. The ld and ldFor just show the counts for 1+ such linked entity. med - (default) - The ld and ldFor show identifier level info. high - All details are shown. | https://genboree.org/cspec/SequenceVariantInterpretation/id?detail=low https://genboree.org/cspec/SequenceVariantInterpretation/id?detail=med https://genboree.org/cspec/SequenceVariantInterpretation/id?detail=high |
fields | Coming soon (Full list of fields will be added in a separate section.) | Comma separated list of fields to get in the API response | https://genboree.org/cspec/SequenceVariantInterpretation/id?detail=low&fields=entId,ldhId |
pg | Integer Default: 1 Min:1 | Page number to be retrieved | |
pgSize | Integer Default: 250 Min 1; Max: 250 | Number of results in each page | https://genboree.org/cspec/SequenceVariantInterpretation/id?pg=6&pgSize=250&detail=low&fields=entId |
The table below lists the key fields returned in the API response.
Key Fields | Description | Example |
ld | This entity is a linked data object for these entities | "ld": [ { "CriteriaCode": [ … ] }, {"RuleSet": [ … ] }, { "Gene": [ … ] } ], Here, "CriteriaCode", "RuleSet" and "Gene" are the linked data entities for the variant "CA000176" |
ldFor | This entity is linked data FOR these other entities | "ldFor": [ { "Gene": [ … ] } ], SequenceVariantInterpretation “CA000176” is linked data FOR the Gene “TP53” |
entId | Identifier of entity in the external data source | "entId": "GN016", where "GN016" - ClinGen Allele Registry identifier for “SequenceVariantInterpretation” |
entIri | IRI of entity in the external data source | "entIri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1097", where the IRI is the “link” to this entity in the external data source |
entType | Type of entity | "entType": "SequenceVariantInterpretation", |
ldhId | CSpec identifier (Note: If data is embedded within CSpec, this will be the only identifier) | "ldhId": "41889804", |
ldhIri | CSpec IRI (Note: If data is embedded within CSpec, this will be the only IRI) | "ldhIri": "https://genboree.org/cspec/SequenceVariantInterpretation/id/41889804" |
entContent | Excerpts from external data source | "entContent": {...} The excerpt content will be different for each entity type. Detailed documentation for the excerpt content stored for each type of entity will be added soon. |
modifier | Person who added this entity to CSpec | "modifier": "johndoe", |
modified | Modification timestamp value | "modified": "2019-10-03T17:04:35.395Z", |
The Criteria Specifiication Registry provides RESTful JSON-LD APIs to browse and search content. Responses are returned in JSON-LD format. Listed below are examples of JSON-LD API endpoints.
Service URL: https://genboree.org/cspec/
Several REST JOSN-LD API endpoints are available to GET links and excerpts from CSpec. Detailed API documentation will be released soon.
Endpoints | Description | Example |
/api/context/{type} | Context to a specific entity type | https://genboree.org/cspec/api/context/SequenceVariantInterpretation |
/api/{type}/id/{val} | Specific JSON-LD based identity-based lookup for an entity type | https://genboree.org/cspec/api/SequenceVariantInterpretation/id/GN016 |
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