The CFDE Gene Regulation Linked Data Hub provides RESTful-APIs to browse and search content. Responses are returned in JSON format.
Service URL: https://genboree.org/ldh
The CFDE GeneReg LDH is collaborating with multiple Data Coordination Centers and other databases to connect gene regulatory information and knowledge from multiple sources. The following is a list of API documentations that potentially will be connected by LDH:
DCC/Database | Tool developed | Landing page | Smart-API documentation |
Metabolomics | MetGene (Gene-Metabolites) | ||
Library of Integrated Network-Based Cellular Signatures(LINCS) | SigCom LINCS (Gene-Gene expression) | https://smart-api.info/ui/fdb3ecfcf5006a142d3f5522930324f1 (Data) https://smart-api.info/ui/75cfc060ea7bec431a356c00c4a67c74 (Metadata) | |
Illuminating the Druggable Genome (IDG) | Pharos (Gene-Drug-Disease) |
Several REST API endpoints are available to GET links and excerpts from LDH. Detailed API docs will be released soon.
Endpoints | Description | Example |
/srvc | LDH Service; lists all entity types and counts | |
/id/{val} | Non-specific identity-based lookup | |
| /{type} | Get info about an LDH entity type | https://genboree.org/cfde-gene-dev/ENCODERegulatoryElementEvidence |
| /{type}/id | Paged list; Batch entity retrieval | |
/{type}/id/{val} | Specific identity-based lookup for an entity type | |
| /{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/cfde-gene-dev/Variant/id/CA13203640/ld https://genboree.org/cfde-gene-dev/Variant/id/CA13203640/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/cfde-gene-dev/Variant/id/CA13203640/types https://genboree.org/cfde-gene-dev/Variant/id/CA13203640/types/ld https://genboree.org/cfde-gene-dev/Variant/id/CA13203640/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/cfde-gene-dev/Variant/id?ids=CA13203640,CA213258351,CA13252026 |
types | Comma separated list of entity types | Allows filtering the results to show certain entity types only | https://genboree.org/cfde-gene-dev/Variant/id/CA13203640?types=xqtlEvidence |
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/cfde-gene-dev/Variant/id?detail=low https://genboree.org/cfde-gene-dev/Variant/id?detail=med |
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/cfde-gene-dev/Variant/id?detail=low&fields=entId,ldhId |
pg | Integer Default: 1 Min:1 | Page number to be retrieved | https://genboree.org/cfde-gene-dev/Variant/id?pg=1&pgSize=250&detail=low&fields=entId,ldhId |
pgSize | Integer Default: 250 Min 1; Max: 250 | Number of results in each page | https://genboree.org/cfde-gene-dev/Variant/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": [ { "AlleleSpecificEvidence": [ … ] }, {"xqtlEvidence": [ … ] }] Here, "AlleleSpecificEvidence" and "xqtlEvidence" are the linked data entities for the Variant "CA13203640" |
ldFor | This entity is linked data FOR these other entities | "ldFor": [ { "RegulatoryElement": [ … ] } ], Regulatory Element “EH38E2924876” is linked data FOR the Variant “CA13203640” |
entId | Identifier of entity in the external data source | "entId": "CA13203640", where "CA13203640" - ClinGen Allele Registry identifier for “Variant” |
entIri | IRI of entity in the external data source | "entIri": "http://reg.genome.network/allele/CA13203640", where the IRI is the “link” to this entity in the external data source |
entType | Type of entity | "entType": "Variant", |
ldhId | LDH identifier (Note: If data is embedded within LDH, this will be the only identifier) | "ldhId": "1341485989", |
ldhIri | LDH IRI (Note: If data is embedded within LDH, this will be the only IRI) | "ldhIri": "https://genboree.org/cfde-gene-dev/Variant/id/1341485989" |
entAliases (not applicable here) | List of aliases for the entity in other external data sources. Includes: id, label and iri | "entAliases": [ { "id": "177629", "iri": "https://www.ncbi.nlm.nih.gov/clinvar/variation/177629/", "label": "ClinVar" }], where "177629" is an alias for this allele "CA015944" in ClinVar |
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. |
entContentSrc (not applicable here) | Metadata about the excerpt content at the external data source. Includes: src, ver, iri and genomeBuild | "entContentSrc": { "genomeBuild": "GRCh37", "source": "gnomAD", "url": "http://gnomad.broadinstitute.org/", "ver": "v2.1.1"}, |
modifier | Person who added this entity to LDH | "modifier": "johndoe", |
modified | Modification timestamp value | "modified": "2019-10-03T17:04:35.395Z", |
