Introduction to CFDE GeneReg LDH Web Services

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

Collaborating Data Coordination Center Web Services

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)

https://bdcw.org/MetGENE/ 

https://smart-api.info/ui/342e4cec92030d74efd84b61650fb0ea 

Library of Integrated Network-Based Cellular Signatures(LINCS)

SigCom LINCS (Gene-Gene expression)

https://maayanlab.cloud/sigcom-lincs#/ 

https://smart-api.info/ui/fdb3ecfcf5006a142d3f5522930324f1 (Data) 

https://smart-api.info/ui/75cfc060ea7bec431a356c00c4a67c74 (Metadata) 

Illuminating the Druggable Genome (IDG)

Pharos (Gene-Drug-Disease)

https://pharos.nih.gov/ 

https://smart-api.info/ui/b8399f43cd71264faca4d798c793aa30 

CFDE GeneReg LDH API Endpoints

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

https://genboree.org/cfde-gene-dev/srvc 

/id/{val}

Non-specific identity-based lookup

https://genboree.org/cfde-gene-dev/id/CA13203640 

/{type}

Get info about an LDH entity type

https://genboree.org/cfde-gene-dev/ENCODERegulatoryElementEvidence 

/{type}/id

Paged list; Batch entity retrieval

https://genboree.org/cfde-gene-dev/Variant/id 

/{type}/id/{val}

Specific identity-based lookup for an entity type

https://genboree.org/cfde-gene-dev/Variant/id/CA13203640 

/{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

CFDE GeneReg LDH API Modifiers

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


https://genboree.org/cfde-gene-dev/Variant/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/cfde-gene-dev/Variant/id?detail=low&fields=entId,ldhId

https://genboree.org/cfde-gene-dev/xqtlEvidence/id?detail=high&fields=entId,entContent.GTExIri,entContent.eQTL

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 

Key Fields in CFDE GeneReg LDH API Response

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",