Query examples
View query:
- List available beacons
- Show information about a beacon
- List supported genomes
- List supported chromosomes
- List supported alleles
- Query a specific beacon
- Query beacon with a specific genome
- Query all beacons
- Filter reponses for a specific beacon
- Aggregate responses of all beacons via beacon of beacons
List beacons
Query:
GET http://localhost:8080/beacon-of-beacons/rest/beacons
Response:
[
{
"aggregator": false,
"id": "thousandgenomes",
"name": "1000 Genomes Project",
"organization": "Google"
},
{
"aggregator": false,
"id": "thousandgenomes-phase3",
"name": "1000 Genomes Project - Phase 3",
"organization": "Google"
},
{
"aggregator": false,
"id": "amplab",
"name": "AMPLab",
"organization": "APMLab"
},
{
"aggregator": true,
"id": "bob",
"name": "Beacon of Beacons",
"organization": "Global Alliance for Genomics and Health"
},
{
"aggregator": false,
"id": "cafe-cardiokit",
"name": "Cafe CardioKit",
"organization": "University of Leicester"
},
{
"aggregator": true,
"id": "cafe-variome",
"name": "Cafe Variome",
"organization": "University of Leicester"
},
{
"aggregator": false,
"id": "cafe-central",
"name": "Cafe Variome Central",
"organization": "University of Leicester"
},
{
"aggregator": false,
"id": "clinvar",
"name": "ClinVar",
"organization": "UCSC"
},
{
"aggregator": false,
"id": "ebi",
"name": "EMBL-EBI",
"organization": "EBI"
},
{
"aggregator": false,
"id": "curoverse-ref",
"name": "GA4GH Example Data",
"organization": "Curoverse"
},
{
"aggregator": true,
"id": "google",
"name": "Google Genomics Public Data",
"organization": "Google"
},
{
"aggregator": false,
"id": "platinum",
"name": "Illumina Platinum Genomes",
"organization": "Google"
},
{
"aggregator": false,
"id": "kaviar",
"name": "Known VARiants",
"organization": "Institute for Systems Biology"
},
{
"aggregator": false,
"id": "lovd",
"name": "Leiden Open Variation",
"organization": "UCSC"
},
{
"aggregator": false,
"id": "ncbi",
"name": "NCBI",
"organization": "NCBI"
},
{
"aggregator": false,
"id": "curoverse",
"name": "PGP",
"organization": "Curoverse"
},
{
"aggregator": false,
"id": "uniprot",
"name": "UniProt",
"organization": "UCSC"
},
{
"aggregator": false,
"id": "wtsi",
"name": "Wellcome Trust Sanger Institute",
"organization": "WTSI"
}
]Show information about a beacon
Query:
GET http://localhost:8080/beacon-of-beacons/rest/beacons/wtsi
Response:
{
"aggregator": false,
"id": "wtsi",
"name": "Wellcome Trust Sanger Institute",
"organization": "WTSI"
}
Alternatively, just filter the list using the optional "beacon" parameter. Example:
GET http://localhost:8080/beacon-of-beacons/rest/beacons?beacon=wtsi
Response:
[
{
"aggregator": false,
"id": "wtsi",
"name": "Wellcome Trust Sanger Institute",
"organization": "WTSI"
}
]
List supported genomes
Query:
GET http://localhost:8080/beacon-of-beacons/rest/references
Response:
[
{
"item": "HG38"
},
{
"item": "HG19"
},
{
"item": "HG18"
},
{
"item": "HG17"
},
{
"item": "HG16"
}
]
List supported chromosomes
Query:
GET http://localhost:8080/beacon-of-beacons/rest/chromosomes
Response:
[
{
"item": "CHR22"
},
{
"item": "CHR21"
},
{
"item": "CHR20"
},
{
"item": "CHR19"
},
{
"item": "CHR18"
},
{
"item": "CHR17"
},
{
"item": "CHR16"
},
{
"item": "CHR15"
},
{
"item": "CHR14"
},
{
"item": "CHR13"
},
{
"item": "CHR12"
},
{
"item": "CHR11"
},
{
"item": "CHR10"
},
{
"item": "CHR9"
},
{
"item": "CHR8"
},
{
"item": "CHR7"
},
{
"item": "CHR6"
},
{
"item": "CHR5"
},
{
"item": "CHR4"
},
{
"item": "CHR3"
},
{
"item": "CHR2"
},
{
"item": "CHR1"
},
{
"item": "CHRX"
},
{
"item": "CHRY"
},
{
"item": "CHRMT"
}
]
List supported alleles
Query:
GET http://localhost:8080/beacon-of-beacons/rest/alleles
Response:
[
{
"item": "A"
},
{
"item": "C"
},
{
"item": "G"
},
{
"item": "T"
},
{
"item": "D"
},
{
"item": "I"
}
]
Query a specific beacon
Query:
GET http://localhost:8080/beacon-of-beacons/rest/responses/lovd?chrom=1&pos=808922&allele=T
Response:
{
"beacon": {
"aggregator": false,
"id": "lovd",
"name": "Leiden Open Variation",
"organization": "UCSC"
},
"query": {
"allele": "T",
"chromosome": "CHR1",
"position": 808922,
"reference": null
},
"response": false
}
As you can see, the beacon responded with its own info, the query details and a response field denoting whether a match was found (true) or not (false). Null value is used to describe a problem, e.g. an invalid query. Some beacons, for example, do not support allele strings of length>1 or X/Y chromosomes.
Query beacon with a specific genome
Query:
GET http://localhost:8080/beacon-of-beacons/rest/responses/amplab?chrom=15&pos=41087870&allele=A&ref=hg19
Response:
{
"beacon": {
"aggregator": false,
"id": "amplab",
"name": "AMPLab",
"organization": "APMLab"
},
"query": {
"allele": "A",
"chromosome": "CHR15",
"position": 41087870,
"reference": "HG19"
},
"response": true
}
Query all beacons
Query:
GET http://localhost:8080/beacon-of-beacons/rest/responses?chrom=14&pos=106833421&allele=A
Response:
[
{
"beacon": {
"aggregator": false,
"id": "thousandgenomes",
"name": "1000 Genomes Project",
"organization": "Google"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "thousandgenomes-phase3",
"name": "1000 Genomes Project - Phase 3",
"organization": "Google"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "amplab",
"name": "AMPLab",
"organization": "APMLab"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": true
},
{
"beacon": {
"aggregator": true,
"id": "bob",
"name": "Beacon of Beacons",
"organization": "Global Alliance for Genomics and Health"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": true
},
{
"beacon": {
"aggregator": false,
"id": "cafe-cardiokit",
"name": "Cafe CardioKit",
"organization": "University of Leicester"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": true,
"id": "cafe-variome",
"name": "Cafe Variome",
"organization": "University of Leicester"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "cafe-central",
"name": "Cafe Variome Central",
"organization": "University of Leicester"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "clinvar",
"name": "ClinVar",
"organization": "UCSC"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "ebi",
"name": "EMBL-EBI",
"organization": "EBI"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "curoverse-ref",
"name": "GA4GH Example Data",
"organization": "Curoverse"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": true,
"id": "google",
"name": "Google Genomics Public Data",
"organization": "Google"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "platinum",
"name": "Illumina Platinum Genomes",
"organization": "Google"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "kaviar",
"name": "Known VARiants",
"organization": "Institute for Systems Biology"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "lovd",
"name": "Leiden Open Variation",
"organization": "UCSC"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "ncbi",
"name": "NCBI",
"organization": "NCBI"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": true
},
{
"beacon": {
"aggregator": false,
"id": "curoverse",
"name": "PGP",
"organization": "Curoverse"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "uniprot",
"name": "UniProt",
"organization": "UCSC"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
},
{
"beacon": {
"aggregator": false,
"id": "wtsi",
"name": "Wellcome Trust Sanger Institute",
"organization": "WTSI"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": false
}
]
Filter reponses for a specific beacon
Query:
GET http://localhost:8080/beacon-of-beacons/rest/responses?chrom=14&pos=106833421&allele=A&beacon=amplab
Response:
[
{
"beacon": {
"aggregator": false,
"id": "amplab",
"name": "AMPLab",
"organization": "APMLab"
},
"query": {
"allele": "A",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": true
}
]
Aggregate responses of all beacons via beacon of beacons
If you want to utilize the "beacon of beacons" feature and are only interested in whether any of the existing beacons have a particular variant, treat Beacon of Beacons as a beacon itself and let it perform the aggregation. Query:
GET http://localhost:8080/beacon-of-beacons/rest/responses/bob?chrom=14&pos=106833421&allele=D
Response:
{
"beacon": {
"aggregator": true,
"id": "bob",
"name": "Beacon of Beacons",
"organization": "Global Alliance for Genomics and Health"
},
"query": {
"allele": "D",
"chromosome": "CHR14",
"position": 106833421,
"reference": null
},
"response": true
}