Introduction

The Exome Aggregation Consortium (ExAC) Browser is a product created at the Broad Institue. It contains genomic information ono ver 60,000 individuals who were sequenced through a variety of projects. You can learn more about this project at the ExAC web site (exac.broadinstitute.org).

As part of the NIH BD2K PIC-SURE Center of Excellence http://www.pic-sure.org the HMS Department of Biomedical informatics https://dbmi.hms.harvard.edu extended the ExAC application by providing a REST service. These services enable a user to integrate ExAC services into their own tools, querying the variant information and returning the data in an easy to use JSON format.

More informations here: http://avillach-lab.hms.harvard.edu

You can see the changes we made on GitHub

/rest/awesome

This call returns information about a gene given its name. Further refinement can be accomplished by setting the service parameter so that only specific information is returned (e.g. Variants in that gene). This is accomplished through a redirect to the URL with the ExAC gene identifier.

Parameter Description
query required The name of the gene
service optional The type of gene information you would like returned

NOTE: This REST call will return a 301(Redirect) which will redirect the user to the correct page. Please make sure the you enable your application to follow redirects.

/rest/awesome?query=CHD8&service=variants_in_gene
            					
            				
Variant

Various levels of detail about a variant can be obtained by calling any of the variant REST calls with the Variant Id (
CHROMOSOME-POSITION-REFERENCE-VARIANT).

/rest/variant

This call returns all information about a variant in the ExAC database.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/14-21853913-T-C
            					
            				
/rest/variant/variant

This call returns information about the variant itself including the gene that it is in, the frequency of it in the database, and what transcripts it could be found in.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/variant/14-21853913-T-C
            					
            				
/rest/variant/base_coverage

This call returns information about a variants base coverage.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/base_coverage/14-21853913-T-C
            					
            				
/rest/variant/consequences

This call returns information about any genotypic consequences from this variantion.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/consequences/14-21853913-T-C
            					
            				
/rest/variant/any_covered

This call returns a boolean if this variant is found in any individuals.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/any_covered/14-21853913-T-C
            					
            				
/rest/variant/ordered_csqs

This call returns information about the CSQS of the variant.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/ordered_csqs/14-21853913-T-C
            					
            				
/rest/variant/metrics

This call will return various metric information about the variant.

Parameter Description
Variant Id required The Variant Id is a string that identifies the gene, position, reference amino acid, and the variant. In the following format:
CHROMOSOME-POSITION-REFERENCE-VARIANT
/rest/variant/metrics/14-21853913-T-C
            					
            				
Gene

Various levels of detail on variants in the ExAC database can be found by the Ensembl gene id. If the Ensembl id is not known then the search tool can be used.

/rest/gene

This call returns all the variant information in the ExAC database from the gene level.

Parameter Description
Gene Id required The Ensembl gene Id
/rest/gene/ENSG00000169174
            					
            				
/rest/gene/transcript

This call returns all the transcripts in a gene.

Parameter Description
Gene Id required The Ensembl gene Id
/rest/gene/transcript/ENSG00000169174
            					
            				
/rest/gene/variants_in_gene

This call returns all the variant information in a gene.

Parameter Description
Gene Id required The Ensembl gene Id
/rest/gene/variants_in_gene/ENSG00000169174
            					
            				
/rest/gene/variants_in_transcript

This call returns all the variant information in a gene plus what transcript(s) the variant is in.

Parameter Description
Gene Id required The Ensembl gene Id
/rest/gene/variants_in_transcript/ENSG00000169174
            					
            				
/rest/gene/transcripts_in_gene

This call returns all the transcripts in a gene.

Parameter Description
Gene Id required The Ensembl gene Id
/rest/gene/transcripts_in_gene/ENSG00000169174
            					
            				
/rest/gene/coverage_stats

This call returns all the coverage statistics for every varaint in a gene.

Parameter Description
Gene Id required The Ensembl gene Id
/rest/gene/coverage_stats/ENSG00000169174
            					
            				
Transcript

Various levels of detail on variants in the ExAC database can be found by the Ensembl variant id.

/rest/transcript

This call returns all the variant information in the ExAC database from the variant level.

Parameter Description
Transcript Id required The Ensembl transcript Id
/rest/transcript/ENST00000407236
            					
            				
/rest/transcript/transcript

This call returns infromation about the transcript such as its exons, start, stop, and strand.

Parameter Description
Transcript Id required The Ensembl transcript Id
/rest/transcript/transcript/ENST00000407236
            					
            				
/rest/transcript/variants_in_transcript

This call returns all the variants in a transcript.

Parameter Description
Transcript Id required The Ensembl transcript Id
/rest/transcript/variants_in_transcript/ENST00000407236
            					
            				
/rest/transcript/coverage_stats

This call returns all the coverage statistical information in a transcript.

Parameter Description
Transcript Id required The Ensembl transcript Id
/rest/transcript/coverage_stats/ENST00000407236
            					
            				
/rest/transcript/gene

This call returns the gene information that this transcript is part of.

Parameter Description
Transcript Id required The Ensembl transcript Id
/rest/transcript/gene/ENST00000407236
            					
            				
Region

Various levels of detail on variants, gene, and transcipts in the ExAC database that can be found in that region.

/rest/region

This call returns all the variant, gene, and transcript information in this region.

Parameter Description
Region required The Region is a string that identifies the chromosome, start and stop position you want to look in. In the following format:
CHROMOSOME-START-STOP
/rest/region/22-46615715-46615880
            					
            				
/rest/region/genes_in_region

This call returns all the genes that are in this region.

Parameter Description
Region required The Region is a string that identifies the chromosome, start and stop position you want to look in. In the following format:
CHROMOSOME-START-STOP
/rest/region/genes_in_region/22-46615715-46615880
            					
            				
/rest/region/variants_in_region

This call returns all variants in the region.

Parameter Description
Region required The Region is a string that identifies the chromosome, start and stop position you want to look in. In the following format:
CHROMOSOME-START-STOP
/rest/region/variants_in_region/22-46615715-46615880
            					
            				
/rest/region/coverage_array

This call returns all the coverage information in this region.

Parameter Description
Region required The Region is a string that identifies the chromosome, start and stop position you want to look in. In the following format:
CHROMOSOME-START-STOP
/rest/region/coverage_array/22-46615715-46615880
            					
            				
dbSNP

All variant information in the ExAC database at the position associated with dbSNP.

/rest/dbsnp

Returns all the variant information at the dbSNP position.

Parameter Description
dbSNP required The dbSNP identifier
/rest/dbsnp/rs1800234
            					
            				
Bulk Query

All bulk queries require a POST call with a request body that contains an JSON array of variant strings(CHROMOSOME-POSITION-REFERENCE-VARIANT)

/rest/bulk/variant

This call returns an array of information about the variants found in the ExAC database.

Body
A JSON array of variant strings(CHROMOSOME-POSITION-REFERENCE-VARIANT).

/rest/bulk/variant
[
"14-21853913-T-C",
"14-21854139-A-G",
"22-46615746-A-G"
]
								
            				
/rest/bulk/variant/variant

This call returns an array of information about the variants passed to it including the gene(s) that they are in, the frequency of it in the database, and what transcripts it could be found in.

Body
A JSON array of variant strings(CHROMOSOME-POSITION-REFERENCE-VARIANT).

/rest/bulk/variant/variant
[
"14-21853913-T-C",
"14-21854139-A-G",
"22-46615746-A-G"
]