AraGWAS API
REST API for AraGWAS
# Install the command line client
$ pip install coreapi-cli
associations
list
List all associations meeting the filtering criteria sorted by score.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
chr | The chromosome of interest. Multiple choices can be chained when accessing programmatically. |
maf | The MAF filter, options are 1 (for <1%), 1-5 (for 1-5%), 5-10 (for 5-10%) and 10 (for >10%). Multiple choices can be chained when accessing programmatically. |
mac | The MAC filter, options are 0 (for MAC≤5) and 5 (for MAC>5), default is 5. Multiple choices can be chained when accessing programmatically. |
annotation | The SNP annotation filter, options are ns (for non-synonymous coding), s (for synonymous coding), in (for introns) and i (for intergenic). Multiple choices can be chained when accessing programmatically. |
type | The SNP type filter, options are genic and non-genic. |
significant | The significance filter, options are 0 for no filtering, p for permutation-threshold filtering and b for Bonferroni-threshold filtering. Default is p. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action associations list -p chr=... -p maf=... -p mac=... -p annotation=... -p type=... -p significant=...
aggregated_statistics
Retrieve the aggregation percentage for associations meeting filters criteria.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
chr | The chromosome of interest. Multiple choices can be chained when accessing programmatically. |
maf | The MAF filter, options are 1 (for <1%), 1-5 (for 1-5%), 5-10 (for 5-10%) and 10 (for >10%). Multiple choices can be chained when accessing programmatically. |
mac | The MAC filter, options are 0 (for MAC≤5) and 5 (for MAC>5), default is 5. Multiple choices can be chained when accessing programmatically. |
annotation | The SNP annotation filter, options are ns (for non-synonymous coding), s (for synonymous coding), in (for introns) and i (for intergenic). Multiple choices can be chained when accessing programmatically. |
type | The SNP type filter, options are genic and non-genic. |
significant | The significance filter, options are 0 for no filtering, p for permutation-threshold filtering and b for Bonferroni-threshold filtering. Default is p. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action associations aggregated_statistics -p chr=... -p maf=... -p mac=... -p annotation=... -p type=... -p significant=...
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action associations count
genes
list
List all genes in the database. Can add 'chrom', 'start' and 'end' as params in the url request.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
chr | The chromosome of interest of the search region |
start | The begininning of the search region |
end | The end of the search region |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genes list -p chr=... -p start=... -p end=...
top_list
Retrieve the top genes based on the number of significant associations and provide full gene information.
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genes top_list
read
Retrieve information about a specific gene.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | The name of the gene |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genes read -p id=...
aggregated_statistics
Retrieve the aggregation percentage for associations meeting the filtering criteria for this gene.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | The name of the gene for which statistics should be computed. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
maf | The MAF filter, options are 1 (for <1%), 1-5 (for 1-5%), 5-10 (for 5-10%) and 10 (for >10%). Multiple choices can be chained when accessing programmatically. |
mac | The MAC filter, options are 0 (for MAC≤5) and 5 (for MAC>5), default is 5. Multiple choices can be chained when accessing programmatically. |
annotation | The SNP annotation filter, options are ns (for non-synonymous coding), s (for synonymous coding), in (for introns) and i (for intergenic). Multiple choices can be chained when accessing programmatically. |
type | The SNP type filter, options are genic and non-genic. |
significant | The significance filter, options are 0 for no filtering, p for permutation-threshold filtering and b for Bonferroni-threshold filtering. Default is p. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genes aggregated_statistics -p maf=... -p mac=... -p annotation=... -p type=... -p significant=... -p id=...
associations
Return associations meeting the filtering criteria for the selected gene.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | The name of the gene for which associations should be loaded. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
maf | The MAF filter, options are 1 (for <1%), 1-5 (for 1-5%), 5-10 (for 5-10%) and 10 (for >10%). Multiple choices can be chained when accessing programmatically. |
mac | The MAC filter, options are 0 (for MAC≤5) and 5 (for MAC>5), default is 5. Multiple choices can be chained when accessing programmatically. |
annotation | The SNP annotation filter, options are ns (for non-synonymous coding), s (for synonymous coding), in (for introns) and i (for intergenic). Multiple choices can be chained when accessing programmatically. |
type | The SNP type filter, options are genic and non-genic. |
significant | The significance filter, options are 0 for no filtering, p for permutation-threshold filtering and b for Bonferroni-threshold filtering. Default is p. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genes associations -p maf=... -p mac=... -p annotation=... -p type=... -p significant=... -p id=...
genotypes
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genotypes list
read
Retrieve information about a specific genotype.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this genotype. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action genotypes read -p id=...
phenotypes
list
List available phenotypes.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action phenotypes list -p page=...
read
Retrieve information about a specific phenotype.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this phenotype. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action phenotypes read -p id=...
studies
Get a list of studies for a specific phenotype.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this phenotype. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action phenotypes studies -p id=...
search
search_results
Display results based on search term.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
query_term required | Search term |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action search search_results -p query_term=...
studies
list
List all available GWA studies.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action studies list -p page=...
read
Retrieve information about a specific GWA study.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this study. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action studies read -p id=...
aggregated_statistics
Retrieve the aggregation statistics of the top assocations meeting the filtering criteria for a study and a specific set of filters.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this study. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
chr | The chromosome of interest. Multiple choices can be chained when accessing programmatically. |
maf | The MAF filter, options are 1 (for <1%), 1-5 (for 1-5%), 5-10 (for 5-10%) and 10 (for >10%). Multiple choices can be chained when accessing programmatically. |
mac | The MAC filter, options are 0 (for MAC≤5) and 5 (for MAC>5), default is 5. Multiple choices can be chained when accessing programmatically. |
annotation | The SNP annotation filter, options are ns (for non-synonymous coding), s (for synonymous coding), in (for introns) and i (for intergenic). Multiple choices can be chained when accessing programmatically. |
type | The SNP type filter, options are genic and non-genic. |
significant | The significance filter, options are 0 for no filtering, p for permutation-threshold filtering and b for Bonferroni-threshold filtering. Default is p. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action studies aggregated_statistics -p chr=... -p maf=... -p mac=... -p annotation=... -p type=... -p significant=... -p id=...
top_associations
Retrieve top associations meeting the filtering criteria for the selected study.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this study. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
chr | The chromosome of interest. Multiple choices can be chained when accessing programmatically. |
maf | The MAF filter, options are 1 (for <1%), 1-5 (for 1-5%), 5-10 (for 5-10%) and 10 (for >10%). Multiple choices can be chained when accessing programmatically. |
mac | The MAC filter, options are 0 (for MAC≤5) and 5 (for MAC>5), default is 5. Multiple choices can be chained when accessing programmatically. |
annotation | The SNP annotation filter, options are ns (for non-synonymous coding), s (for synonymous coding), in (for introns) and i (for intergenic). Multiple choices can be chained when accessing programmatically. |
type | The SNP type filter, options are genic and non-genic. |
significant | The significance filter, options are 0 for no filtering, p for permutation-threshold filtering and b for Bonferroni-threshold filtering. Default is p. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action studies top_associations -p chr=... -p maf=... -p mac=... -p annotation=... -p type=... -p significant=... -p id=...
top_genes_and_snp_type
Get genes and SNP type that got the most significant associations for a specific study. The returned fields will be empty if there are no significant associations for the selected study.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this study. |
# Load the schema document
$ coreapi get https://aragwas.1001genomes.org/docs/
# Interact with the API endpoint
$ coreapi action studies top_genes_and_snp_type -p id=...