MyGene.info Gene Query v3 API.

• MyGene.info gene query service

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  • GETGene query service/v3/query
    Make gene query and return matching gene list. Support JSONP and CORS as well.
    
    

    Parameter	Value	Type	Location	Description
    q		string	query	query string. Examples: "CDK2", "NM_052827", "204639_at". The detailed query syntax can be found at http://docs.mygene.info/en/latest/doc/query_service.html
    fields		string	query	a comma-separated fields to limit the fields returned from the matching gene hits. The supported field names can be found from any gene object (e.g. http://mygene.info/v3/gene/1017). Note that it supports dot notation as well, e.g., you can pass "refseq.rna". If "fields=all", all available fields will be returned. Default: "symbol,name,taxid,entrezgene,ensemblgene".
    species		string	query	can be used to limit the gene hits from given species. You can use "common names" for nine common species (human, mouse, rat, fruitfly, nematode, zebrafish, thale-cress, frog and pig). All other species, you can provide their taxonomy ids. Multiple species can be passed using comma as a separator. Passing “all” will query against all available species. Default: human,mouse,rat.
    size		integer	query	the maximum number of matching gene hits to return (with a cap of 1000 at the moment). Default: 10.
    from		integer	query	the number of matching gene hits to skip, starting from 0. Combining with "size" parameter, this can be useful for paging. Default: 0.
    sort		string	query	the comma-separated fields to sort on. Prefix with "-" for descending order, otherwise in ascending order. Default: sort by matching scores in decending order.
    facets		string	query	a single field or comma-separated fields to return facets, for example, “facets=taxid”, “facets=taxid,type_of_gene”.
    species_facet_filter		string	query	relevant when faceting on species (i.e., “facets=taxid” are passed). It’s used to pass species filter without changing the scope of faceting, so that the returned facet counts won’t change. Either species name or taxonomy id can be used, just like “species” parameter above.
    entrezonly		string	query	when passed as “true” or “1”, the query returns only the hits with valid Entrez gene ids. Default: false.
    ensemblonly		string	query	when passed as “true” or “1”, the query returns only the hits with valid Ensembl gene ids. Default: false.
    callback		string	query	you can pass a "callback" parameter to make a JSONP call.
    dotfield		string	query	control the format of the returned fields when passed "fields" parameter contains dot notation, e.g. "fields=refseq.rna". If "true" or "1", the returned data object contains a single "refseq.rna" field, otherwise ("false" or "0"), a single "refseq" field with a sub-field of "rna". Default: true.
    filter		string	query	alias for "fields" parameter.
    limit		integer	query	alias for "size" parameter.
    skip		integer	query	alias for "from" parameter.
    email		string	query	If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.

  • POSTGene query service via POST/v3/query
    Make gene queries in batch
    
    

    Parameter	Value	Type	Location	Description
    q		string	query	multiple query terms seperated by comma (also support "+" or white space), but no wildcard, e.g., "q=1017,1018" or "q=CDK2+BTK"
    scopes		string	query	specify one or more fields (separated by comma) as the search "scopes", e.g., "scopes=entrezgene", "scopes=entrezgene,ensemblgene". The available "fields" can be passed to "scopes" parameter are listed here: http://mygene.info/doc/query_service.html#available-fields. Default: "scopes=entrezgene,ensemblgene,retired" (either Entrez or Ensembl gene ids).
    fields		string	query	a comma-separated fields to limit the fields returned from the matching gene hits. The supported field names can be found from any gene object (e.g. http://mygene.info/v3/gene/1017). Note that it supports dot notation as well, e.g., you can pass "refseq.rna". If "fields=all", all available fields will be returned. Default: "symbol,name,taxid,entrezgene,ensemblgene".
    species		string	query	can be used to limit the gene hits from given species. You can use "common names" for nine common species (human, mouse, rat, fruitfly, nematode, zebrafish, thale-cress, frog and pig). All other species, you can provide their taxonomy ids. Multiple species can be passed using comma as a separator. Default: human,mouse,rat.
    dotfield		string	query	control the format of the returned fields when passed "fields" parameter contains dot notation, e.g. "fields=refseq.rna". If "true" or "1", the returned data object contains a single "refseq.rna" field, otherwise ("false" or "0"), a single "refseq" field with a sub-field of "rna". Default: true.
    email		string	query	If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.

  • GETGene query service by genome interval/v3/query
    Make gene query by genome interval and return genes within that region. Support JSONP and CORS as well.
    
    

    Parameter	Value	Type	Location	Description
    q		string	query	genome interval in format of "chr#:start-end", e.g., chr1:151,073,054-151,383,976 (comma allowed). For human genes, the interval query is against hg38 by default, but you can still use hg19.chr1:151,073,054-151,383,976 to query against hg19 genome assembly
    fields		string	query	a comma-separated fields to limit the fields returned from the matching gene hits. The supported field names can be found from any gene object (e.g. http://mygene.info/v3/gene/1017). Note that it supports dot notation as well, e.g., you can pass "refseq.rna". If "fields=all", all available fields will be returned. Default: "symbol,name,taxid,entrezgene,ensemblgene".
    species		string	query	Optional, do the genome interval query for the given species. You can use "common names" for nine common species (human, mouse, rat, fruitfly, nematode, zebrafish, thale-cress, frog and pig). Any other species, you can provide its taxonomy id. Default: human.
    size		integer	query	the maximum number of matching gene hits to return (with a cap of 1000 at the moment). Default: 10.
    from		integer	query	the number of matching gene hits to skip, starting from 0. Combining with "size" parameter, this can be useful for paging. Default: 0.
    sort		string	query	the comma-separated fields to sort on. Prefix with "-" for descending order, otherwise in ascending order. Default: sort by matching scores in decending order.
    entrezonly		string	query	when passed as “true” or “1”, the query returns only the hits with valid Entrez gene ids. Default: false.
    ensemblonly		string	query	when passed as “true” or “1”, the query returns only the hits with valid Ensembl gene ids. Default: false.
    callback		string	query	you can pass a "callback" parameter to make a JSONP call.
    dotfield		string	query	control the format of the returned fields when passed "fields" parameter contains dot notation, e.g. "fields=refseq.rna". If "true" or "1", the returned data object contains a single "refseq.rna" field, otherwise ("false" or "0"), a single "refseq" field with a sub-field of "rna". Default: true.
    filter		string	query	alias for "fields" parameter.
    limit		integer	query	alias for "size" parameter.
    skip		integer	query	alias for "from" parameter.
    email		string	query	If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.

• MyGene.info gene annotation services

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  • GETGene annotation service/v3/gene/:geneid
    Retrieve gene annotation based on Entrez or Ensembl gene id, support JSONP and CORS as well.
    
    

    Parameter	Value	Type	Location	Description
    geneid		string	query	Entrez or Ensembl gene id, e,g., 1017, ENSG00000170248. A retired Entrez Gene id works too if it is replaced by a new one, e.g., 245794
    fields		string	query	a comma-separated fields to limit the fields returned from the matching gene hits. The supported field names can be found from any gene object (e.g. http://mygene.info/v3/gene/1017). Note that it supports dot notation as well, e.g., you can pass "refseq.rna". If "fields=all", all available fields will be returned. Default: "symbol,name,taxid,entrezgene,ensemblgene".
    callback		string	query	you can pass a "callback" parameter to make a JSONP call.
    filter		string	query	alias for "fields" parameter.
    dotfield		string	query	control the format of the returned fields when passed "fields" parameter contains dot notation, e.g. "fields=refseq.rna". If "true" or "1", the returned data object contains a single "refseq.rna" field, otherwise ("false" or "0"), a single "refseq" field with a sub-field of "rna". Default: true.
    email		string	query	If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.

  • POSTGene annotation service via POST/v3/gene
    Make gene queries in batch for a list of Entrez or Ensembl gene ids
    
    

    Parameter	Value	Type	Location	Description
    ids		string	query	multiple geneids seperated by comma, e.g., "ids=1017,1018" or "ids=695,ENSG00000123374". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.
    fields		string	query	a comma-separated fields to limit the fields returned from the matching gene hits. The supported field names can be found from any gene object (e.g. http://mygene.info/v3/gene/1017). Note that it supports dot notation as well, e.g., you can pass "refseq.rna". If "fields=all", all available fields will be returned. Default: "symbol,name,taxid,entrezgene,ensemblgene".
    species		string	query	Optional, can be used to limit the gene hits from given species. You can use "common names" for nine common species (human, mouse, rat, fruitfly, nematode, zebrafish, thale-cress, frog and pig). All other species, you can provide their taxonomy ids. Multiple species can be passed using comma as a separator. Default: all.
    dotfield		string	query	control the format of the returned fields when passed "fields" parameter contains dot notation, e.g. "fields=refseq.rna". If "true" or "1", the returned data object contains a single "refseq.rna" field, otherwise ("false" or "0"), a single "refseq" field with a sub-field of "rna". Default: true.
    email		string	query	If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.

• MyGene.info metadata service

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  • GETMetadata service/v3/metadata
    Get metadata about the data available from MyGene.info.
    
    

    Parameter	Value	Type	Location	Description
    callback		string	query	you can pass a "callback" parameter to make a JSONP call.