{ "opencollection": "1.0.0", "info": { "name": "NCBI Datasets BioSample Gene API", "version": "v2" }, "request": { "auth": { "type": "apikey", "key": "api-key", "value": "{{api-key}}", "placement": "header" } }, "items": [ { "info": { "name": "Gene", "type": "folder" }, "items": [ { "info": { "name": "Get a gene data package by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_ids/download", "params": [ { "name": "gene_ids", "value": "", "type": "path", "description": "One or more NCBI GeneIDs" }, { "name": "include_annotation_type", "value": "", "type": "query", "description": "Specify which sequence files to include in the data package." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Limit the contents of the sequence files and tabular product report to the specified RNA and protein accessions" }, { "name": "aux_report", "value": "", "type": "query", "description": "Specify additional report files to include in the data package. The gene data report is always included, and its inclusion is not affected by this parameter." }, { "name": "tabular_reports", "value": "", "type": "query", "description": "Specify which tabular report files to include in the data package." }, { "name": "filename", "value": "", "type": "query", "description": "Output file name." } ] }, "docs": "Download a gene data package including sequence, annotation and data reports, as a compressed zip archive, by GeneID." }, { "info": { "name": "Get a gene data package", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/download", "params": [ { "name": "filename", "value": "", "type": "query", "description": "Output file name." } ], "body": { "type": "json", "data": "{}" } }, "docs": "Download a gene data package including sequence, annotation and data reports, as a compressed zip archive." }, { "info": { "name": "Get gene reports by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_ids", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "gene_ids", "value": "", "type": "path", "description": "One or more NCBI GeneIDs" }, { "name": "locus_tags", "value": "", "type": "query", "description": "Gene locus tags" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene summary by GeneID. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)" }, { "info": { "name": "Get gene metadata by RefSeq Accession", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/accession/:accessions", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "accessions", "value": "", "type": "path", "description": "One or more RefSeq nucleotide or protein accessions" }, { "name": "locus_tags", "value": "", "type": "query", "description": "Gene locus tags" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene summary by RefSeq Accession. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)" }, { "info": { "name": "Get gene metadata by gene symbol", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/:symbols/taxon/:taxon", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "symbols", "value": "", "type": "path", "description": "One or more gene symbols" }, { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol" }, { "name": "locus_tags", "value": "", "type": "query", "description": "Gene locus tags" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene summary by by gene symbol. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)" }, { "info": { "name": "Get gene reports by taxonomic identifier", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/taxon/:taxon", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at" }, { "name": "locus_tags", "value": "", "type": "query", "description": "Gene locus tags" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene summary for a specified NCBI Taxonomy ID or name (common or scientific). By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)" }, { "info": { "name": "Get gene metadata as JSON", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene", "body": { "type": "json", "data": "{}" } }, "docs": "Get a gene summary. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)" }, { "info": { "name": "Get a gene data report by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_ids/dataset_report", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "gene_ids", "value": "", "type": "path", "description": "One or more NCBI GeneIDs" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene data report by GeneID. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene data report by RefSeq nucleotide or protein accession", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/accession/:accessions/dataset_report", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "accessions", "value": "", "type": "path", "description": "One or more RefSeq nucleotide or protein accessions" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene data report by RefSeq nucleotide or protein accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene data report by symbol and taxon", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/:symbols/taxon/:taxon/dataset_report", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "symbols", "value": "", "type": "path", "description": "One or more gene symbols" }, { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." } ] }, "docs": "Get a gene data report by gene symbol and taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene data report by taxon", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/taxon/:taxon/dataset_report", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." } ] }, "docs": "Get a gene data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene data report by locus tag", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/locus_tag/:locus_tags/dataset_report", "params": [ { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "locus_tags", "value": "", "type": "path", "description": "Gene locus tags" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "sort.field", "value": "", "type": "query" } ] }, "docs": "Get a gene data report by gene locus tag. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene data report", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/dataset_report", "body": { "type": "json", "data": "{}" } }, "docs": "Get a gene data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene product report by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_ids/product_report", "params": [ { "name": "gene_ids", "value": "", "type": "path", "description": "One or more NCBI GeneIDs" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene product report by GeneID. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene product report by RefSeq nucleotide or protein accession", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/accession/:accessions/product_report", "params": [ { "name": "accessions", "value": "", "type": "path", "description": "One or more RefSeq nucleotide or protein accessions" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." }, { "name": "sort.field", "value": "", "type": "query" }, { "name": "sort.direction", "value": "", "type": "query" } ] }, "docs": "Get a gene product report by RefSeq nucleotide or protein accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene product report by symbol and taxon", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/:symbols/taxon/:taxon/product_report", "params": [ { "name": "symbols", "value": "", "type": "path", "description": "One or more gene symbols" }, { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." } ] }, "docs": "Get a gene product report by symbol and taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene product report by taxon", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/taxon/:taxon/product_report", "params": [ { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "tax_search_subtree", "value": "", "type": "query", "description": "If true, include genes from taxonomic ranks below the requested taxon." } ] }, "docs": "Get a gene product report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene product report by locus tag", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/locus_tag/:locus_tags/product_report", "params": [ { "name": "locus_tags", "value": "", "type": "path", "description": "Gene locus tags" }, { "name": "table_fields", "value": "", "type": "query", "description": "Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "table_format", "value": "", "type": "query", "description": "Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "include_tabular_header", "value": "", "type": "query", "description": "Specify when to include the table header when requesting a tabular report." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." }, { "name": "query", "value": "", "type": "query", "description": "Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name." }, { "name": "types", "value": "", "type": "query", "description": "Limit to genes matching the specified gene type." }, { "name": "accession_filter", "value": "", "type": "query", "description": "Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`." }, { "name": "sort.field", "value": "", "type": "query" } ] }, "docs": "Get a gene product report by gene locus tag. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a gene product report", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/product_report", "body": { "type": "json", "data": "{}" } }, "docs": "Get a gene product report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats." }, { "info": { "name": "Get a download summary of a gene data package by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_ids/download_summary", "params": [ { "name": "gene_ids", "value": "", "type": "path", "description": "One or more NCBI GeneIDs" }, { "name": "include_annotation_type", "value": "", "type": "query", "description": "Specify which sequence files to include in the data package." }, { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "fasta_filter", "value": "", "type": "query", "description": "Limit the FASTA sequences in the datasets package to these transcript and protein accessions (deprecated)" }, { "name": "accession_filter", "value": "", "type": "query", "description": "Limit the contents of the sequence files and tabular product report to the specified RNA and protein accessions" }, { "name": "aux_report", "value": "", "type": "query", "description": "Specify additional report files to include in the data package. The gene data report is always included, and its inclusion is not affected by this parameter." }, { "name": "tabular_reports", "value": "", "type": "query", "description": "Specify which tabular report files to include in the data package." } ] }, "docs": "Get a download summary of a gene data package, including counts and estimated package size, in JSON format." }, { "info": { "name": "Get a download summary of a gene data package", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/download_summary", "body": { "type": "json", "data": "{}" } }, "docs": "Get a download summary of a gene data package, including counts and estimated package size, in JSON format." }, { "info": { "name": "Get gene counts by taxon", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/taxon/:taxon/counts", "params": [ { "name": "taxon", "value": "", "type": "path", "description": "Taxon for provided gene symbol" } ] }, "docs": "Get gene counts by taxon in JSON format." }, { "info": { "name": "Get gene counts by taxon", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/taxon/counts", "body": { "type": "json", "data": "{}" } }, "docs": "Get gene counts by taxon in JSON format." }, { "info": { "name": "Get a gene data report for a gene ortholog set by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_id/orthologs", "params": [ { "name": "gene_id", "value": "", "type": "path", "description": "One or more NCBI GeneIDs" }, { "name": "returned_content", "value": "", "type": "query", "description": "Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts." }, { "name": "taxon_filter", "value": "", "type": "query", "description": "Limit to genes from the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank." }, { "name": "page_size", "value": "", "type": "query", "description": "The maximum number of gene reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results." }, { "name": "page_token", "value": "", "type": "query", "description": "A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved." } ] }, "docs": "Get a gene data report for a gene ortholog set by GeneID in JSON format." }, { "info": { "name": "Get a gene data report for a gene ortholog set by GeneID", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/orthologs", "body": { "type": "json", "data": "{}" } }, "docs": "Get a gene data report for a gene ortholog set by GeneID in JSON format." }, { "info": { "name": "Get gene links by GeneID", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/:gene_ids/links", "params": [ { "name": "gene_ids", "value": "", "type": "path", "description": "One or more NCBI GeneIDs, limited to 100" } ] }, "docs": "Get links to available gene resources in JSON format." }, { "info": { "name": "Get gene links by GeneID", "type": "http" }, "http": { "method": "POST", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/links", "body": { "type": "json", "data": "{}" } }, "docs": "Get links to available gene resources in JSON format." }, { "info": { "name": "Get gene counts per chromosome by taxon and annotation name", "type": "http" }, "http": { "method": "GET", "url": "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/taxon/:taxon/annotation/:annotation_name/chromosome_summary", "params": [ { "name": "taxon", "value": "", "type": "path", "description": "NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank, with an anntoated genome" }, { "name": "annotation_name", "value": "", "type": "path", "description": "Annotation name corresponding to the provided taxon" } ] }, "docs": "Get gene counts per chromosome by taxon and annotation name in JSON format." } ] } ], "bundled": true }