openapi: 3.0.1 info: title: NCBI Datasets BioSample Gene API version: v2 description: '### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability. ' servers: - url: https://api.ncbi.nlm.nih.gov/datasets/v2 security: - ApiKeyAuthHeader: [] tags: - name: Gene description: '#### Options to download gene data, including the associated sequence and metadata. These gene services allow you to get gene metadata as a data report or download gene, transcript and protein sequence, and metadata, as a gene data package, for all genes in NCBI Gene. ' paths: /gene/id/{gene_ids}/download: get: summary: Get a gene data package by GeneID description: Download a gene data package including sequence, annotation and data reports, as a compressed zip archive, by GeneID. tags: - Gene operationId: download_gene_package responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/zip: schema: format: binary type: string description: Zip compressed stream parameters: - name: gene_ids description: One or more NCBI GeneIDs in: path required: true schema: type: array items: type: integer examples: example-0: value: 59067 summary: Human IL21, interleukin 21 example-1: value: - 59067 - 50615 summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor - name: include_annotation_type description: Specify which sequence files to include in the data package. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2Fasta' examples: example-0: value: - FASTA_RNA - FASTA_PROTEIN summary: Include RNA and protein sequence files example-1: value: - FASTA_CDS - FASTA_5P_UTR - FASTA_3P_UTR summary: Include coding sequence, and 5' and 3' UTRs - name: accession_filter description: Limit the contents of the sequence files and tabular product report to the specified RNA and protein accessions in: query required: false schema: type: array items: type: string examples: example-0: value: NM_021803.4 summary: Human IL21 MANE Select transcript - name: aux_report 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. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' examples: example-0: value: PRODUCT_REPORT summary: Add the gene product report - name: tabular_reports description: Specify which tabular report files to include in the data package. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' examples: example-0: value: - DATASET_REPORT - PRODUCT_REPORT summary: Include tabular gene and gene product reports - name: filename description: Output file name. in: query required: false schema: type: string default: ncbi_dataset.zip /gene/download: post: summary: Get a gene data package description: Download a gene data package including sequence, annotation and data reports, as a compressed zip archive. tags: - Gene operationId: download_gene_package_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/zip: schema: format: binary type: string description: Zip compressed stream requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneDatasetRequest' examples: Multiple GeneID examples: description: Human interleukin 21 and interleukin 21 receptor genes, with RNA and protein sequence files, and both gene and product reports value: gene_ids: - 59067 - 50615 include_annotation_type: - FASTA_RNA - FASTA_PROTEIN aux_report: - DATASET_REPORT - PRODUCT_REPORT parameters: - name: filename description: Output file name. in: query required: false schema: type: string default: ncbi_dataset.zip /gene/id/{gene_ids}: get: deprecated: true summary: Get gene reports by GeneID description: '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)' tags: - Gene operationId: gene_reports_by_id responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: gene_ids description: One or more NCBI GeneIDs in: path required: true schema: type: array items: type: integer examples: example-0: value: 59067 summary: Human IL21, interleukin 21 example-1: value: - 59067 - 50615 summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor - name: locus_tags description: Gene locus tags in: query required: false schema: type: array items: type: string examples: example-0: value: b0001 summary: E. coli thrL, thr operon leader peptide example-1: value: - YER095W - YML032C summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52 - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/accession/{accessions}: get: deprecated: true summary: Get gene metadata by RefSeq Accession description: '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)' tags: - Gene operationId: gene_metadata_by_accession responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: accessions description: One or more RefSeq nucleotide or protein accessions in: path required: true schema: type: array items: type: string examples: example-0: value: NM_021803.4 summary: Human interleukin 21 mRNA example-1: value: - NP_068575.1 - NP_851564.1 summary: Human interleukin 21 and interleukin 21 receptor proteins - name: locus_tags description: Gene locus tags in: query required: false schema: type: array items: type: string examples: example-0: value: b0001 summary: E. coli thrL, thr operon leader peptide example-1: value: - YER095W - YML032C summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52 - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/symbol/{symbols}/taxon/{taxon}: get: deprecated: true summary: Get gene metadata by gene symbol description: '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)' tags: - Gene operationId: gene_metadata_by_tax_and_symbol responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: symbols description: One or more gene symbols in: path required: true schema: type: array items: type: string examples: example-0: value: GNAS summary: Human GNAS, GNAS complex locus - name: taxon description: NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy ID for human example-1: value: human summary: Common Name example-2: value: Homo sapiens summary: Scientific Name - name: locus_tags description: Gene locus tags in: query required: false schema: type: array items: type: string examples: example-0: value: b0001 summary: E. coli thrL, thr operon leader peptide example-1: value: - YER095W - YML032C summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52 - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/taxon/{taxon}: get: deprecated: true summary: Get gene reports by taxonomic identifier description: '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)' tags: - Gene operationId: gene_reports_by_taxon responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: taxon description: NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy Identifier example-1: value: human summary: Common Name example-2: value: Homo sapiens summary: Scientific Name - name: locus_tags description: Gene locus tags in: query required: false schema: type: array items: type: string examples: example-0: value: b0001 summary: E. coli thrL, thr operon leader peptide example-1: value: - YER095W - YML032C summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52 - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene: post: deprecated: true summary: Get gene metadata as JSON description: '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)' tags: - Gene operationId: gene_metadata_by_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequest' examples: Multiple GeneID examples: description: Human interleukin 21 and interleukin 21 receptor genes value: gene_ids: - 59067 - 50615 /gene/id/{gene_ids}/dataset_report: get: summary: Get a gene data report by GeneID description: '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.' tags: - Gene operationId: gene_dataset_reports_by_id responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: gene_ids description: One or more NCBI GeneIDs in: path required: true schema: type: array items: type: integer examples: example-0: value: 59067 summary: Human IL21, interleukin 21 example-1: value: - 59067 - 50615 summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/accession/{accessions}/dataset_report: get: summary: Get a gene data report by RefSeq nucleotide or protein accession description: '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.' tags: - Gene operationId: gene_dataset_report_by_accession responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: accessions description: One or more RefSeq nucleotide or protein accessions in: path required: true schema: type: array items: type: string examples: example-0: value: NM_021803.4 summary: Human interleukin 21 mRNA example-1: value: - NP_068575.1 - NP_851564.1 summary: Human interleukin 21 and interleukin 21 receptor proteins - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/symbol/{symbols}/taxon/{taxon}/dataset_report: get: summary: Get a gene data report by symbol and taxon description: '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.' tags: - Gene operationId: gene_dataset_report_by_tax_and_symbol responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: symbols description: One or more gene symbols in: path required: true schema: type: array items: type: string examples: example-0: value: GNAS summary: Human GNAS, GNAS complex locus - name: taxon description: NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy ID for human example-1: value: human summary: Common Name example-2: value: Homo sapiens summary: Scientific Name - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false /gene/taxon/{taxon}/dataset_report: get: summary: Get a gene data report by taxon description: '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.' tags: - Gene operationId: gene_dataset_reports_by_taxon responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: taxon description: NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy Identifier example-1: value: human summary: Common Name example-2: value: Homo sapiens summary: Scientific Name - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false /gene/locus_tag/{locus_tags}/dataset_report: get: summary: Get a gene data report by locus tag description: '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.' tags: - Gene operationId: gene_dataset_reports_by_locus_tag responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: locus_tags description: Gene locus tags in: path required: true schema: type: array items: type: string examples: example-0: value: b0001 summary: E. coli thrL, thr operon leader peptide example-1: value: - YER095W - YML032C summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52 - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: sort.field in: query required: false schema: type: string /gene/dataset_report: post: summary: Get a gene data report description: '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.' tags: - Gene operationId: gene_dataset_report responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequest' examples: Multiple GeneID examples: description: Human interleukin 21 and interleukin 21 receptor genes value: gene_ids: - 59067 - 50615 /gene/id/{gene_ids}/product_report: get: summary: Get a gene product report by GeneID description: '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.' tags: - Gene operationId: gene_product_reports_by_id responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: gene_ids description: One or more NCBI GeneIDs in: path required: true schema: type: array items: type: integer examples: example-0: value: 59067 summary: Human IL21, interleukin 21 example-1: value: - 59067 - 50615 summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/accession/{accessions}/product_report: get: summary: Get a gene product report by RefSeq nucleotide or protein accession description: '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.' tags: - Gene operationId: gene_product_report_by_accession responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: accessions description: One or more RefSeq nucleotide or protein accessions in: path required: true schema: type: array items: type: string examples: example-0: value: NM_021803.4 summary: Human interleukin 21 mRNA example-1: value: - NP_068575.1 - NP_851564.1 summary: Human interleukin 21 and interleukin 21 receptor proteins - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /gene/symbol/{symbols}/taxon/{taxon}/product_report: get: summary: Get a gene product report by symbol and taxon description: '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.' tags: - Gene operationId: gene_product_report_by_tax_and_symbol responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: symbols description: One or more gene symbols in: path required: true schema: type: array items: type: string examples: example-0: value: GNAS summary: Human GNAS, GNAS complex locus - name: taxon description: NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy ID for human example-1: value: human summary: Common Name example-2: value: Homo sapiens summary: Scientific Name - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false /gene/taxon/{taxon}/product_report: get: summary: Get a gene product report by taxon description: '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.' tags: - Gene operationId: gene_product_reports_by_taxon responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: taxon description: NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy Identifier example-1: value: human summary: Common Name example-2: value: Homo sapiens summary: Scientific Name - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: tax_search_subtree description: If true, include genes from taxonomic ranks below the requested taxon. in: query required: false schema: type: boolean default: false /gene/locus_tag/{locus_tags}/product_report: get: summary: Get a gene product report by locus tag description: '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.' tags: - Gene operationId: gene_product_reports_by_locus_tags responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string parameters: - name: locus_tags description: Gene locus tags in: path required: true schema: type: array items: type: string examples: example-0: value: b0001 summary: E. coli thrL, thr operon leader peptide example-1: value: - YER095W - YML032C summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52 - name: table_fields 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`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - gene-id - gene-type - description summary: GeneID, type and description - name: table_format 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`.' in: query required: false schema: type: string examples: example-0: value: summary summary: This template, valid for both gene report types, specifies a basic set of fields available from the report example-1: value: gene-ontology summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string - name: query description: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. in: query required: false schema: type: string examples: example-0: value: A2M immunoglobulin summary: Gene name or description - name: types description: Limit to genes matching the specified gene type. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneType' examples: example-0: value: PROTEIN_CODING summary: Protein coding genes example-1: value: ncRNA summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes example-2: value: PSEUDO summary: Pseudogenes - name: accession_filter description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.' in: query required: false schema: type: array items: type: string examples: example-0: value: - NM_001407959.1 - NM_001408458.1 summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively - name: sort.field in: query required: false schema: type: string /gene/product_report: post: summary: Get a gene product report description: '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.' tags: - Gene operationId: gene_product_report responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' text/tab-separated-values: schema: type: string requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneDatasetReportsRequest' examples: Multiple GeneID examples: description: Human interleukin 21 and interleukin 21 receptor genes value: gene_ids: - 59067 - 50615 /gene/id/{gene_ids}/download_summary: get: summary: Get a download summary of a gene data package by GeneID description: Get a download summary of a gene data package, including counts and estimated package size, in JSON format. tags: - Gene operationId: gene_download_summary_by_id responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2DownloadSummary' parameters: - name: gene_ids description: One or more NCBI GeneIDs in: path required: true schema: type: array items: type: integer examples: example-0: value: 59067 summary: Human IL21, interleukin 21 example-1: value: - 59067 - 50615 summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor - name: include_annotation_type description: Specify which sequence files to include in the data package. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2Fasta' examples: example-0: value: - FASTA_RNA - FASTA_PROTEIN summary: Include RNA and protein sequence files example-1: value: - FASTA_CDS - FASTA_5P_UTR - FASTA_3P_UTR summary: Include coding sequence, and 5' and 3' UTRs - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2GeneDatasetRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: fasta_filter description: Limit the FASTA sequences in the datasets package to these transcript and protein accessions (deprecated) in: query required: false schema: type: array items: type: string - name: accession_filter description: Limit the contents of the sequence files and tabular product report to the specified RNA and protein accessions in: query required: false schema: type: array items: type: string examples: example-0: value: NM_021803.4 summary: Human IL21 MANE Select transcript - name: aux_report 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. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' examples: example-0: value: PRODUCT_REPORT summary: Add the gene product report - name: tabular_reports description: Specify which tabular report files to include in the data package. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' examples: example-0: value: - DATASET_REPORT - PRODUCT_REPORT summary: Include tabular gene and gene product reports /gene/download_summary: post: summary: Get a download summary of a gene data package description: Get a download summary of a gene data package, including counts and estimated package size, in JSON format. tags: - Gene operationId: gene_download_summary_by_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2DownloadSummary' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneDatasetRequest' examples: Multiple GeneID examples: description: Human interleukin 21 and interleukin 21 receptor genes, with RNA and protein sequence files, and both gene and product reports value: gene_ids: - 59067 - 50615 include_annotation_type: - FASTA_RNA - FASTA_PROTEIN aux_report: - DATASET_REPORT - PRODUCT_REPORT /gene/taxon/{taxon}/counts: get: summary: Get gene counts by taxon description: Get gene counts by taxon in JSON format. tags: - Gene operationId: gene_counts_for_taxon responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2GeneCountsByTaxonReply' parameters: - name: taxon description: Taxon for provided gene symbol in: path required: true schema: type: string examples: example-0: value: '9606' summary: NCBI Taxonomy ID for human example-1: value: human summary: Common name example-2: value: Homo sapiens summary: Scientific name /gene/taxon/counts: post: summary: Get gene counts by taxon description: Get gene counts by taxon in JSON format. tags: - Gene operationId: gene_counts_for_taxon_by_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2GeneCountsByTaxonReply' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneCountsByTaxonRequest' examples: Single TaxID example: description: NCBI Taxonomy ID for human value: taxon: '9606' /gene/id/{gene_id}/orthologs: get: summary: Get a gene data report for a gene ortholog set by GeneID description: Get a gene data report for a gene ortholog set by GeneID in JSON format. tags: - Gene operationId: gene_orthologs_by_id responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' parameters: - name: gene_id description: One or more NCBI GeneIDs in: path required: true schema: type: integer examples: example-0: value: 2778 summary: Human GNAS, GNAS complex locus example-1: value: 2 summary: Human A2M, alpha-2-macroglobulin - name: returned_content description: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. in: query required: false schema: $ref: '#/components/schemas/v2OrthologRequestContentType' examples: example-0: value: IDS_ONLY summary: Return abbreviated report with GeneIDs example-1: value: COUNTS_ONLY summary: Return abbreviated report with GeneIDs, transcript and protein counts - name: taxon_filter description: Limit to genes from the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank. in: query required: false schema: type: array items: type: string examples: example-0: value: - '9606' - '10090' summary: NCBI Taxonomy IDs for human and mouse example-1: value: house mouse summary: Common name example-2: value: Homo sapiens summary: Scientific name - name: page_size 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. in: query required: false schema: type: integer default: 20 - name: page_token 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. in: query required: false schema: type: string /gene/orthologs: post: summary: Get a gene data report for a gene ortholog set by GeneID description: Get a gene data report for a gene ortholog set by GeneID in JSON format. tags: - Gene operationId: gene_orthologs_by_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2reportsGeneDataReportPage' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2OrthologRequest' examples: Single GeneID example: description: Primate gene orthologs of the human gene, GNAS complex locus value: gene_id: 2778 taxon_filter: - primates /gene/id/{gene_ids}/links: get: summary: Get gene links by GeneID description: Get links to available gene resources in JSON format. tags: - Gene operationId: gene_links_by_id responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2GeneLinksReply' parameters: - name: gene_ids description: One or more NCBI GeneIDs, limited to 100 in: path required: true schema: type: array items: type: integer examples: example-0: value: 59067 summary: Human IL21, interleukin 21 example-1: value: - 59067 - 50615 summary: Human IL21 and ILR21R, interleukin 21 and interleukin 21 receptor /gene/links: post: summary: Get gene links by GeneID description: Get links to available gene resources in JSON format. tags: - Gene operationId: gene_links_by_id_by_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2GeneLinksReply' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GeneLinksRequest' examples: Multiple GeneID examples: description: Human interleukin 21 and interleukin 21 receptor genes value: gene_ids: - 59067 - 50615 /gene/taxon/{taxon}/annotation/{annotation_name}/chromosome_summary: get: summary: Get gene counts per chromosome by taxon and annotation name description: Get gene counts per chromosome by taxon and annotation name in JSON format. tags: - Gene operationId: gene_chromosome_summary responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/json: schema: $ref: '#/components/schemas/v2GeneChromosomeSummaryReply' parameters: - name: taxon description: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank, with an anntoated genome in: path required: true schema: type: string examples: example-0: value: '9117' summary: NCBI Taxonomy ID for Grus americana example-1: value: Whooping crane summary: Common Name example-2: value: Grus americana summary: Scientific Name - name: annotation_name description: Annotation name corresponding to the provided taxon in: path required: true schema: type: string examples: example-0: value: GCF_028858705.1-RS_2023_03 summary: NCBI Grus americana Annotation Release GCF_028858705.1-RS_2023_03 components: schemas: v2GeneDatasetRequestContentType: type: string enum: - COMPLETE - IDS_ONLY default: COMPLETE v2OrthologRequestContentType: type: string enum: - COMPLETE - IDS_ONLY default: COMPLETE v2DownloadSummaryDehydrated: type: object properties: estimated_file_size_mb: type: integer url: type: string cli_download_command_line: type: string cli_rehydrate_command_line: type: string v2reportsWarning: type: object properties: gene_warning_code: $ref: '#/components/schemas/v2reportsWarningGeneWarningCode' reason: type: string message: type: string replaced_id: $ref: '#/components/schemas/v2reportsWarningReplacedId' unrecognized_identifier: type: string v2reportsTranscript: type: object properties: accession_version: type: string title: RefSeq transcript accession with version name: type: string title: RefSeq transcript name length: type: integer title: RefSeq transcript length in nucleotides cds: $ref: '#/components/schemas/v2reportsSeqRangeSet' genomic_locations: type: array items: $ref: '#/components/schemas/v2reportsGenomicLocation' ensembl_transcript: type: string title: Ensembl transcript accession with version protein: $ref: '#/components/schemas/v2reportsProtein' type: $ref: '#/components/schemas/v2reportsTranscriptTranscriptType' title: Indicates transcript protein-coding potential and whether it was computationally predicted select_category: $ref: '#/components/schemas/v2reportsTranscriptSelectCategory' v2reportsOrientation: type: string enum: - none - plus - minus default: none v2GeneCountsByTaxonReply: type: object properties: report: type: array items: $ref: '#/components/schemas/v2GeneCountsByTaxonReplyGeneTypeAndCount' v2reportsTranscriptTranscriptType: type: string enum: - UNKNOWN - PROTEIN_CODING - NON_CODING - PROTEIN_CODING_MODEL - NON_CODING_MODEL default: UNKNOWN v2reportsGeneSummary: type: object properties: source: type: string title: Source of the gene summary description: type: string title: Gene summary text itself that describes the gene date: type: string title: Date that the gene summary was last updated v2GeneLinksReply: type: object properties: gene_links: type: array items: $ref: '#/components/schemas/v2GeneLinksReplyGeneLink' v2DownloadSummaryFileSummary: type: object properties: file_count: type: integer size_mb: type: number format: float v2reportsGeneOntology: type: object properties: assigned_by: type: string title: The database that made the annotation molecular_functions: type: array items: $ref: '#/components/schemas/v2reportsProcessMetadata' biological_processes: type: array items: $ref: '#/components/schemas/v2reportsProcessMetadata' cellular_components: type: array items: $ref: '#/components/schemas/v2reportsProcessMetadata' v2reportsMapLocation: type: object properties: map_type: $ref: '#/components/schemas/v2reportsMapLocationMapType' title: Type of mapping; can be "Cytogenetic" or "Genetic" map_value: type: string title: Location of the gene in mapping coordinates v2reportsErrorGeneErrorCode: type: string enum: - UNKNOWN_GENE_ERROR_CODE - INCOMPLETE_LOOKUP_SYMBOL - INVALID_TAXON_GENE_ARGUMENT default: UNKNOWN_GENE_ERROR_CODE v2GeneDatasetRequest: type: object properties: gene_ids: type: array items: type: integer include_annotation_type: type: array items: $ref: '#/components/schemas/v2Fasta' returned_content: $ref: '#/components/schemas/v2GeneDatasetRequestContentType' title: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. fasta_filter: type: array items: type: string accession_filter: type: array items: type: string aux_report: type: array items: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' tabular_reports: type: array items: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' table_fields: type: array items: type: string table_report_type: $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType' title: Specify the report from which the table fields will be taken. This is currently deprecated - use tabular_reports instead. v2SortField: type: object properties: field: type: string direction: $ref: '#/components/schemas/v2SortDirection' v2reportsProcessMetadata: type: object properties: name: type: string title: Gene ontology term name go_id: type: string title: Gene ontology identifier evidence_code: type: string title: Indicates how the annotation is supported qualifier: type: string title: Explicitly link gene products to GO terms reference: $ref: '#/components/schemas/v2reportsReference' title: Source of evidence supporting the GO annotation v2GeneChromosomeSummaryReply: type: object properties: gene_chromosome_summaries: type: array items: $ref: '#/components/schemas/v2GeneChromosomeSummaryReplyGeneChromosomeSummary' v2reportsTranscriptTypeCount: type: object properties: type: $ref: '#/components/schemas/v2reportsTranscriptTranscriptType' title: Type of transcript count: type: integer title: Number of transcripts of a particular type v2reportsGeneType: type: string enum: - UNKNOWN - tRNA - rRNA - snRNA - scRNA - snoRNA - PROTEIN_CODING - PSEUDO - TRANSPOSON - miscRNA - ncRNA - BIOLOGICAL_REGION - OTHER default: UNKNOWN title: 'NB: GeneType values match Entrez Gene' v2DownloadSummaryAvailableFiles: type: object properties: all_genomic_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' genome_gff: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' genome_gbff: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' rna_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' prot_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' genome_gtf: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' cds_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' sequence_report: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' annotation_report: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' v2GeneLinksReplyGeneLinkType: type: string enum: - DEFAULT - GENE_LINK - GDV_LINK - ORTHOLOG_LINK - MCGV_LINK default: DEFAULT title: Types of gene links that may be returned v2GeneDatasetRequestGeneDatasetReportType: type: string enum: - DATASET_REPORT - PRODUCT_REPORT default: DATASET_REPORT v2GeneCountsByTaxonRequest: type: object properties: taxon: type: string title: Taxon for provided gene symbol v2DownloadSummary: type: object properties: record_count: type: integer title: The number of records for the requested filter. assembly_count: type: integer title: For backwards compatability with old VirusDatasetSummary resource_updated_on: type: string format: date-time title: The latest date on which the resource was updated. hydrated: $ref: '#/components/schemas/v2DownloadSummaryHydrated' dehydrated: $ref: '#/components/schemas/v2DownloadSummaryDehydrated' errors: type: array items: $ref: '#/components/schemas/v2reportsError' messages: type: array items: $ref: '#/components/schemas/v2reportsMessage' available_files: $ref: '#/components/schemas/v2DownloadSummaryAvailableFiles' v2reportsRnaType: type: string enum: - rna_UNKNOWN - premsg - tmRna default: rna_UNKNOWN v2reportsErrorAssemblyErrorCode: type: string enum: - UNKNOWN_ASSEMBLY_ERROR_CODE - INVALID_BIOPROJECT_IDS - NO_ASSEMBLIES_FOR_BIOPROJECTS - INVALID_TAXON - MISSING_SEARCH_FIELD - INVALID_BIOSAMPLE_IDS - NO_ASSEMBLIES_FOR_BIOSAMPLE_IDS - NO_ASSEMBLIES_FOR_ASSEMBLY_NAMES - INVALID_WGS_ACCESSIONS - NO_ASSEMBLIES_FOR_WGS_ACCESSIONS default: UNKNOWN_ASSEMBLY_ERROR_CODE v2reportsRange: type: object properties: begin: type: string format: uint64 title: Sequence start position end: type: string format: uint64 title: Sequence stop position orientation: $ref: '#/components/schemas/v2reportsOrientation' title: Direction relative to the genome order: type: integer title: The position of this sequence in a group of sequences ribosomal_slippage: type: integer title: When ribosomal slippage is desired, fill out slippage amount between this and previous range. v2reportsGeneDescriptor: type: object properties: gene_id: type: string format: uint64 title: NCBI Gene ID symbol: type: string title: Gene symbol description: type: string title: Gene name tax_id: type: string format: uint64 title: NCBI Taxonomy ID for the organism taxname: type: string title: Taxonomic name of the organism common_name: type: string title: Common name of the organism type: $ref: '#/components/schemas/v2reportsGeneType' title: Type of gene rna_type: $ref: '#/components/schemas/v2reportsRnaType' orientation: $ref: '#/components/schemas/v2reportsOrientation' title: Direction of the gene relative to the genome coordinates reference_standards: type: array items: $ref: '#/components/schemas/v2reportsGenomicRegion' genomic_regions: type: array items: $ref: '#/components/schemas/v2reportsGenomicRegion' chromosomes: type: array items: type: string nomenclature_authority: $ref: '#/components/schemas/v2reportsNomenclatureAuthority' swiss_prot_accessions: type: array items: type: string ensembl_gene_ids: type: array items: type: string omim_ids: type: array items: type: string synonyms: type: array items: type: string alternate_names: type: array items: type: string replaced_gene_id: type: string format: uint64 title: The NCBI Gene ID for the gene that was merged into the current gene record annotations: type: array items: $ref: '#/components/schemas/v2reportsAnnotation' transcript_count: type: integer title: Number of transcripts encoded by the gene protein_count: type: integer title: Number of proteins encoded by the gene transcript_type_counts: type: array items: $ref: '#/components/schemas/v2reportsTranscriptTypeCount' gene_groups: type: array items: $ref: '#/components/schemas/v2reportsGeneGroup' summary: type: array items: $ref: '#/components/schemas/v2reportsGeneSummary' gene_ontology: $ref: '#/components/schemas/v2reportsGeneOntology' locus_tag: type: string map_locations: type: array items: $ref: '#/components/schemas/v2reportsMapLocation' v2reportsErrorVirusErrorCode: type: string enum: - UNKNOWN_VIRUS_ERROR_CODE default: UNKNOWN_VIRUS_ERROR_CODE v2reportsGeneReportMatch: type: object properties: gene: $ref: '#/components/schemas/v2reportsGeneDescriptor' product: $ref: '#/components/schemas/v2reportsProductDescriptor' query: type: array items: type: string warnings: type: array items: $ref: '#/components/schemas/v2reportsWarning' warning: $ref: '#/components/schemas/v2reportsWarning' errors: type: array items: $ref: '#/components/schemas/v2reportsError' v2IncludeTabularHeader: type: string enum: - INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY - INCLUDE_TABULAR_HEADER_ALWAYS - INCLUDE_TABULAR_HEADER_NEVER default: INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY v2reportsErrorTaxonomyErrorCode: type: string enum: - UNKNOWN_TAXONOMY_ERROR_CODE - INVALID_TAXONOMY_TAXON default: UNKNOWN_TAXONOMY_ERROR_CODE v2reportsGeneDataReportPage: type: object properties: reports: type: array items: $ref: '#/components/schemas/v2reportsGeneReportMatch' messages: type: array items: $ref: '#/components/schemas/v2reportsMessage' total_count: type: integer title: The total count of available genes (ignoring the page_size parameter). next_page_token: type: string title: A token that can be sent as `page_token` to retrieve the next page. If this field is omitted, there are no subsequent pages. rpcStatus: type: object properties: code: type: integer format: int32 message: type: string details: type: array items: $ref: '#/components/schemas/protobufAny' v2reportsTranscriptSelectCategory: type: string enum: - SELECT_UNKNOWN - REFSEQ_SELECT - MANE_SELECT - MANE_PLUS_CLINICAL default: SELECT_UNKNOWN v2GeneDatasetReportsRequest: type: object properties: returned_content: $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType' title: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. gene_ids: type: array items: type: integer accessions: type: array items: type: string symbols_for_taxon: $ref: '#/components/schemas/v2GeneDatasetReportsRequestSymbolsForTaxon' taxon: type: string title: NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at locus_tags: type: array items: type: string table_fields: type: array items: type: string table_format: type: string title: '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`.' include_tabular_header: $ref: '#/components/schemas/v2IncludeTabularHeader' title: Specify when to include the table header when requesting a tabular report. page_size: type: integer title: 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. page_token: type: string title: 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. query: type: string title: Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name. types: type: array items: $ref: '#/components/schemas/v2GeneType' accession_filter: type: array items: type: string tax_search_subtree: type: boolean title: If true, include genes from taxonomic ranks below the requested taxon. sort: type: array items: $ref: '#/components/schemas/v2SortField' v2Fasta: type: string enum: - FASTA_UNSPECIFIED - FASTA_GENE - FASTA_RNA - FASTA_PROTEIN - FASTA_GENE_FLANK - FASTA_CDS - FASTA_5P_UTR - FASTA_3P_UTR default: FASTA_UNSPECIFIED v2reportsError: type: object properties: assembly_error_code: $ref: '#/components/schemas/v2reportsErrorAssemblyErrorCode' gene_error_code: $ref: '#/components/schemas/v2reportsErrorGeneErrorCode' organelle_error_code: $ref: '#/components/schemas/v2reportsErrorOrganelleErrorCode' virus_error_code: $ref: '#/components/schemas/v2reportsErrorVirusErrorCode' taxonomy_error_code: $ref: '#/components/schemas/v2reportsErrorTaxonomyErrorCode' reason: type: string message: type: string invalid_identifiers: type: array items: type: string v2GeneType: type: string enum: - UNKNOWN - tRNA - rRNA - snRNA - scRNA - snoRNA - PROTEIN_CODING - PSEUDO - TRANSPOSON - miscRNA - ncRNA - BIOLOGICAL_REGION - OTHER default: UNKNOWN title: 'NB: GeneType values match Entrez Gene' v2GeneDatasetReportsRequestSymbolsForTaxon: type: object properties: symbols: type: array items: type: string taxon: type: string title: NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol v2reportsProductDescriptor: type: object properties: gene_id: type: string format: uint64 title: NCBI Gene ID symbol: type: string title: gene symbol description: type: string title: gene name tax_id: type: string format: uint64 title: NCBI Taxonomy ID for the organism taxname: type: string title: Taxonomic name of the organism common_name: type: string title: Common name of the organism type: $ref: '#/components/schemas/v2reportsGeneType' title: Type of gene rna_type: $ref: '#/components/schemas/v2reportsRnaType' title: Type of RNA transcripts: type: array items: $ref: '#/components/schemas/v2reportsTranscript' transcript_count: type: integer title: Number of transcripts encoded by the gene protein_count: type: integer title: Number of proteins encoded by the gene transcript_type_counts: type: array items: $ref: '#/components/schemas/v2reportsTranscriptTypeCount' v2reportsGenomicLocation: type: object properties: genomic_accession_version: type: string sequence_name: type: string genomic_range: $ref: '#/components/schemas/v2reportsRange' exons: type: array items: $ref: '#/components/schemas/v2reportsRange' v2reportsGenomicRegion: type: object properties: gene_range: $ref: '#/components/schemas/v2reportsSeqRangeSet' title: The range of this Gene record on this genomic region. type: $ref: '#/components/schemas/v2reportsGenomicRegionGenomicRegionType' title: Type of genomic region v2reportsGenomicRegionGenomicRegionType: type: string enum: - UNKNOWN - REFSEQ_GENE - PSEUDOGENE - BIOLOGICAL_REGION - OTHER default: UNKNOWN v2GeneChromosomeSummaryReplyGeneChromosomeSummary: type: object properties: name: type: string count: type: integer accession: type: string v2GeneCountsByTaxonReplyGeneTypeAndCount: type: object properties: gene_type: type: string count: type: integer v2GeneDatasetReportsRequestContentType: type: string enum: - COMPLETE - IDS_ONLY - COUNTS_ONLY default: COMPLETE title: Specify a specific group of values to be returned for dataset reports. These options do not apply to product reports. v2reportsMaturePeptide: type: object properties: accession_version: type: string name: type: string length: type: integer v2DownloadSummaryHydrated: type: object properties: estimated_file_size_mb: type: integer url: type: string cli_download_command_line: type: string v2reportsNomenclatureAuthority: type: object properties: authority: type: string title: The nomenclature authority for this gene record identifier: type: string title: The nomenclature authority identifier for this gene record v2reportsMessage: type: object properties: error: $ref: '#/components/schemas/v2reportsError' warning: $ref: '#/components/schemas/v2reportsWarning' v2reportsSeqRangeSet: type: object properties: accession_version: type: string title: NCBI Accession.version of the sequence range: type: array items: $ref: '#/components/schemas/v2reportsRange' v2OrthologRequest: type: object properties: gene_id: type: integer title: One or more NCBI GeneIDs returned_content: $ref: '#/components/schemas/v2OrthologRequestContentType' title: Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts. taxon_filter: type: array items: type: string page_size: type: integer title: 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. page_token: type: string title: 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. v2reportsWarningGeneWarningCode: type: string enum: - UNKNOWN_GENE_WARNING_CODE - ACCESSION_VERSION_MISMATCH - REPLACED_GENE_ID - DISCONTINUED_GENE_ID - UNRECOGNIZED_GENE_ID - UNRECOGNIZED_GENE_SYMBOL - UNRECOGNIZED_ACCESSION - UNRECOGNIZED_TAX_TOKEN - NO_GENE_ANNOTATION_FOUND - ABOVE_SPECIES_TAXON default: UNKNOWN_GENE_WARNING_CODE v2reportsMapLocationMapType: type: string enum: - Unknown - Cytogenetic - Genetic default: Unknown v2reportsErrorOrganelleErrorCode: type: string enum: - UNKNOWN_ORGANELLE_ERROR_CODE - INVALID_ORGANELLE_TAXON - NO_ORGANELLES_FOR_ACCESSION default: UNKNOWN_ORGANELLE_ERROR_CODE v2reportsProtein: type: object properties: accession_version: type: string title: RefSeq protein accession with version name: type: string title: Protein name length: type: integer title: Protein length in amino acids isoform_name: type: string title: Protein isoform name ensembl_protein: type: string title: Ensembl protein accession with version mature_peptides: type: array items: $ref: '#/components/schemas/v2reportsMaturePeptide' v2reportsReference: type: object properties: pmids: type: array items: type: string format: uint64 v2reportsGeneGroup: type: object properties: id: type: string title: Gene group identifier, currently these only include gene ortholog sets method: type: string title: Method used to calculate the gene group, currently this only includes "NCBI Ortholog" v2reportsAnnotation: type: object properties: assembly_accession: type: string title: Genome assembly accession assembly_name: type: string title: Genome assembly name annotation_name: type: string title: Genome annotation name annotation_release_date: type: string title: Genome annotation release date genomic_locations: type: array items: $ref: '#/components/schemas/v2reportsGenomicLocation' v2GeneLinksReplyGeneLink: type: object properties: gene_id: type: integer title: The matching gene id gene_link_type: $ref: '#/components/schemas/v2GeneLinksReplyGeneLinkType' title: The type of link, e.g. gdv link or ortholog set resource_link: type: string title: A link to a gene resource resource_id: type: string title: A resource ID, provided if gene-id is not used for the link, e.g. the ortholog id. v2SortDirection: type: string enum: - SORT_DIRECTION_UNSPECIFIED - SORT_DIRECTION_ASCENDING - SORT_DIRECTION_DESCENDING default: SORT_DIRECTION_UNSPECIFIED protobufAny: type: object properties: type_url: type: string value: type: string format: byte v2GeneLinksRequest: type: object properties: gene_ids: type: array items: type: integer v2reportsWarningReplacedId: type: object properties: requested: type: string returned: type: string securitySchemes: ApiKeyAuth: type: apiKey in: query name: api_key ApiKeyAuthHeader: type: apiKey in: header name: api-key externalDocs: description: Interactively explore genome assembly datasets url: https://www.ncbi.nlm.nih.gov/datasets/genomes/