--- type: "firecrawl-provider" description: "NCBI Gene, the U.S. National Center for Biotechnology Information's database of genes across organisms: search genes by symbol, name or Entrez query; read one gene's official symbol and aliases, NCBI summary with who provided it, chromosome and genomic location, RefSeq and MANE Select transcripts, GeneRIF publications and UniProt, Ensembl, HGNC and OMIM cross-references; and list its orthologs in other species. Uses the NCBI Datasets v2 API and E-utilities anonymously. NCBI places no restrictions on the data; every output carries an attribution line and gene page URLs." use_when: "NCBI Gene, the U.S. National Center for Biotechnology Information's database of genes across organisms: search genes by symbol, name or Entrez query; read one gene's official symbol and aliases, NCBI summary with who provided it, chromosome and genomic location, RefSeq and MANE Select transcripts, GeneRIF publications and UniProt, Ensembl, HGNC and OMIM cross-references; and list its orthologs in other species. Uses the NCBI Datasets v2 API and E-utilities anonymously. NCBI places no restrictions on the data; every output carries an attribution line and gene page URLs." categories: "Health" capabilities: 3 credits_per_call: 5 --- # NCBI Gene on Firecrawl Alexandria NCBI Gene, the U.S. National Center for Biotechnology Information's database of genes across organisms: search genes by symbol, name or Entrez query; read one gene's official symbol and aliases, NCBI summary with who provided it, chromosome and genomic location, RefSeq and MANE Select transcripts, GeneRIF publications and UniProt, Ensembl, HGNC and OMIM cross-references; and list its orthologs in other species. Uses the NCBI Datasets v2 API and E-utilities anonymously. NCBI places no restrictions on the data; every output carries an attribution line and gene page URLs. - Categories: Health - Category index: [Health category](https://firecrawl.dev/alexandria/agents/categories/health) - Provider key: `gene-ncbi-nlm-nih-gov` - Access: Firecrawl credits - Cost: 5 credits per call ## More - [Human guide](https://firecrawl.dev/app/alexandria/gene-ncbi-nlm-nih-gov) - [OpenAPI spec](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/openapi.json) ## Capabilities - [Get](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/genes/get): One NCBI Gene record, by GeneID (`7157`), by official symbol or alias in an organism (`symbol`, with `organism` defaulting to human, 9606), or by an ncbi.nlm.nih.gov/gene URL: symbol, aliases and full name, NCBI summary with who provided it and when, chromosome and genomic locations, RefSeqGene, MANE/RefSeq Select and other RefSeq transcripts with Ensembl IDs, GeneRIF PubMed IDs, and UniProt, Ensembl, HGNC/MGI and OMIM IDs. `resolution` says how the input matched; replaced GeneIDs are followed and reported, and an alias several genes share returns `gene: null` with the `candidates`. Unknown, discontinued and wrong-organism inputs are `not_found`. - [Orthologs](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/genes/orthologs): Orthologs of one gene from NCBI's ortholog sets: give the gene as for `get` (`gene_id`, `symbol` with `organism`, or `url`) and optionally `taxa` (taxonomy IDs or names at any rank: `mouse`, `Danio rerio`, `rodents`) to keep only those organisms. Each ortholog is a gene row with GeneID, symbol, organism, location and cross-references, in NCBI's order; the set pages with `limit` and `offset`. A gene without orthologs, or none in the taxa, returns an empty list. - [Search](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/genes/search): Search NCBI Gene by symbol, name or Entrez query (`BRCA1`, `insulin receptor`, `kinase[Gene/Protein Name] AND 17[chr]`), optionally in one organism and of one gene type. Results come in Entrez relevance order, each with the GeneID, symbol, name, organism, location, aliases and UniProt, Ensembl, HGNC/MGI and OMIM IDs; an empty result is a valid empty page. ## 1. Choose this provider when NCBI Gene, the U.S. National Center for Biotechnology Information's database of genes across organisms: search genes by symbol, name or Entrez query; read one gene's official symbol and aliases, NCBI summary with who provided it, chromosome and genomic location, RefSeq and MANE Select transcripts, GeneRIF publications and UniProt, Ensembl, HGNC and OMIM cross-references; and list its orthologs in other species. Uses the NCBI Datasets v2 API and E-utilities anonymously. NCBI places no restrictions on the data; every output carries an attribution line and gene page URLs. ## 2. Minimal request Call `POST https://api.firecrawl.dev/v2/scrape` with `{ alexandria: { provider, capability, options } }`. For a batch, send `{ alexandria: [...] }` with up to 10 calls. ```json { "provider": "gene-ncbi-nlm-nih-gov", "capability": "genes/get", "options": { "gene_id": "7157" } } ``` ## 3. Add provider options Use only the options needed for the task: - `gene_id` (string): NCBI GeneID, e.g. `7157` or `GeneID:7157`. Example: `7157` - `organism` (string): Organism for `symbol`: NCBI taxonomy ID or name (`9606`, `human`, `Mus musculus`, `zebrafish`). Defaults to human (9606). Only with `symbol`. Example: `` - `symbol` (string): Official gene symbol or alias, case-insensitive, e.g. `TP53`, `p53`, `HER2`, `Trp53`. Looked up in `organism`. Example: `TP53` - `url` (string): NCBI Gene page URL, e.g. `https://www.ncbi.nlm.nih.gov/gene/7157` (also `/gene/?term=7157` and `/datasets/gene/7157/`). Example: `https://www.ncbi.nlm.nih.gov/gene/7157` ## 4. Request through your preferred interface ### JavaScript ```javascript const result = await firecrawl.scrape({ alexandria: { provider: "gene-ncbi-nlm-nih-gov", capability: "genes/get", options: { gene_id: "7157", }, }, }); ``` ### Python ```python result = firecrawl.scrape_alexandria({ "provider": "gene-ncbi-nlm-nih-gov", "capability": "genes/get", "options": { "gene_id": "7157" } }) ``` ### cURL ```sh curl https://api.firecrawl.dev/v2/scrape \ -H "Authorization: Bearer $FIRECRAWL_API_KEY" \ -H "Content-Type: application/json" \ -d '{ "alexandria": { "provider": "gene-ncbi-nlm-nih-gov", "capability": "genes/get", "options": { "gene_id": "7157" } } }' ``` ### CLI ```sh firecrawl scrape 'gene-ncbi-nlm-nih-gov/genes/get' \ --options '{"gene_id":"7157"}' ``` ### MCP Call the FCX MCP retrieve tool with this object: ```json { "provider": "gene-ncbi-nlm-nih-gov", "capability": "genes/get", "options": { "gene_id": "7157" } } ``` Ask for only the returned fields needed by the task. ## 5. Full request shape ```json { "provider": "gene-ncbi-nlm-nih-gov", "capability": "genes/get", "options": { "gene_id": "7157" } } ``` ## 6. Response data The response includes `success`, `provider`, `capability`, `creditsCost` and `data`. This example shows the provider payload in `data`: ```json { "candidates": [], "gene": { "aliases": [ "P53", "BCC7", "LFS1", "BMFS5", "TRP53" ], "chromosomes": [ "17" ], "ensembl_gene_ids": [ "ENSG00000141510" ], "gene_id": "7157", "generifs": { "count": 9982, "pmids": [ "39469578", "39454005", "39436667", "39390510", "39368467", "39324446", "39321806", "39312196", "39289671", "39283177", "39242607", "39207627", "39173856", "39148095", "39134014", "39126833", "39074355", "39062707", "39060302", "39018356" ] }, "genomic_locations": [ { "assembly": "GRCh38.p14", "assembly_accession": "GCF_000001405.40", "end": 7687490, "sequence_accession": "NC_000017.11", "sequence_name": "17", "start": 7668421, "strand": "minus" }, { "assembly": "T2T-CHM13v2.0", "assembly_accession": "GCF_009914755.1", "end": 7591594, "sequence_accession": "NC_060941.1", "sequence_name": "17", "start": 7572544, "strand": "minus" } ], "locus_tag": null, "map_location": "17p13.1", "name": "tumor protein p53", "nomenclature": { "authority": "HGNC", "id": "HGNC:11998" }, "omim_ids": [ "191170" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "other_names": [ "antigen NY-CO-13", "cellular tumor antigen p53", "mutant tumor protein 53", "phosphoprotein p53", "transformation-related protein 53", "tumor protein 53", "tumor supressor p53" ], "refseq": { "gene": "NG_017013.2", "protein_count": 25, "select_transcript": { "accession": "NM_000546.6", "ensembl_protein": "ENSP00000269305.4", "ensembl_transcript": "ENST00000269305.9", "name": "transcript variant 1", "protein": "NP_000537.3", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": "mane_select", "type": "protein_coding" }, "transcript_count": 26, "transcripts": [ { "accession": "NM_000546.6", "ensembl_protein": "ENSP00000269305.4", "ensembl_transcript": "ENST00000269305.9", "name": "transcript variant 1", "protein": "NP_000537.3", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": "mane_select", "type": "protein_coding" }, { "accession": "NM_001126112.3", "ensembl_protein": "ENSP00000391478.2", "ensembl_transcript": "ENST00000445888.7", "name": "transcript variant 2", "protein": "NP_001119584.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126113.3", "ensembl_protein": "ENSP00000398846.2", "ensembl_transcript": "ENST00000455263.7", "name": "transcript variant 4", "protein": "NP_001119585.1", "protein_name": "cellular tumor antigen p53 isoform c", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126114.3", "ensembl_protein": "ENSP00000391127.2", "ensembl_transcript": "ENST00000420246.7", "name": "transcript variant 3", "protein": "NP_001119586.1", "protein_name": "cellular tumor antigen p53 isoform b", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126115.2", "ensembl_protein": "ENSP00000481179.1", "ensembl_transcript": "ENST00000504937.5", "name": "transcript variant 5", "protein": "NP_001119587.1", "protein_name": "cellular tumor antigen p53 isoform d", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126116.2", "ensembl_protein": "ENSP00000478499.1", "ensembl_transcript": "ENST00000510385.5", "name": "transcript variant 6", "protein": "NP_001119588.1", "protein_name": "cellular tumor antigen p53 isoform e", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126117.2", "ensembl_protein": "ENSP00000484409.1", "ensembl_transcript": "ENST00000504290.5", "name": "transcript variant 7", "protein": "NP_001119589.1", "protein_name": "cellular tumor antigen p53 isoform f", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126118.2", "ensembl_protein": "ENSP00000478219.1", "ensembl_transcript": "ENST00000610292.4", "name": "transcript variant 8", "protein": "NP_001119590.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276695.3", "ensembl_protein": "ENSP00000480868.1", "ensembl_transcript": "ENST00000610538.4", "name": "transcript variant 4", "protein": "NP_001263624.1", "protein_name": "cellular tumor antigen p53 isoform h", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276696.3", "ensembl_protein": "ENSP00000482222.1", "ensembl_transcript": "ENST00000622645.4", "name": "transcript variant 3", "protein": "NP_001263625.1", "protein_name": "cellular tumor antigen p53 isoform i", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276697.3", "ensembl_protein": "ENSP00000484375.1", "ensembl_transcript": "ENST00000619186.4", "name": "transcript variant 5", "protein": "NP_001263626.1", "protein_name": "cellular tumor antigen p53 isoform j", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276698.3", "ensembl_protein": "ENSP00000481401.1", "ensembl_transcript": "ENST00000618944.4", "name": "transcript variant 6", "protein": "NP_001263627.1", "protein_name": "cellular tumor antigen p53 isoform k", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276699.3", "ensembl_protein": "ENSP00000477531.1", "ensembl_transcript": "ENST00000610623.4", "name": "transcript variant 7", "protein": "NP_001263628.1", "protein_name": "cellular tumor antigen p53 isoform l", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276760.3", "ensembl_protein": "ENSP00000481638.1", "ensembl_transcript": "ENST00000620739.4", "name": "transcript variant 1", "protein": "NP_001263689.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276761.3", "ensembl_protein": "ENSP00000482537.1", "ensembl_transcript": "ENST00000619485.4", "name": "transcript variant 2", "protein": "NP_001263690.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407262.1", "ensembl_protein": "ENSP00000426252.2", "ensembl_transcript": "ENST00000503591.3", "name": "transcript variant 9", "protein": "NP_001394191.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407263.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 9", "protein": "NP_001394192.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407264.1", "ensembl_protein": "ENSP00000593626.1", "ensembl_transcript": "ENST00000923567.2", "name": "transcript variant 10", "protein": "NP_001394193.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407265.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 10", "protein": "NP_001394194.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407266.1", "ensembl_protein": "ENSP00000424104.2", "ensembl_transcript": "ENST00000508793.6", "name": "transcript variant 11", "protein": "NP_001394195.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407267.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 11", "protein": "NP_001394196.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407268.1", "ensembl_protein": "ENSP00000352610.4", "ensembl_transcript": "ENST00000359597.8", "name": "transcript variant 12", "protein": "NP_001394197.1", "protein_name": "cellular tumor antigen p53 isoform b", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407269.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 12", "protein": "NP_001394198.1", "protein_name": "cellular tumor antigen p53 isoform i", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407270.1", "ensembl_protein": "ENSP00000745782.1", "ensembl_transcript": "ENST00001075976.1", "name": "transcript variant 13", "protein": "NP_001394199.1", "protein_name": "cellular tumor antigen p53 isoform b", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407271.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 13", "protein": "NP_001394200.1", "protein_name": "cellular tumor antigen p53 isoform i", "select_category": null, "type": "protein_coding" } ] }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/7157", "summary": { "date": "2016-12", "provided_by": "RefSeq", "text": "This gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoforms. Additional isoforms have also been shown to result from the use of alternate translation initiation codons from identical transcript variants (PMIDs: 12032546, 20937277). [provided by RefSeq, Dec 2016]" }, "symbol": "TP53", "type": "protein_coding", "uniprot_ids": [ "P04637" ] }, "license": { "attribution": "Data from NCBI Gene, National Center for Biotechnology Information, U.S. National Library of Medicine (https://www.ncbi.nlm.nih.gov/gene/).", "name": "Public domain (NCBI)", "url": "https://www.ncbi.nlm.nih.gov/home/about/policies/" }, "observed_at_ms": 1792529971704, "resolution": { "gene_id": "7157", "input": "7157", "matched_on": "gene_id", "note": null, "organism": null, "replaced_gene_id": null } } ``` ## API reference-derived contract The following capability contract is generated from the same normalized Alexandria API reference exposed in the API spec. ### Get - Capability: `genes/get` - Description: One NCBI Gene record, by GeneID (`7157`), by official symbol or alias in an organism (`symbol`, with `organism` defaulting to human, 9606), or by an ncbi.nlm.nih.gov/gene URL: symbol, aliases and full name, NCBI summary with who provided it and when, chromosome and genomic locations, RefSeqGene, MANE/RefSeq Select and other RefSeq transcripts with Ensembl IDs, GeneRIF PubMed IDs, and UniProt, Ensembl, HGNC/MGI and OMIM IDs. `resolution` says how the input matched; replaced GeneIDs are followed and reported, and an alias several genes share returns `gene: null` with the `candidates`. Unknown, discontinued and wrong-organism inputs are `not_found`. - Instructions: When you have a gene symbol, alias, GeneID or NCBI Gene URL and need what the gene is, where it lies, its canonical transcript, its curated literature, or its IDs in UniProt, Ensembl, HGNC and OMIM. - Cost: 5 credits per call - Capability file: [Get](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/genes/get) Accepted options: - `gene_id` (string): NCBI GeneID, e.g. `7157` or `GeneID:7157`. Example: `7157` - `organism` (string): Organism for `symbol`: NCBI taxonomy ID or name (`9606`, `human`, `Mus musculus`, `zebrafish`). Defaults to human (9606). Only with `symbol`. Example: `` - `symbol` (string): Official gene symbol or alias, case-insensitive, e.g. `TP53`, `p53`, `HER2`, `Trp53`. Looked up in `organism`. Example: `TP53` - `url` (string): NCBI Gene page URL, e.g. `https://www.ncbi.nlm.nih.gov/gene/7157` (also `/gene/?term=7157` and `/datasets/gene/7157/`). Example: `https://www.ncbi.nlm.nih.gov/gene/7157` Response schema example: ```json { "candidates": [], "gene": { "aliases": [ "P53", "BCC7", "LFS1", "BMFS5", "TRP53" ], "chromosomes": [ "17" ], "ensembl_gene_ids": [ "ENSG00000141510" ], "gene_id": "7157", "generifs": { "count": 9982, "pmids": [ "39469578", "39454005", "39436667", "39390510", "39368467", "39324446", "39321806", "39312196", "39289671", "39283177", "39242607", "39207627", "39173856", "39148095", "39134014", "39126833", "39074355", "39062707", "39060302", "39018356" ] }, "genomic_locations": [ { "assembly": "GRCh38.p14", "assembly_accession": "GCF_000001405.40", "end": 7687490, "sequence_accession": "NC_000017.11", "sequence_name": "17", "start": 7668421, "strand": "minus" }, { "assembly": "T2T-CHM13v2.0", "assembly_accession": "GCF_009914755.1", "end": 7591594, "sequence_accession": "NC_060941.1", "sequence_name": "17", "start": 7572544, "strand": "minus" } ], "locus_tag": null, "map_location": "17p13.1", "name": "tumor protein p53", "nomenclature": { "authority": "HGNC", "id": "HGNC:11998" }, "omim_ids": [ "191170" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "other_names": [ "antigen NY-CO-13", "cellular tumor antigen p53", "mutant tumor protein 53", "phosphoprotein p53", "transformation-related protein 53", "tumor protein 53", "tumor supressor p53" ], "refseq": { "gene": "NG_017013.2", "protein_count": 25, "select_transcript": { "accession": "NM_000546.6", "ensembl_protein": "ENSP00000269305.4", "ensembl_transcript": "ENST00000269305.9", "name": "transcript variant 1", "protein": "NP_000537.3", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": "mane_select", "type": "protein_coding" }, "transcript_count": 26, "transcripts": [ { "accession": "NM_000546.6", "ensembl_protein": "ENSP00000269305.4", "ensembl_transcript": "ENST00000269305.9", "name": "transcript variant 1", "protein": "NP_000537.3", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": "mane_select", "type": "protein_coding" }, { "accession": "NM_001126112.3", "ensembl_protein": "ENSP00000391478.2", "ensembl_transcript": "ENST00000445888.7", "name": "transcript variant 2", "protein": "NP_001119584.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126113.3", "ensembl_protein": "ENSP00000398846.2", "ensembl_transcript": "ENST00000455263.7", "name": "transcript variant 4", "protein": "NP_001119585.1", "protein_name": "cellular tumor antigen p53 isoform c", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126114.3", "ensembl_protein": "ENSP00000391127.2", "ensembl_transcript": "ENST00000420246.7", "name": "transcript variant 3", "protein": "NP_001119586.1", "protein_name": "cellular tumor antigen p53 isoform b", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126115.2", "ensembl_protein": "ENSP00000481179.1", "ensembl_transcript": "ENST00000504937.5", "name": "transcript variant 5", "protein": "NP_001119587.1", "protein_name": "cellular tumor antigen p53 isoform d", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126116.2", "ensembl_protein": "ENSP00000478499.1", "ensembl_transcript": "ENST00000510385.5", "name": "transcript variant 6", "protein": "NP_001119588.1", "protein_name": "cellular tumor antigen p53 isoform e", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126117.2", "ensembl_protein": "ENSP00000484409.1", "ensembl_transcript": "ENST00000504290.5", "name": "transcript variant 7", "protein": "NP_001119589.1", "protein_name": "cellular tumor antigen p53 isoform f", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001126118.2", "ensembl_protein": "ENSP00000478219.1", "ensembl_transcript": "ENST00000610292.4", "name": "transcript variant 8", "protein": "NP_001119590.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276695.3", "ensembl_protein": "ENSP00000480868.1", "ensembl_transcript": "ENST00000610538.4", "name": "transcript variant 4", "protein": "NP_001263624.1", "protein_name": "cellular tumor antigen p53 isoform h", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276696.3", "ensembl_protein": "ENSP00000482222.1", "ensembl_transcript": "ENST00000622645.4", "name": "transcript variant 3", "protein": "NP_001263625.1", "protein_name": "cellular tumor antigen p53 isoform i", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276697.3", "ensembl_protein": "ENSP00000484375.1", "ensembl_transcript": "ENST00000619186.4", "name": "transcript variant 5", "protein": "NP_001263626.1", "protein_name": "cellular tumor antigen p53 isoform j", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276698.3", "ensembl_protein": "ENSP00000481401.1", "ensembl_transcript": "ENST00000618944.4", "name": "transcript variant 6", "protein": "NP_001263627.1", "protein_name": "cellular tumor antigen p53 isoform k", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276699.3", "ensembl_protein": "ENSP00000477531.1", "ensembl_transcript": "ENST00000610623.4", "name": "transcript variant 7", "protein": "NP_001263628.1", "protein_name": "cellular tumor antigen p53 isoform l", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276760.3", "ensembl_protein": "ENSP00000481638.1", "ensembl_transcript": "ENST00000620739.4", "name": "transcript variant 1", "protein": "NP_001263689.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001276761.3", "ensembl_protein": "ENSP00000482537.1", "ensembl_transcript": "ENST00000619485.4", "name": "transcript variant 2", "protein": "NP_001263690.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407262.1", "ensembl_protein": "ENSP00000426252.2", "ensembl_transcript": "ENST00000503591.3", "name": "transcript variant 9", "protein": "NP_001394191.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407263.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 9", "protein": "NP_001394192.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407264.1", "ensembl_protein": "ENSP00000593626.1", "ensembl_transcript": "ENST00000923567.2", "name": "transcript variant 10", "protein": "NP_001394193.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407265.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 10", "protein": "NP_001394194.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407266.1", "ensembl_protein": "ENSP00000424104.2", "ensembl_transcript": "ENST00000508793.6", "name": "transcript variant 11", "protein": "NP_001394195.1", "protein_name": "cellular tumor antigen p53 isoform a", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407267.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 11", "protein": "NP_001394196.1", "protein_name": "cellular tumor antigen p53 isoform g", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407268.1", "ensembl_protein": "ENSP00000352610.4", "ensembl_transcript": "ENST00000359597.8", "name": "transcript variant 12", "protein": "NP_001394197.1", "protein_name": "cellular tumor antigen p53 isoform b", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407269.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 12", "protein": "NP_001394198.1", "protein_name": "cellular tumor antigen p53 isoform i", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407270.1", "ensembl_protein": "ENSP00000745782.1", "ensembl_transcript": "ENST00001075976.1", "name": "transcript variant 13", "protein": "NP_001394199.1", "protein_name": "cellular tumor antigen p53 isoform b", "select_category": null, "type": "protein_coding" }, { "accession": "NM_001407271.1", "ensembl_protein": null, "ensembl_transcript": null, "name": "transcript variant 13", "protein": "NP_001394200.1", "protein_name": "cellular tumor antigen p53 isoform i", "select_category": null, "type": "protein_coding" } ] }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/7157", "summary": { "date": "2016-12", "provided_by": "RefSeq", "text": "This gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoforms. Additional isoforms have also been shown to result from the use of alternate translation initiation codons from identical transcript variants (PMIDs: 12032546, 20937277). [provided by RefSeq, Dec 2016]" }, "symbol": "TP53", "type": "protein_coding", "uniprot_ids": [ "P04637" ] }, "license": { "attribution": "Data from NCBI Gene, National Center for Biotechnology Information, U.S. National Library of Medicine (https://www.ncbi.nlm.nih.gov/gene/).", "name": "Public domain (NCBI)", "url": "https://www.ncbi.nlm.nih.gov/home/about/policies/" }, "observed_at_ms": 1792529971704, "resolution": { "gene_id": "7157", "input": "7157", "matched_on": "gene_id", "note": null, "organism": null, "replaced_gene_id": null } } ``` ### Orthologs - Capability: `genes/orthologs` - Description: Orthologs of one gene from NCBI's ortholog sets: give the gene as for `get` (`gene_id`, `symbol` with `organism`, or `url`) and optionally `taxa` (taxonomy IDs or names at any rank: `mouse`, `Danio rerio`, `rodents`) to keep only those organisms. Each ortholog is a gene row with GeneID, symbol, organism, location and cross-references, in NCBI's order; the set pages with `limit` and `offset`. A gene without orthologs, or none in the taxa, returns an empty list. - Instructions: To find the mouse, rat, zebrafish or other species' counterpart of a gene, or which species share it. - Cost: 5 credits per call - Capability file: [Orthologs](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/genes/orthologs) Accepted options: - `gene_id` (string): NCBI GeneID, e.g. `7157` or `GeneID:7157`. Example: `7157` - `limit` (number): Orthologs per page. Example: `20` - `offset` (number): Zero-based index of the first ortholog; pass `next_offset` for the next page. Example: `0` - `organism` (string): Organism for `symbol`: NCBI taxonomy ID or name (`9606`, `human`, `Mus musculus`, `zebrafish`). Defaults to human (9606). Only with `symbol`. Example: `` - `symbol` (string): Official gene symbol or alias, case-insensitive, e.g. `TP53`, `p53`, `HER2`, `Trp53`. Looked up in `organism`. Example: `TP53` - `taxa` (string[]): Only orthologs in these organisms: NCBI taxonomy IDs or names at any rank, e.g. `["mouse", "zebrafish"]`, `["10090"]`, `["rodents"]`. Example: `["mouse","zebrafish"]` - `url` (string): NCBI Gene page URL, e.g. `https://www.ncbi.nlm.nih.gov/gene/7157` (also `/gene/?term=7157` and `/datasets/gene/7157/`). Example: `https://www.ncbi.nlm.nih.gov/gene/7157` Response schema example: ```json { "candidates": [], "gene": { "gene_id": "7157", "name": "tumor protein p53", "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/7157", "symbol": "TP53" }, "license": { "attribution": "Data from NCBI Gene, National Center for Biotechnology Information, U.S. National Library of Medicine (https://www.ncbi.nlm.nih.gov/gene/).", "name": "Public domain (NCBI)", "url": "https://www.ncbi.nlm.nih.gov/home/about/policies/" }, "limit": 20, "next_offset": null, "observed_at_ms": 1792529987246, "offset": 0, "orthologs": [ { "aliases": [ "bbl", "bfy", "bhy", "p44", "p53", "Tp53" ], "chromosomes": [ "11" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSMUSG00000059552" ], "gene_id": "22059", "map_location": "11 B3", "name": "transformation related protein 53", "nomenclature": { "authority": "MGI", "id": "MGI:98834" }, "omim_ids": [], "organism": { "common_name": "house mouse", "scientific_name": "Mus musculus", "taxon_id": 10090 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/22059", "status": "live", "symbol": "Trp53", "type": "protein_coding", "uniprot_ids": [ "P02340" ] }, { "aliases": [ "p53", "brp53", "drp53", "fb40d06", "wu:fb40d06", "zgc:111919", "etID22686.5" ], "chromosomes": [ "5" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSDARG00180036740" ], "gene_id": "30590", "map_location": null, "name": "tumor protein p53", "nomenclature": { "authority": "ZFIN", "id": "ZDB-GENE-990415-270" }, "omim_ids": [], "organism": { "common_name": "zebrafish", "scientific_name": "Danio rerio", "taxon_id": 7955 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/30590", "status": "live", "symbol": "tp53", "type": "protein_coding", "uniprot_ids": [ "P79734" ] } ], "resolution": { "gene_id": "7157", "input": "TP53", "matched_on": "symbol", "note": null, "organism": "9606", "replaced_gene_id": null }, "taxa": [ "mouse", "zebrafish" ], "total_count": 2 } ``` ### Search - Capability: `genes/search` - Description: Search NCBI Gene by symbol, name or Entrez query (`BRCA1`, `insulin receptor`, `kinase[Gene/Protein Name] AND 17[chr]`), optionally in one organism and of one gene type. Results come in Entrez relevance order, each with the GeneID, symbol, name, organism, location, aliases and UniProt, Ensembl, HGNC/MGI and OMIM IDs; an empty result is a valid empty page. - Instructions: To find genes from a name, keyword or partial symbol, or all genes matching a criterion. With a known symbol and organism, `get` resolves the gene directly. - Cost: 5 credits per call - Capability file: [Search](https://firecrawl.dev/alexandria/agents/providers/gene-ncbi-nlm-nih-gov/genes/search) Accepted options: - `gene_type` (string): Only genes of this type. Example: `protein_coding` - `include_discontinued` (boolean): Also list replaced and discontinued records (`status` says which; a replaced row names its `current_gene_id`). Default: current genes only. Example: `false` - `limit` (number): Results per page. Example: `10` - `offset` (number): Zero-based index of the first result; pass `next_offset` for the next page. Example: `0` - `organism` (string): Only genes of this organism: NCBI taxonomy ID (`9606`) or scientific or common name (`Homo sapiens`, `mouse`, `Danio rerio`). Without it, results span all organisms. Example: `9606` - `query` (string, required): Free text or Entrez Gene query syntax: a symbol (`BRCA1`), a name (`insulin receptor`), or fielded terms such as `CAP[sym]` (symbol or alias), `TP53[preferred symbol]`, `kinase[Gene/Protein Name]`, `17[chr]`, combined with AND, OR, NOT. Example: `BRCA1` Response schema example: ```json { "entrez_query": "(BRCA1) AND txid9606[orgn] AND genetype protein coding[Properties] AND alive[prop]", "gene_type": "protein_coding", "include_discontinued": false, "license": { "attribution": "Data from NCBI Gene, National Center for Biotechnology Information, U.S. National Library of Medicine (https://www.ncbi.nlm.nih.gov/gene/).", "name": "Public domain (NCBI)", "url": "https://www.ncbi.nlm.nih.gov/home/about/policies/" }, "limit": 5, "messages": [], "next_offset": 5, "observed_at_ms": 1792529961855, "offset": 0, "organism": "9606", "query": "BRCA1", "query_translation": "BRCA1[All Fields] AND txid9606[orgn] AND genetype protein coding[Properties] AND alive[prop]", "results": [ { "aliases": [ "IRIS", "PSCP", "BRCAI", "BRCC1", "FANCS", "PNCA4", "RNF53", "BROVCA1", "PPP1R53" ], "chromosomes": [ "17" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSG00000012048" ], "gene_id": "672", "map_location": "17q21.31", "name": "BRCA1 DNA repair associated", "nomenclature": { "authority": "HGNC", "id": "HGNC:1100" }, "omim_ids": [ "113705" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/672", "status": "live", "symbol": "BRCA1", "type": "protein_coding", "uniprot_ids": [ "P38398" ] }, { "aliases": [ "FAD", "FACD", "FAD1", "GLM3", "BRCC2", "FANCD", "PNCA2", "FANCD1", "XRCC11", "BROVCA2" ], "chromosomes": [ "13" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSG00000139618" ], "gene_id": "675", "map_location": "13q13.1", "name": "BRCA2 DNA repair associated", "nomenclature": { "authority": "HGNC", "id": "HGNC:1101" }, "omim_ids": [ "600185" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/675", "status": "live", "symbol": "BRCA2", "type": "protein_coding", "uniprot_ids": [ "P51587" ] }, { "aliases": [ "RECA", "BRCC5", "FANCR", "MRMV2", "HRAD51", "RAD51A", "HsRad51", "HsT16930" ], "chromosomes": [ "15" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSG00000051180" ], "gene_id": "5888", "map_location": "15q15.1", "name": "RAD51 recombinase", "nomenclature": { "authority": "HGNC", "id": "HGNC:9817" }, "omim_ids": [ "179617" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/5888", "status": "live", "symbol": "RAD51", "type": "protein_coding", "uniprot_ids": [ "Q06609" ] }, { "aliases": [], "chromosomes": [ "2" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSG00000138376" ], "gene_id": "580", "map_location": "2q35", "name": "BRCA1 associated RING domain 1", "nomenclature": { "authority": "HGNC", "id": "HGNC:952" }, "omim_ids": [ "601593" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/580", "status": "live", "symbol": "BARD1", "type": "protein_coding", "uniprot_ids": [ "Q99728" ] }, { "aliases": [ "UBM2", "UVM2", "KURIS", "TPDS1", "UCHL2", "hucep-6", "HUCEP-13" ], "chromosomes": [ "3" ], "current_gene_id": null, "ensembl_gene_ids": [ "ENSG00000163930" ], "gene_id": "8314", "map_location": "3p21.1", "name": "BRCA1 associated deubiquitinase 1", "nomenclature": { "authority": "HGNC", "id": "HGNC:950" }, "omim_ids": [ "603089" ], "organism": { "common_name": "human", "scientific_name": "Homo sapiens", "taxon_id": 9606 }, "source_url": "https://www.ncbi.nlm.nih.gov/gene/8314", "status": "live", "symbol": "BAP1", "type": "protein_coding", "uniprot_ids": [ "Q92560" ] } ], "source_url": "https://www.ncbi.nlm.nih.gov/gene/?term=%28BRCA1%29+AND+txid9606%5Borgn%5D+AND+genetype+protein+coding%5BProperties%5D+AND+alive%5Bprop%5D", "total_count": 1512 } ```