# NCBI Gene Lookup — Genomics API for Pharma R\&D (`azureblue/ncbi-gene-scraper`) Actor Search NCBI Gene via E-utilities. Returns gene symbol, full name, chromosome location, map locus, aliases, OMIM ID, organism and functional summary. - **URL**: https://apify.com/azureblue/ncbi-gene-scraper.md - **Developed by:** [azureblue](https://apify.com/azureblue) (community) - **Categories:** Developer tools - **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, NaN bookmarks - **User rating**: No ratings yet ## Pricing $7.50 / 1,000 results This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events. Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event ## What's an Apify Actor? Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases. In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours, and optionally produces a well-defined JSON output, datasets with results, or files in key-value store. In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server. Actors are written with capital "A". ## How to integrate an Actor? If asked about integration, you help developers integrate Actors into their projects. You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready. The best way to integrate Actors is as follows. In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python.md): ```bash pip install apify-client ``` In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md): ````bash # MacOS / Linux curl -fsSL https://apify.com/install-cli.sh | bash # Windows irm https://apify.com/install-cli.ps1 | iex ```bash In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp.md). If your project is in a different language, use the [REST API](https://docs.apify.com/api/v2.md). For usage examples, see the [API](#api) section below. For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt). # README ## NCBI Gene Database Scraper Search the [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/) database via E-utilities. Returns structured gene records including symbol, full name, chromosome location, map locus, aliases, OMIM ID, and functional summary — for any organism. ### Features - E-utilities esearch + esummary pipeline (same infrastructure as PubMed) - Filter by organism (default: Homo sapiens, supports any NCBI taxonomy name) - Wildcard search: `BRCA*` matches BRCA1, BRCA2, etc. - Returns chromosomal coordinates (accession, start, stop, exon count) - Includes OMIM cross-reference where available - No API key required ### Input | Field | Type | Required | Default | Description | |-------|------|----------|---------|-------------| | `geneName` | string | ✅ | — | Gene symbol or name, e.g. `BRCA1` or `insulin receptor` | | `organism` | string | | `Homo sapiens` | Organism filter (NCBI taxonomy name) | | `maxResults` | integer | | 50 | Max gene records (1–5,000) | ### Output ```json { "geneId": "672", "symbol": "BRCA1", "fullName": "BRCA1 DNA repair associated", "chromosome": "17", "location": "17q21.31", "aliases": ["BRCAI", "BRCC1", "IRIS", "PNCA4", "RNF53"], "organism": "Homo sapiens", "summary": "This gene encodes a nuclear phosphoprotein that plays a role in maintaining genomic stability and acts as a tumor suppressor...", "omimId": "113705", "chrAccession": "NC_000017.11", "chrStart": 43044294, "chrStop": 43170245, "exonCount": 24, "url": "https://www.ncbi.nlm.nih.gov/gene/672" } ```` ### Use Cases #### 1. Cancer Gene Panel Annotation A molecular diagnostics company builds an annotation pipeline for a targeted NGS panel: they input 300 cancer-related gene names and retrieve chromosomal coordinates, OMIM IDs and functional descriptions for all of them in minutes. #### 2. Pharmacogenomics Database A research group building a drug-gene interaction database scrapes NCBI Gene for all genes involved in drug metabolism (e.g. `CYP*` wildcard) — getting aliases, chromosome locations and summaries as seed data. #### 3. Medical Genetics Education A genetics professor generates weekly problem sets by querying genes related to the lecture topic (e.g. `collagen`) and exporting the results as a structured dataset for students to analyze chromosomal distribution and disease associations. ### Data Source [NCBI Gene E-utilities API](https://www.ncbi.nlm.nih.gov/books/NBK25499/) — NCBI/NIH, no API key required (rate-limited at 3 req/sec). ### Pricing Pay-per-result. 100 genes ≈ $0.50–$1.00. # Actor input Schema ## `geneName` (type: `string`): Gene symbol or name to search. Example: 'BRCA1' or 'insulin receptor'. Use \* for wildcard: 'BRCA\*'. ## `organism` (type: `string`): Organism to filter results. Use NCBI taxonomy name. ## `maxResults` (type: `integer`): Maximum number of gene records to retrieve (1–5,000). ## Actor input object example ```json { "geneName": "BRCA1", "organism": "Homo sapiens", "maxResults": 50 } ``` # Actor output Schema ## `dataset` (type: `string`): Open the run's default dataset to view, filter and export the scraped items. # API You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup. ## JavaScript example ```javascript import { ApifyClient } from 'apify-client'; // Initialize the ApifyClient with your Apify API token // Replace the '' with your token const client = new ApifyClient({ token: '', }); // Prepare Actor input const input = { "geneName": "BRCA1" }; // Run the Actor and wait for it to finish const run = await client.actor("azureblue/ncbi-gene-scraper").call(input); // Fetch and print Actor results from the run's dataset (if any) console.log('Results from dataset'); console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`); const { items } = await client.dataset(run.defaultDatasetId).listItems(); items.forEach((item) => { console.dir(item); }); // 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs ``` ## Python example ```python from apify_client import ApifyClient # Initialize the ApifyClient with your Apify API token # Replace '' with your token. client = ApifyClient("") # Prepare the Actor input run_input = { "geneName": "BRCA1" } # Run the Actor and wait for it to finish run = client.actor("azureblue/ncbi-gene-scraper").call(run_input=run_input) # Fetch and print Actor results from the run's dataset (if there are any) print("💾 Check your data here: https://console.apify.com/storage/datasets/" + run["defaultDatasetId"]) for item in client.dataset(run["defaultDatasetId"]).iterate_items(): print(item) # 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start ``` ## CLI example ```bash echo '{ "geneName": "BRCA1" }' | apify call azureblue/ncbi-gene-scraper --silent --output-dataset ``` ## MCP server setup ```json { "mcpServers": { "apify": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=azureblue/ncbi-gene-scraper", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "NCBI Gene Lookup — Genomics API for Pharma R&D", "description": "Search NCBI Gene via E-utilities. Returns gene symbol, full name, chromosome location, map locus, aliases, OMIM ID, organism and functional summary.", "version": "1.0", "x-build-id": "YD1BWfidfOzfi9aKZ" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/azureblue~ncbi-gene-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-azureblue-ncbi-gene-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } }, "/acts/azureblue~ncbi-gene-scraper/runs": { "post": { "operationId": "runs-sync-azureblue-ncbi-gene-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor and returns information about the initiated run in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/runsResponseSchema" } } } } } } }, "/acts/azureblue~ncbi-gene-scraper/run-sync": { "post": { "operationId": "run-sync-azureblue-ncbi-gene-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } } }, "components": { "schemas": { "inputSchema": { "type": "object", "required": [ "geneName" ], "properties": { "geneName": { "title": "Gene Name or Symbol", "type": "string", "description": "Gene symbol or name to search. Example: 'BRCA1' or 'insulin receptor'. Use * for wildcard: 'BRCA*'." }, "organism": { "title": "Organism", "type": "string", "description": "Organism to filter results. Use NCBI taxonomy name.", "default": "Homo sapiens" }, "maxResults": { "title": "Maximum Results", "minimum": 1, "maximum": 5000, "type": "integer", "description": "Maximum number of gene records to retrieve (1–5,000).", "default": 50 } } }, "runsResponseSchema": { "type": "object", "properties": { "data": { "type": "object", "properties": { "id": { "type": "string" }, "actId": { "type": "string" }, "userId": { "type": "string" }, "startedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "finishedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "status": { "type": "string", "example": "READY" }, "meta": { "type": "object", "properties": { "origin": { "type": "string", "example": "API" }, "userAgent": { "type": "string" } } }, "stats": { "type": "object", "properties": { "inputBodyLen": { "type": "integer", "example": 2000 }, "rebootCount": { "type": "integer", "example": 0 }, "restartCount": { "type": "integer", "example": 0 }, "resurrectCount": { "type": "integer", "example": 0 }, "computeUnits": { "type": "integer", "example": 0 } } }, "options": { "type": "object", "properties": { "build": { "type": "string", "example": "latest" }, "timeoutSecs": { "type": "integer", "example": 300 }, "memoryMbytes": { "type": "integer", "example": 1024 }, "diskMbytes": { "type": "integer", "example": 2048 } } }, "buildId": { "type": "string" }, "defaultKeyValueStoreId": { "type": "string" }, "defaultDatasetId": { "type": "string" }, "defaultRequestQueueId": { "type": "string" }, "buildNumber": { "type": "string", "example": "1.0.0" }, "containerUrl": { "type": "string" }, "usage": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "integer", "example": 1 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } }, "usageTotalUsd": { "type": "number", "example": 0.00005 }, "usageUsd": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "number", "example": 0.00005 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } } } } } } } } } ```