# iCite NIH Research Publications Scraper (`crawlerbros/icite-scraper`) Actor

Scrape NIH iCite - search PubMed biomedical publications, fetch by PubMed IDs, or browse by year. Returns citation counts, relative citation ratios, abstracts, DOIs, and full PubMed links.

- **URL**: https://apify.com/crawlerbros/icite-scraper.md
- **Developed by:** [Crawler Bros](https://apify.com/crawlerbros) (community)
- **Categories:** Agents, Developer tools, Automation
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, NaN bookmarks
- **User rating**: No ratings yet

## Pricing

from $3.00 / 1,000 results

This Actor is paid per event and usage. You are charged both the fixed price for specific events and for Apify platform usage.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

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

## iCite NIH Research Publications Scraper

Extract biomedical research publications from the [NIH iCite database](https://icite.od.nih.gov/) — the authoritative source for PubMed citation metrics used by the National Institutes of Health. Search by keyword, retrieve specific papers by PubMed ID, or browse publications by year. Every record includes citation counts, relative citation ratios, DOIs, abstracts, and direct PubMed links.

### What You Can Do

- **Search publications** — find research papers matching any keyword or phrase (e.g., "CRISPR", "machine learning", "COVID-19 vaccine")
- **Lookup by PubMed ID** — retrieve specific papers using their PMID numbers
- **Browse by year** — collect all publications from a given year or date range
- **Filter by year** — narrow search results to a specific publication period

### Input

| Field | Type | Description |
|---|---|---|
| **Mode** | Select | `searchPublications`, `getByPmids`, or `browseByYear` |
| **Search query** | Text | Keyword or phrase (required for `searchPublications`) |
| **PubMed IDs** | JSON array | List of PubMed IDs to look up (required for `getByPmids`) |
| **Year from** | Integer | Earliest publication year (required for `browseByYear`, optional filter for other modes) |
| **Year to** | Integer | Latest publication year (optional) |
| **Max items** | Integer | Cap on total records returned (1–1000, default 20) |

#### Example Inputs

**Search for machine learning papers:**
```json
{
  "mode": "searchPublications",
  "query": "machine learning",
  "maxItems": 50
}
````

**Retrieve specific papers by PubMed ID:**

```json
{
  "mode": "getByPmids",
  "pmids": [28212749, 30049766, 32907876],
  "maxItems": 100
}
```

**Browse publications from a specific year:**

```json
{
  "mode": "browseByYear",
  "yearFrom": 2022,
  "yearTo": 2023,
  "maxItems": 200
}
```

### Output

Each record represents one biomedical research publication:

| Field | Type | Description |
|---|---|---|
| `pmid` | Integer | PubMed ID (unique identifier) |
| `pubmedUrl` | String | Direct link to the paper on PubMed |
| `doi` | String | Digital Object Identifier (when available) |
| `title` | String | Full publication title |
| `authors` | Array of strings | Author names |
| `year` | Integer | Publication year |
| `journal` | String | Journal name |
| `citationCount` | Integer | Number of times this paper has been cited |
| `referencesCount` | Integer | Number of references in this paper |
| `relativeCitationRatio` | Float | NIH field-normalized citation metric (1.0 = average) |
| `isResearchArticle` | Boolean | Whether classified as a primary research article |
| `abstract` | String | Publication abstract (when available) |
| `scrapedAt` | String | ISO 8601 timestamp of when the record was scraped |

#### Example Output Record

```json
{
  "pmid": 28212749,
  "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/28212749/",
  "doi": "10.1038/nature21349",
  "title": "A deep learning approach to antibiotic discovery",
  "authors": ["Stokes JM", "Yang K", "Swanson K"],
  "year": 2020,
  "journal": "Cell",
  "citationCount": 1842,
  "referencesCount": 56,
  "relativeCitationRatio": 28.4,
  "isResearchArticle": true,
  "abstract": "Due to the rapid emergence of antibiotic-resistant bacteria...",
  "scrapedAt": "2024-01-15T10:30:00+00:00"
}
```

### Data Source

Data is sourced from the **NIH iCite API** (`https://icite.od.nih.gov/api/pubs`), a free public API maintained by the National Institutes of Health with no authentication required. iCite provides citation metrics for all articles indexed in PubMed — over 35 million biomedical publications.

### Use Cases

- **Literature reviews** — systematically collect papers on a research topic
- **Citation analysis** — identify highly cited papers using the Relative Citation Ratio (RCR)
- **Research trend analysis** — track publication volume and impact over time
- **Academic research** — build datasets for scientometric studies
- **Grant writing** — find and cite relevant prior art efficiently

### FAQs

**Is this API free to use?**
Yes. The NIH iCite API is a public, open-access service with no API key required.

**How many records can I retrieve?**
Up to 1,000 records per run using the `maxItems` setting. For larger datasets, run the actor multiple times with different year ranges or queries.

**What is the Relative Citation Ratio (RCR)?**
RCR is a field-normalized citation metric developed by NIH. A value of 1.0 means the paper is cited at the average rate for its field. Papers with RCR > 2.0 are considered highly impactful.

**Are all PubMed articles available?**
The iCite database covers the majority of PubMed articles with citation data. Some very recent or specialized articles may not yet have citation metrics.

**Can I search for a specific author?**
Use `mode=searchPublications` with a query like `"author name"` or search by a known PubMed ID.

**How current is the data?**
NIH updates iCite citation metrics weekly.

# Actor input Schema

## `mode` (type: `string`):

Which data-collection mode to run.

## `query` (type: `string`):

Keyword or phrase to search (mode=searchPublications). Example: `machine learning`, `CRISPR gene therapy`.

## `pmids` (type: `array`):

List of PubMed IDs (integers or strings) to look up directly. Example: `[1234567, 9876543]`.

## `yearFrom` (type: `integer`):

Include only publications from this year onward. Required for mode=browseByYear.

## `yearTo` (type: `integer`):

Include only publications up to this year (inclusive). Optional — defaults to the same as yearFrom if omitted in browseByYear mode.

## `maxItems` (type: `integer`):

Maximum number of records to emit (1–1000).

## Actor input object example

```json
{
  "mode": "searchPublications",
  "query": "machine learning",
  "pmids": [],
  "maxItems": 20
}
```

# Actor output Schema

## `publications` (type: `string`):

Dataset containing all scraped NIH iCite research publications.

# 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 '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "mode": "searchPublications",
    "query": "machine learning",
    "pmids": [],
    "maxItems": 20
};

// Run the Actor and wait for it to finish
const run = await client.actor("crawlerbros/icite-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 '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "mode": "searchPublications",
    "query": "machine learning",
    "pmids": [],
    "maxItems": 20,
}

# Run the Actor and wait for it to finish
run = client.actor("crawlerbros/icite-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 '{
  "mode": "searchPublications",
  "query": "machine learning",
  "pmids": [],
  "maxItems": 20
}' |
apify call crawlerbros/icite-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "command": "npx",
            "args": [
                "mcp-remote",
                "https://mcp.apify.com/?tools=crawlerbros/icite-scraper",
                "--header",
                "Authorization: Bearer <YOUR_API_TOKEN>"
            ]
        }
    }
}

```

## OpenAPI specification

```json
{
    "openapi": "3.0.1",
    "info": {
        "title": "iCite NIH Research Publications Scraper",
        "description": "Scrape NIH iCite - search PubMed biomedical publications, fetch by PubMed IDs, or browse by year. Returns citation counts, relative citation ratios, abstracts, DOIs, and full PubMed links.",
        "version": "1.0",
        "x-build-id": "GzHEEAAgkWb3RDhBQ"
    },
    "servers": [
        {
            "url": "https://api.apify.com/v2"
        }
    ],
    "paths": {
        "/acts/crawlerbros~icite-scraper/run-sync-get-dataset-items": {
            "post": {
                "operationId": "run-sync-get-dataset-items-crawlerbros-icite-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": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK"
                    }
                }
            }
        },
        "/acts/crawlerbros~icite-scraper/runs": {
            "post": {
                "operationId": "runs-sync-crawlerbros-icite-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor and returns information about the initiated run in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$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": {
                                    "$ref": "#/components/schemas/runsResponseSchema"
                                }
                            }
                        }
                    }
                }
            }
        },
        "/acts/crawlerbros~icite-scraper/run-sync": {
            "post": {
                "operationId": "run-sync-crawlerbros-icite-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$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": [
                    "mode"
                ],
                "properties": {
                    "mode": {
                        "title": "Mode",
                        "enum": [
                            "searchPublications",
                            "getByPmids",
                            "browseByYear"
                        ],
                        "type": "string",
                        "description": "Which data-collection mode to run.",
                        "default": "searchPublications"
                    },
                    "query": {
                        "title": "Search query",
                        "type": "string",
                        "description": "Keyword or phrase to search (mode=searchPublications). Example: `machine learning`, `CRISPR gene therapy`.",
                        "default": "machine learning"
                    },
                    "pmids": {
                        "title": "PubMed IDs (mode=getByPmids)",
                        "type": "array",
                        "description": "List of PubMed IDs (integers or strings) to look up directly. Example: `[1234567, 9876543]`.",
                        "default": []
                    },
                    "yearFrom": {
                        "title": "Year from",
                        "minimum": 1900,
                        "maximum": 2100,
                        "type": "integer",
                        "description": "Include only publications from this year onward. Required for mode=browseByYear."
                    },
                    "yearTo": {
                        "title": "Year to",
                        "minimum": 1900,
                        "maximum": 2100,
                        "type": "integer",
                        "description": "Include only publications up to this year (inclusive). Optional — defaults to the same as yearFrom if omitted in browseByYear mode."
                    },
                    "maxItems": {
                        "title": "Max items",
                        "minimum": 1,
                        "maximum": 1000,
                        "type": "integer",
                        "description": "Maximum number of records to emit (1–1000).",
                        "default": 20
                    }
                }
            },
            "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
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }
}
```