# ChEMBL Biotherapeutic Sequence Master (`nexgenwatch/chembl-biotherapeutic-sequence-master`) Actor

One structured record per ChEMBL biotherapeutic — the molecule id, the HELM notation, the biocomponent array, and the description. A master index over ChEMBL's ~23,849 biotherapeutics, keyed and deduplicated on molecule_chembl_id.

- **URL**: https://apify.com/nexgenwatch/chembl-biotherapeutic-sequence-master.md
- **Developed by:** [NexGen Watch](https://apify.com/nexgenwatch) (community)
- **Categories:** Automation, Lead generation, Developer tools
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $13.40 / 1,000 biotherapeutic records

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

Learn more: https://docs.apify.com/actors/running/actors-in-store.md#pay-per-event

## What's an Apify Actor?

An Actor is a serverless cloud program that runs on the Apify platform. It has two run modes.
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.

Apify vocabulary and the platform model are defined once, in the agent quickstart at https://apify.com/agents.md.

## 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.

Do not guess an integration path. Every one of them is in the agent quickstart at https://apify.com/agents.md: the Apify MCP server, Agent Skills with the Apify CLI, the JavaScript and Python clients, the REST API, and the account-free path for an agent with no human to sign in. It also carries the rule on stating cost before the first paid run.

For examples already wired to this Actor's own input schema, see the [API](#api) section below.

Each client library has reference documentation the quickstart does not restate: [JavaScript/TypeScript](https://docs.apify.com/api/client/js/docs.md) (`npm install apify-client`) and [Python](https://docs.apify.com/api/client/python/docs.md) (`pip install apify-client`).

# README

## 🔔 ChEMBL Biotherapeutic Sequence Master

One structured record per **ChEMBL biotherapeutic** — the molecule id, the HELM notation, the biocomponent
array, and the description. A master index over ChEMBL's ~23,849 biotherapeutics, keyed and deduplicated on
`molecule_chembl_id`. Built for biologics, sequence-informatics, and licensing teams who need ChEMBL's
biotherapeutic sequences as clean, verbatim facts.

**Differentiation:** the HELM notation and biocomponents array are carried **verbatim and never chemically
reinterpreted** — the HELM string is validated only as a non-empty string, the biocomponents only as a list,
and both are emitted exactly as ChEMBL publishes them (the array serialized as JSON). No sequence is parsed,
translated, canonicalised, or re-derived. Every row stamps the CC BY-SA share-alike notice.

Output is one `chembl_biotherapeutic` row per result; billing is pay-per-event, the value event being one biotherapeutic record (a $0.02 start fee per run, then $0.02 per biotherapeutic record). Source: www.ebi.ac.uk.

No login, no API key and no CAPTCHA solving are involved: the source is read logged-out with an identified contact User-Agent.

### 📊 Sample Output

[![ChEMBL Biotherapeutic Sequence Master sample output — a table of real biotherapeutic record rows (molecule_chembl_id, helm_notation, chembl_release, release_date) from run x3SMABwsbinT34XrY on build 0.1.5](https://api.apify.com/v2/key-value-stores/80Y7h3rmVN5CWK7Mw/records/chembl-biotherapeutic-sequence-master-sample)](https://apify.com/nexgenwatch/chembl-biotherapeutic-sequence-master?fpr=2ayu9b)

Real rows from run `x3SMABwsbinT34XrY` on build 0.1.5 (2026-09-19), the same input as the Quick start below — every value is as the source published it (emails masked, long text shortened):

| molecule_chembl_id | helm_notation | chembl_release | release_date | license | attribution |
|---|---|---|---|---|---|
| CHEMBL448105 | PEPTIDE1{A.L.Y.A.S.K.L.S.\[am]}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL266571 | PEPTIDE1{\[meR].K.P.W.\[Tle].L}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL268600 | PEPTIDE1{\[X833].\[dP].W.\[Tle].\[X454]}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL6562 | PEPTIDE1{\[X12].\[dP].W.\[Tle].\[X454]}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL380726 | PEPTIDE1{K.P.W.\[Tle].L}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL427604 | PEPTIDE1{\[X12].\[dP].W.I.L}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL265671 | PEPTIDE1{\[X500].\[dP].W.\[Tle].\[X454]}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |
| CHEMBL266306 | PEPTIDE1{K.F.Y.C.N.G.K.R.V.C.V.C.R.\[am]}$$$$ | ChEMBL_37 | ChEMBL_37 | CC BY-SA 3.0 | ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/) |

The run finished with the status message: `NORMAL: 50 unique rows (0 duplicates collapsed) from ChEMBL_37. billable=50`

### ✅ What you get

Each row is flat JSON with these fields (from the dataset schema and the sample run; a field the source does not publish for a given row is `null`):

- `record_type` (string/null) — e.g. `chembl_biotherapeutic`
- `molecule_chembl_id` (string/null) — e.g. `CHEMBL448105`
- `helm_notation` (string/null) — e.g. `PEPTIDE1{A.L.Y.A.S.K.L.S.[am]}$$$$`
- `helm_valid` (string/integer/boolean/null) — e.g. `True`
- `biocomponents` (string/null) — e.g. `[]`
- `component_count` (string/integer/boolean/null) — e.g. `0`
- `description` (string/null) — null in every sample row
- `chembl_release` (string/null) — e.g. `ChEMBL_37`
- `source` (string/null) — e.g. `chembl-biotherapeutic-sequence-master`
- `release_date` (string/null) — e.g. `ChEMBL_37`
- `source_url` (string/null) — e.g. `https://www.ebi.ac.uk/chembl/api/data/biotherapeutic.json`
- `observed_at` (string/null) — e.g. `2026-09-19T00:18:47Z`
- `license` (string/null) — e.g. `CC BY-SA 3.0`
- `attribution` (string/null) — e.g. `ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/)`
- `terminal` (string/null) — null in every sample row
- `reported_total` (string/integer/boolean/null) — null in every sample row
- `raw_seen` (string/integer/boolean/null) — null in every sample row
- `duplicates` (string/integer/boolean/null) — null in every sample row
- `unique_found` (string/integer/boolean/null) — null in every sample row
- `delivered` (string/integer/boolean/null) — null in every sample row
- `scope` (string/null) — null in every sample row
- `note` (string/null) — null in every sample row

**✅ What you get**

- `record_type` (string/null) — e.g. `chembl_biotherapeutic`
- `molecule_chembl_id` (string/null) — e.g. `CHEMBL448105`
- `helm_notation` (string/null) — e.g. `PEPTIDE1{A.L.Y.A.S.K.L.S.[am]}$$$$`
- `helm_valid` (string/integer/boolean/null) — e.g. `True`
- `biocomponents` (string/null) — e.g. `[]`
- `component_count` (string/integer/boolean/null) — e.g. `0`
- `description` (string/null) — null in every sample row
- `chembl_release` (string/null) — e.g. `ChEMBL_37`
- `source` (string/null) — e.g. `chembl-biotherapeutic-sequence-master`
- `release_date` (string/null) — e.g. `ChEMBL_37`
- `source_url` (string/null) — e.g. `https://www.ebi.ac.uk/chembl/api/data/biotherapeutic.json`
- `observed_at` (string/null) — e.g. `2026-09-18T23:24:09Z`
- `license` (string/null) — e.g. `CC BY-SA 3.0`
- `attribution` (string/null) — e.g. `ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/)`
- `terminal` (string/null) — null in every sample row
- `reported_total` (string/integer/boolean/null) — null in every sample row
- `raw_seen` (string/integer/boolean/null) — null in every sample row
- `duplicates` (string/integer/boolean/null) — null in every sample row
- `unique_found` (string/integer/boolean/null) — null in every sample row
- `delivered` (string/integer/boolean/null) — null in every sample row
- `scope` (string/null) — null in every sample row
- `note` (string/null) — null in every sample row

### ⚙️ Sample inputs

**1. Quick start — the Store example (this is what the sample above came from)**

```json
{
  "maxRecords": 50
}
```

The sample run charged exactly: 2 × $0.02 apify-actor-start + 50 × $0.02 biotherapeutic_record = **$1.04** on the Free tier — every delivered row was billed.

**2. A smaller, narrowed run**

```json
{
  "maxRecords": 5
}
```

Caps the run at 5 rows — about $0.12 on the Free tier ($0.02 start + 5 × $0.02).

**3. A full-size run**

```json
{
  "maxRecords": 23849
}
```

Up to 23849 rows (the schema default for `maxRecords`) — about $477.00 on the Free tier ($0.02 start + 23849 × $0.02) if the source has that many.

### 🧾 JSON sample record

One real record from run `x3SMABwsbinT34XrY`, exactly as it lands in the dataset (emails masked, long text shortened):

```json
{
  "record_type": "chembl_biotherapeutic",
  "molecule_chembl_id": "CHEMBL448105",
  "helm_notation": "PEPTIDE1{A.L.Y.A.S.K.L.S.[am]}$$$$",
  "helm_valid": true,
  "biocomponents": "[]",
  "component_count": 0,
  "description": null,
  "chembl_release": "ChEMBL_37",
  "source": "chembl-biotherapeutic-sequence-master",
  "release_date": "ChEMBL_37",
  "source_url": "https://www.ebi.ac.uk/chembl/api/data/biotherapeutic.json",
  "observed_at": "2026-09-19T00:18:47Z",
  "license": "CC BY-SA 3.0",
  "attribution": "ChEMBL / EMBL-EBI (https://www.ebi.ac.uk/chembl/)"
}
```

### 🔧 How it works

**Source.** The actor reads www.ebi.ac.uk — endpoints: `https://www.ebi.ac.uk`, `https://www.ebi.ac.uk/chembl/`, `https://www.ebi.ac.uk/chembl/api/data/biotherapeutic.json`. Public pages and feeds only; nothing behind a login.

**Transport.** Plain HTTPS from the Apify platform, no proxy. robots.txt is read first and a disallowed path is never fetched. Every request carries an identified contact User-Agent. Pacing: `CRAWL_DELAY`=10.0.

**Charging.** Each biotherapeutic record is charged at the moment it is pushed (`biotherapeutic_record`); a row that fails to charge is not delivered, so the dataset count always equals the charged count.

**🔧 How it works**

**Source**

The public, keyless ChEMBL REST API at EMBL-EBI — `https://www.ebi.ac.uk/chembl/api/data/biotherapeutic.json`,
paginated, serialized at a **10-second crawl delay**, no parallel fan-out. robots.txt on `www.ebi.ac.uk` is
honoured; the `/chembl` path is permitted.

**Fidelity**

`helm_notation` and `biocomponents` are reproduced exactly as ChEMBL publishes them; `helm_valid` and
`component_count` are structural flags only. Nothing about the sequence chemistry is inferred.

**Licence & attribution**

ChEMBL is released by EMBL-EBI under **Creative Commons Attribution-ShareAlike 3.0 (CC BY-SA 3.0)**:

- **Attribution:** ChEMBL / EMBL-EBI — https://www.ebi.ac.uk/chembl/
- **Release:** stamped per record (`chembl_release`).
- **ShareAlike:** redistribution or derivative works must be licensed under the same CC BY-SA 3.0.

Every record carries `license` = `CC BY-SA 3.0` and `attribution`.

**What is not done.** No login, no cookie or CAPTCHA bypass, no private or personal-account data, no browser automation.

### 💰 Pricing example

| Event | Free | Bronze | Silver | Gold |
|---|---|---|---|---|
| Actor Start (`apify-actor-start`) | $0.02 | $0.02 | $0.02 | $0.02 |
| Biotherapeutic Record (`biotherapeutic_record`) | $0.02 | $0.018 | $0.016 | $0.0134 |

Worked at the live Free-tier price:

- 8 biotherapeutic records: $0.02 start + 8 × $0.02 = **$0.18**
- 25 biotherapeutic records: $0.02 start + 25 × $0.02 = **$0.52**
- 100 biotherapeutic records: $0.02 start + 100 × $0.02 = **$2.02**

A run that delivers zero rows charges the $0.02 start fee only. A BLOCKED run (source refused) fails loud and charges no value event. The start fee is charged once per GB of run memory; the default run memory is 4096 MB.

Yield on the sample run: `NORMAL: 50 unique rows (0 duplicates collapsed) from ChEMBL_37. billable=50`. `maxRecords` is a hard ceiling on what is delivered and billed, never a target.

### ⚖️ Legal & ToS

This actor reads public, logged-out pages and feeds published by www.ebi.ac.uk. It collects only what the source publishes to any visitor, keeps to the source's robots rules (checked on every run), identifies itself with a contact User-Agent, and does not access accounts, private data or anything behind authentication. Use the output in line with the source's terms and your local law; the intended use is B2B research and monitoring.

### ❓ FAQ

**Q: Do I need an API key or a login?**\
A: No. The source (www.ebi.ac.uk) is read logged-out; the input schema has no key field and the actor carries no secrets.

**Q: Why did my run return 0 rows?**\
A: Read the run's status message. GENUINE_EMPTY means the source was read and had nothing in scope for your input; BLOCKED means the source refused and the run failed without billing a value event — retry later or narrow the input. A zero-row run bills the start fee only.

**Q: How many rows can one run return?**\
A: Up to `maxRecords` (default 23849). Raise the cap for a bigger run; you pay per delivered row.

**Q: How fresh is the data?**\
A: Every run reads the source live at run time; nothing is cached between runs. Put it on a schedule for a continuous feed.

**Q: What formats can I export?**\
A: The dataset downloads as JSON, CSV, Excel, XML or RSS from the run's Dataset tab or the Apify API, and any run can push to a webhook or integration.

**Q: How is this different from the other NexGen Watch actors actors?**\
A: Same output shape and billing model; this one covers www.ebi.ac.uk. The siblings under **Related Actors** cover the other sources or slices — run several on one schedule for a combined feed.

**Q: Are there rate limits?**\
A: The actor paces itself against the source (`CRAWL_DELAY`=10.0) and honours its robots rules; there is no per-buyer limit beyond your Apify plan's concurrency.

### 🆘 Troubleshooting

- **Run FAILED with BLOCKED** → the source refused the request or changed its page shape → nothing was billed beyond the start fee; retry after a while, and if it persists open an Issue with the run id.
- **Status says CAPPED** → your cap (`maxRecords`) was reached → raise it for a bigger run.
- **Input validation error on start** → a field is outside the schema's allowed values → start from the Quick start block and change one field at a time.
- **Run TIMED-OUT** → a very wide request on a slow day → raise the run timeout in Run options or narrow the input; what was delivered before the timeout is still in the dataset.

### 🔗 Related Actors

- [BTS T-100 Airport Traffic](https://apify.com/nexgenwatch/bts-t100-airport-traffic?fpr=2ayu9b) — Structured monthly airport traffic and capacity records from the U.S. DOT Bureau of Transportation Statistics (BTS) T-100 program, read directly from…
- [Bulk Email List Hygiene Check (Syntax · MX · Disposable · Role)](https://apify.com/nexgenwatch/bulk-email-list-verifier?fpr=2ayu9b) — Clean an email list before you send — one email_verification_check row per address, answered from syntax and DNS alone: is the address well-formed, d…
- [Census Address Geography Check](https://apify.com/nexgenwatch/census-address-geography-check?fpr=2ayu9b) — A definitive check: does this business/property address resolve to an official U.S. Census geography, and which one?
- [ChEMBL Clinical-Stage Indication Screen](https://apify.com/nexgenwatch/chembl-clinical-stage-indication-screen?fpr=2ayu9b) — One structured clinical compound record per molecule at or above the clinical phase you set — max_phase, first approval year, molecule type, route fl…
- [ChEMBL Source Document Index](https://apify.com/nexgenwatch/chembl-source-document-index?fpr=2ayu9b) — One structured record per ChEMBL source document — the document id, doc type, and the bibliographic identifiers (DOI, PubMed id, patent id, journal,…
- [ChEMBL Target Assay Definition Screener](https://apify.com/nexgenwatch/chembl-target-assay-definition-screener?fpr=2ayu9b) — One structured record per assay for the ChEMBL target(s) you name — the assay id, type and description, category, organism/tissue/cell, BAO format/la…
- 🏢 **About NexGenData** — NexGen Watch is NexGenData's fleet of more than 300 public data actors built on official sources, pay-per-result. Browse the catalog at [apify.com/nexgenwatch](https://apify.com/nexgenwatch?fpr=2ayu9b).

### ⭐ Found this useful?

If this actor saved you a manual check, a quick **[review on the Apify Store](https://apify.com/nexgenwatch/chembl-biotherapeutic-sequence-master?fpr=2ayu9b)** helps other teams find it. Feature request or a source that changed? Open it from the **Issues** tab — every one is read.

# Actor input Schema

## `moleculeIds` (type: `array`):

Restrict to these ChEMBL molecule ids. Empty = the full biotherapeutic master (~23,849).

## `maxRecords` (type: `integer`):

Max biotherapeutic records delivered (buyer bound; one charge per delivered record). The master holds ~23,849; serialized at a 10-second crawl delay.

## `userAgent` (type: `string`):

Override the transparent crawler UA.

## Actor input object example

```json
{
  "moleculeIds": [],
  "maxRecords": 50
}
```

# Actor output Schema

## `results` (type: `string`):

No description

# 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 = {
    "maxRecords": 50
};

// Run the Actor and wait for it to finish
const run = await client.actor("nexgenwatch/chembl-biotherapeutic-sequence-master").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 = { "maxRecords": 50 }

# Run the Actor and wait for it to finish
run = client.actor("nexgenwatch/chembl-biotherapeutic-sequence-master").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "maxRecords": 50
}' |
apify call nexgenwatch/chembl-biotherapeutic-sequence-master --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,nexgenwatch/chembl-biotherapeutic-sequence-master"
        }
    }
}
```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/oTWpxAclEK70aXWOk/builds/49GEnKtEaKO85OfhP/openapi.json