🔔 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

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)

{
  "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

{
  "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

{
  "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):

{
  "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 — 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) — 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 — A definitive check: does this business/property address resolve to an official U.S. Census geography, and which one?
• ChEMBL Clinical-Stage Indication Screen — 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 — 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 — 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.

⭐ Found this useful?

If this actor saved you a manual check, a quick review on the Apify Store helps other teams find it. Feature request or a source that changed? Open it from the Issues tab — every one is read.