CROssBAR Data API

Name: CROssBAR Data API API
Brand: CROssBAR Data API
Availability: InStock

✓ Official Vendor SpecHealthcareClinical Datanone13 EndpointsREST

For Agents

Query integrated biomedical reference data — ChEMBL molecules and assays, DrugBank drugs, UniProt human proteins, IntAct interactions, EFO and HPO ontologies, and PubChem bioassays and compounds — through one REST API.

Quickstart

Get started with CROssBAR Data API in minutes using your preferred integration method.

# Add to your MCP client config (Claude Desktop, Cursor, Windsurf)
{
  "jentic": {
    "url": "https://api.jentic.com/mcp",
    "auth": "oauth"
  }
}

# Then ask your agent:
"query ebi crossbar drug and protein data"

# → Jentic returns the GET /events tool with parameter schema, agent executes.

Capabilities

What an agent can do with CROssBAR Data API API.

Retrieve ChEMBL molecules, activities, and assays with their associated metadata

Look up DrugBank drug records with structure, indication, and identifier fields

Query UniProt human proteins via the proteins endpoint with selective taxonomy filters

Fetch EFO disease terms and HPO phenotype records for ontology mapping

GET STARTED

Start building with CROssBAR Data API API

Explore with Jentic

View OpenAPI Spec

Use for: Look up ChEMBL activities for a target of interest, Get DrugBank records for a list of drug names, Retrieve UniProt human protein data for selected accessions, Find EFO disease terms matching a search query

Not supported: Does not handle clinical trial enrolment, electronic health records, or patient-identifying data — use for read-only biomedical reference data from ChEMBL, DrugBank, UniProt, IntAct, EFO, HPO, and PubChem only.

The CROssBAR Data API from EMBL-EBI exposes integrated biomedical reference data drawn from ChEMBL, DrugBank, UniProt, IntAct, EFO, HPO, and PubChem behind a single REST surface. Researchers can query molecules, assays, activities, drugs, proteins, EFO disease terms, HPO phenotypes, IntAct molecular interactions, and PubChem bioassays, compounds, and substances. The API powers exploratory pipelines that need cross-database biomedical context without separate integrations for each underlying source.

Use Cases

Patterns agents use CROssBAR Data API API for, with concrete tasks.

★ Drug Discovery Knowledge Aggregation

Researchers building drug discovery pipelines need data spread across ChEMBL, DrugBank, UniProt, and PubChem. The CROssBAR Data API consolidates queries to those sources behind one base URL at www.ebi.ac.uk/Tools/crossbar, returning integrated records for molecules, drugs, proteins, and bioassays. This eliminates the need to maintain four separate clients and credentials for what is effectively one analysis.

Call GET /molecules, GET /drugs, and GET /proteins for a target of interest and merge the results into a single drug-target context object.

Disease and Phenotype Mapping

Translational research teams that need to map clinical concepts to standardised ontologies can query GET /efo for Experimental Factor Ontology disease terms and GET /hpo for Human Phenotype Ontology entries. The records include identifiers and labels that downstream tools use to link patient records to study cohorts and reference data.

Call GET /efo for a candidate disease label and GET /hpo for related phenotype concepts to build an ontology mapping.

Protein Interaction Context for Targets

When evaluating a candidate target, researchers want both the protein record and its known molecular interactions. The CROssBAR Data API exposes UniProt human proteins through GET /proteins and IntAct interactions through GET /intact, so a single integration can pull a target's sequence metadata and its interaction neighbourhood. This supports pathway and network analyses without bouncing between data portals.

Call GET /proteins for a UniProt accession then GET /intact for its known interactions and assemble the resulting graph.

PubChem Bioassay Cross-Reference

PubChem bioassays connect compounds and substances to biological readouts. The CROssBAR Data API exposes GET /pubchem/bioassays, GET /pubchem/bioassays/sids, GET /pubchem/compounds, and GET /pubchem/substances so an analysis can move from a bioassay to its substances and back to compound records inside one workflow. This is useful for hit-triage steps that need provenance from screen back to chemistry.

Call GET /pubchem/bioassays for an assay of interest then GET /pubchem/bioassays/sids for its substance IDs, and GET /pubchem/compounds for the linked compounds.

AI Agent Biomedical Research Assistant

An AI agent supporting a research team can use Jentic to discover CROssBAR endpoints and run multi-source queries on demand. Researchers ask the agent for a drug-target-disease summary and the agent stitches together calls to /molecules, /proteins, /drugs, /efo, and /intact to produce a single grounded answer with EBI-sourced data.

Through Jentic, search 'query ebi crossbar drug data', load the relevant operation schemas, and execute a chained query across /drugs, /proteins, and /intact for a chosen target.

Key Endpoints

13 endpoints — the crossbar data api from embl-ebi exposes integrated biomedical reference data drawn from chembl, drugbank, uniprot, intact, efo, hpo, and pubchem behind a single rest surface.

METHOD

PATH

DESCRIPTION

GET

/activities

Get ChEMBL activities

GET

/molecules

Get ChEMBL molecules

GET

/drugs

Get DrugBank drug records

GET

/proteins

Get UniProt human protein records

GET

/intact

Get IntAct molecular interactions

GET

/efo

Get EFO disease terms

GET

/hpo

Get HPO phenotype data

GET

/pubchem/bioassays

Get PubChem bioassays

GET

/activities

Get ChEMBL activities

GET

/molecules

Get ChEMBL molecules

GET

/drugs

Get DrugBank drug records

GET

/proteins

Get UniProt human protein records

GET

/intact

Get IntAct molecular interactions

GET

Why though Jentic?

Three things that make agents converge on Jentic-routed access.

Credential isolation

The CROssBAR Data API has no required credentials. Jentic still routes the call through its runtime so any future EBI rate-limit or token requirement can be added centrally without changing agent code.

Intent-based discovery

Agents search natural-language intents like 'look up chembl activities' or 'get uniprot human proteins' and Jentic returns the matching CROssBAR operation with its input schema, so the agent calls the right endpoint without reading EBI documentation.

Time to first call

Direct CROssBAR integration takes about a day to handle the per-resource query parameters and JSON shapes for each underlying source. Through Jentic the search-load-execute flow is under an hour.

Related APIs

Alternatives and complements available in the Jentic catalogue.

Complementary

Edamam Food Database API

Nutrition reference data for food research, complementing CROssBAR's drug and protein focus

Use Edamam when the research context shifts from drug-target biology to nutrition or dietary data.

Alternative

eBay Recommendation API

Unrelated commerce recommendations — listed only because it shares the 'recommendation' concept

Do not choose for biomedical work; use only if the task is e-commerce listing recommendations.

Complementary

Ediware API

Email campaign tools that researchers might pair with CROssBAR for stakeholder outreach

Use Ediware when the research workflow needs to notify or update collaborators about CROssBAR query results.

FAQs

Specific to using CROssBAR Data API API through Jentic.

What authentication does the CROssBAR Data API use?

The CROssBAR Data API spec defines no security schemes — endpoints are public over HTTPS at www.ebi.ac.uk/Tools/crossbar. Through Jentic, calls run from Jentic's runtime so any IP-based fair-use throttling at EBI is centralised rather than scattered across agent processes.

Which biomedical sources does the CROssBAR Data API expose?

It integrates ChEMBL (activities, assays, molecules), DrugBank (drugs), UniProt (human proteins), IntAct (molecular interactions), EFO (disease terms), HPO (phenotypes), and PubChem (bioassays, compounds, substances) behind a single REST surface.

What are the rate limits for the CROssBAR Data API?

The OpenAPI spec does not declare rate limits. EMBL-EBI services apply general fair-use throttling at the infrastructure level for high-volume callers. Batch queries by passing larger ID lists per call to reduce request count.

Can I query DrugBank and UniProt in a single workflow with the CROssBAR Data API?

Yes. GET /drugs returns DrugBank records and GET /proteins returns UniProt human protein data, so an agent can call both in one workflow against the same base URL without separate credentials.

How do I query CROssBAR through Jentic?

Search 'query ebi crossbar' in Jentic, load the operation schema for the resource you need (for example GET /molecules or GET /intact), and execute it with the target identifiers. Jentic returns the EBI response payload.

Does the CROssBAR Data API cover non-human proteins?

The proteins endpoint description states it returns proteins collected from UniProt for selected human taxonomy IDs. Non-human protein coverage is not exposed in this spec.