Ncbi Nlm Nih Gov NCBI Datasets API
★ Only Publicly Available OpenAPI DocumentHealthcareClinical DataapiKey107 EndpointsREST
For Agents
Look up genomes, genes, taxonomy, viruses, and BioSample records from NCBI by accession, taxon, or BioProject, and retrieve curated data reports and download summaries.
Use for: I need to fetch a genome assembly report for accession GCF_000001405.40, Retrieve taxonomy details for the species Homo sapiens, Search for SARS-CoV-2 sequences updated in the last 30 days, Get a download summary of a genome data package by taxon
Not supported: Does not handle clinical patient records, sequence read storage, or PubMed literature search — use for genome, gene, taxonomy, and BioSample reference data only.
Jentic publishes the only available OpenAPI specification for NCBI Datasets API, keeping it validated and agent-ready. The NCBI Datasets v2 API provides programmatic access to genome assemblies, gene records, taxonomy, BioSample metadata, prokaryote and virus sequence collections, and organelle datasets curated by the National Center for Biotechnology Information. Researchers, bioinformaticians, and AI agents use it to fetch data reports, sequence reports, and downloadable data packages by accession, taxon, BioProject, or BioSample identifier across 107 endpoints.
Install Jentic One Beta
Connect the NCBI Datasets API to your agent
Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the NCBI Datasets API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.
Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.
1
Step 1: Jentic One Host machine
# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh2
Step 2: Agent machine
# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register # connects your agent to your Jentic One instanceJentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.
Capabilities
What an agent can do with NCBI Datasets API.
Retrieve genome assembly reports by accession, taxon, BioProject, or BioSample identifier
Fetch gene metadata and sequence reports for vertebrate and prokaryote organisms
Look up taxonomy lineage and link nodes between species and higher ranks
Search virus and SARS-CoV-2 sequence collections with annotation details
Generate download summaries and assembly links for bulk data packages
Query BioSample records and resolve accession-to-assembly relationships
Use Cases
Patterns agents use NCBI Datasets API for, with concrete tasks.
★ Genome Assembly Lookup by Accession
Bioinformatics pipelines query the NCBI Datasets API to fetch genome assembly reports by accession (e.g., GCF_000001405.40 for the human reference). The API returns assembly statistics, organism metadata, sequence reports, and download links in a single structured response. Replaces multiple Entrez calls with one v2 endpoint.
Call GET /genome/accession/{accessions}/dataset_report with accession GCF_000001405.40 and parse the assembly statistics
Taxonomy and Gene Cross-Reference
Agents and analysis scripts resolve taxonomy IDs to genome and gene records to support comparative genomics workflows. The NCBI Datasets API exposes taxonomy nodes, lineage queries, and cross-references to genes and BioSamples without requiring a local NCBI mirror. Useful for researchers building species-level dashboards.
Resolve taxon 9606 via the taxonomy endpoints, then call GET /genome/taxon/{taxons}/dataset_report to retrieve human genome assemblies
Virus and Pathogen Surveillance
Public health and research teams pull virus sequence records — including SARS-CoV-2 — from NCBI to track variants, sample collection dates, and submitter metadata. The Datasets API provides structured virus queries with annotation context, replacing manual NCBI website searches and enabling pipelines to refresh on a schedule.
Search the virus endpoints for SARS-CoV-2 records updated since 2026-05-01 and download the resulting accessions
Agent-Driven Genomics Q&A
An AI agent invoked by a researcher answers questions like 'what is the assembly size of the latest mouse reference genome?' by searching Jentic for the right NCBI Datasets operation, loading the schema, and executing the call. Removes the need for the agent to learn NCBI's URL conventions or argument ordering.
Search Jentic for 'fetch mouse genome assembly report' and execute the resolved GET endpoint, returning assembly size to the user
Key Endpoints
107 endpoints — jentic publishes the only available openapi specification for ncbi datasets api, keeping it validated and agent-ready.
METHOD
PATH
DESCRIPTION
GET
/genome/accession/{accessions}/dataset_report
Get genome assembly report by accession
GET
/genome/taxon/{taxons}/dataset_report
Get genome assembly reports by taxon
GET
/genome/accession/{accessions}/download_summary
Preview a genome data package download
GET
/genome/bioproject/{bioprojects}/dataset_report
Get assemblies by BioProject
GET
/genome/biosample/{biosample_ids}/dataset_report
Get assemblies by BioSample
GET
/genome/sequence_accession/{accession}/sequence_assemblies
Resolve sequence accession to assemblies
GET
/genome/accession/{accessions}/dataset_report
Get genome assembly report by accession
GET
/genome/taxon/{taxons}/dataset_report
Get genome assembly reports by taxon
GET
/genome/accession/{accessions}/download_summary
Preview a genome data package download
GET
/genome/bioproject/{bioprojects}/dataset_report
Get assemblies by BioProject
GET
/genome/biosample/{biosample_ids}/dataset_report
Get assemblies by BioSample
GET
/genome/sequence_accession/{accession}/sequence_assemblies
Resolve sequence accession to assemblies
Why Jentic?
Three things that make agents converge on Jentic-routed access.
Credential isolation
The optional NCBI `api-key` header is stored encrypted in the Jentic vault. Agents receive scoped execution tokens — the raw key never enters the agent's context. Unauthenticated calls also work for low-volume use.
Intent-based discovery
Agents search by intent (e.g., 'fetch genome assembly by taxon') and Jentic returns the right NCBI Datasets endpoint with its schema, so the agent can call /genome/taxon/{taxons}/dataset_report without browsing 107 paths.
Time to first call
Direct NCBI Datasets integration: 1-3 days to learn accession patterns, parameter conventions, and large-result pagination. Through Jentic: under 1 hour — search, load schema, execute.
Related APIs
Alternatives and complements available in the Jentic catalogue.
FAQs
Specific to using NCBI Datasets API through Jentic.
Why is there no official OpenAPI spec for NCBI Datasets API?
NCBI does not publish an OpenAPI specification. Jentic generates and maintains this spec so that AI agents and developers can call NCBI Datasets API via structured tooling. It is validated against the live API and kept up to date. Get started at https://app.jentic.com/sign-up.
What authentication does the NCBI Datasets API use?
NCBI Datasets accepts an optional `api-key` header (or `api_key` query parameter) that raises rate limits from 3 requests/second to 10 requests/second. Jentic stores the key in the encrypted vault when supplied; unauthenticated calls also work for low-volume use.
Can I download bulk genome data with this API?
The /genome/.../download_summary endpoints return a preview with the size and contents of a data package. Actual download bytes are streamed from the NCBI download service URL returned in the response — the API itself returns metadata and links, not raw FASTA bytes.
What are the rate limits for the NCBI Datasets API?
NCBI applies 3 requests/second without a key and 10 requests/second with a registered API key. Heavy taxonomy or BioProject batches should use POST endpoints (e.g., POST /genome/dataset_report) which accept arrays of accessions in one call.
How do I look up a genome assembly through Jentic?
Search Jentic for 'fetch genome assembly report by accession', load the schema for GET /genome/accession/{accessions}/dataset_report, and execute it with the desired accession. The agent receives the structured assembly report directly.
Is the NCBI Datasets API free?
Yes. NCBI Datasets is funded by the U.S. National Library of Medicine and is free to use. Registering for an API key only changes rate limits, not pricing.
GET STARTED