BioSamples Series¶

NCBI BioProject records describe the umbrella study or research effort, while BioSample records describe the individual biological materials used in that study. A typical workflow starts from a BioProject accession, finds the linked BioSamples, and then follows those samples to related sequencing runs, assemblies, or other submitted data.

Connections to Sequencing Databases¶

BioProject and BioSample accessions act as shared metadata anchors across many sequence and expression repositories. The BioProject groups the overall study, and each BioSample records the biological source material for one or more experiments. Other databases then attach their own records to those same study and sample identifiers.

In NCBI SRA, sequencing records usually sit below BioSample and BioProject metadata. A BioProject can contain many BioSamples, each BioSample can have one or more SRA experiments, and each experiment can have one or more sequencing runs. This lets a user start with a study accession such as PRJNA..., find the sample accessions such as SAMN..., and then locate the raw read accessions such as SRR..., SRX..., or SRS....

GEO is often used for expression studies, including RNA-seq and array-based experiments. GEO records have their own accessions, such as series (GSE...), samples (GSM...), and platforms (GPL...). For sequencing-based GEO studies, the GEO series or samples may link out to SRA records, and those SRA records may then link back to the relevant BioProject and BioSample records. In practice, GEO often describes the experimental design and processed expression data, while SRA stores the raw sequencing reads.

ENA is the European nucleotide archive and exchanges many sequence records with NCBI through the International Nucleotide Sequence Database Collaboration. ENA uses accessions such as PRJEB... for projects, SAMEA... for samples, ERX... for experiments, and ERR... for runs. These often correspond to the same conceptual levels as NCBI BioProject, BioSample, SRA experiment, and SRA run records, even when the accession prefixes differ.

ArrayExpress, now closely connected with functional genomics data resources at EMBL-EBI, is similar to GEO in that it describes expression experiments and their processed metadata. ArrayExpress studies may point to ENA run or experiment records for raw sequencing data, while array-based studies may remain primarily within ArrayExpress. When the same study is represented in both NCBI and EMBL-EBI systems, BioProject/BioSample-style identifiers help connect the study-level and sample-level metadata to the raw and processed data records.

A common lookup chain is:

BioProject -> BioSample -> SRA/ENA experiment -> SRA/ENA run
GEO series -> GEO sample -> SRA run -> BioSample/BioProject
ArrayExpress experiment -> ENA run/experiment -> sample/project metadata

Fetching Sequencing Data from BioSample Records¶

BioSample database from e-tools API's point of view¶

BioSample database is indexed in the e-tools API. This is the latest information about the BioSamples database as of 2026-04-21:

{
  "header": {
    "type": "einfo",
    "version": "0.3"
  },
  "einforesult": {
    "dbinfo": [
      {
        "dbname": "biosample",
        "menuname": "BioSample",
        "description": "BioSample Database",
        "dbbuild": "Build260430-0301m.1",
        "count": "54057175",
        "lastupdate": "2026/04/30 07:11"
      }
    ]
  }
}

The fields that are indexed in the BioSample database are:

#	name	fullname	description	termcount	isdate	isnumerical	singletoken	hierarchy	ishidden
0	ALL	All Fields	All terms from all searchable fields	462127089	N	N	N	N	N
1	UID	UID	Unique number assigned to publication	0	N	Y	Y	N	Y
2	FILT	Filter	Limits the records	296	N	N	Y	N	N
3	ACCN	Accession	Accession number of sequence	100585623	N	N	Y	N	N
4	TITL	Title	Words in definition line	19553227	N	N	N	N	N
5	PROP	Properties	Classification by source qualifiers and molecular types	4224	N	N	Y	N	N
6	WORD	Text Word	Free text associated with record	313550255	N	N	N	N	N
7	ORGN	Organism	Scientific and common names of organism, and a...	1740903	N	N	Y	Y	N
8	AUTH	Author	Author(s) of publication	192502	N	N	Y	N	N
9	PDAT	Publication Date	Date sequence added to GenBank	9824	Y	N	Y	N	N
10	MDAT	Modification Date	Date of last update	5038	Y	N	Y	N	N
11	ATNM	Attribute Name	Attribute Name	84737	N	N	Y	N	N
12	ATTR	Attribute	Attribute	145899988	N	N	Y	N	N
13	CEN	Submitter Organization	Submitter Organization(s)	128391	N	N	Y	N	N

The links that are indexed in the BioSample database are:

#	name	menu	description	dbto
0	biosample_assembly	Assembly links	Assembly	assembly
1	biosample_biocollections	BioCollections	BioCollections	biocollections
2	biosample_bioproject	BioProject Links	BioProject links	bioproject
3	biosample_dbvar	dbVar Links	Links to dbVar	dbvar
4	biosample_gap	dbGaP Links	Links to dbGap Studies	gap
5	biosample_gds	GEO DataSets Links	GEO DataSets links	gds
6	biosample_nuccore	Nucleotide Links	Nucleotide links	nuccore
7	biosample_omim	OMIM links	OMIM links	omim
8	biosample_pubmed	PubMed Links	PubMed links	pubmed
9	biosample_snp	SNP Links	Related SNP record	snp
10	biosample_sra	SRA Links	Links to SRA experiments	sra
11	biosample_taxonomy	Taxonomy Links	Links to Taxonomy	taxonomy

BioSamples Series¶

Connections to Sequencing Databases¶

Fetching Sequencing Data from BioSample Records¶

BioSample database from e-tools API's point of view¶

Fetching directions from BioSamples series¶