Please use Mélanie Courtot, Luca Cherubin, Adam Faulconbridge, Daniel Vaughan, Matthew Green, David Richardson, Peter Harrison, Patricia L Whetzel, Helen Parkinson, Tony Burdett; BioSamples database: an updated sample metadata hub, Nucleic Acids Research, Volume 47, Issue D1, 8 January 2019, Pages D1172–D1178, https://doi.org/10.1093/nar/gky1061

BioSamples content is updated daily. Information directly submitted or updated in a source should be reflected within 48 hours. However, occasionally daily updates may be missed due to unexpected circumstances.

BioSample accessions always begin with SAM. The next letter is either E or N or D depending if the sample information was originally submitted to EMBL-EBI or NCBI or DDBJ respectively. After that, there may be an A or a G to denote an Assay sample or a Group of samples. Finally there is a numeric component that may or may not be zero-padded.

The Resource Identification, RRID, Initiative began working with the BioSamples databases in the EU and US in order to identify the pancreatic islets used by researchers who are part of the Integrated Islet Distribution Program, IIDP. Recently the leadership of the IIDP, BioSamples and the RRID project came together to add BioSamples in a limited capacity to the RRID project, which will identify the IIDP samples as RRIDs. More information can be found in the blog post and the RRID FAQs.

Bioschemas is an extension of schemas.org, a markup language for website and services to provide consistently structured information. It adds semantic markup to web pages by describing ‘types’ of information, which then have ‘properties’. The BIoSamples team at EMBL-EBi leads the Bioschemas samples specification work and has added BIoschemas export, serialised as JSON-LD, to all our samples pages. Check out an example here.

BioSamples also provides serialisations for other Bioschemas entities embedded in a script tag within the HTML source code, check out examples of the DataCatalog entity as well as the DataSet entity.

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We use ontologies to help refine search queries. This means that your query might match to a synonym or more specific term than you were looking for; e.g. a search for 'human' will match 'homo sapiens'. However, direct matches will be ranked higher in the results.

This website requires cookies, and the limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our Privacy Notice and Terms of Use.

If you submit information to BioSamples please note that we will handle your submission in accordance with our Submission Privacy Notice.

Most of the data in BioSamples has been submitted by third parties, often via one or more other services. This means that we are unable to go back to submitters for corrections or clarifications. Therefore we do not have the same degree of up front quality control as services with specific curators and submission requirements. We do however try to extract the highest quality of information from the data we are given, for example by mapping to ontologies and using ontology expansion for queries.

BioSamples is an open source database. The source code is published here. Licensing information for the source code is on our licensing page. For problems in building your local BioSamples database, please send a pull request or contact us at biosamples@ebi.ac.uk.

SamplesTab services have been deprecated and retired on July 1st 2020. Please use our JSON API for sample submission and update.

The Submitted on date field was added in our release in November 2020. All samples submitted after November 17th 2020 will present this information. Older samples may not have that date - this will be progressively added as our curation pipelines periodically run, or can be added on request at biosamples <at> ebi.ac.uk.

Many users reported confusion interpreting the ID created on field. To address this issue, we have removed the field from the UI. It has been retained in the JSON source as create for advanced users familiar with the BioSamples processing pipelines and documentation. create reflects the date at which the sample accession is created. This attribute is generated by BioSamples. IDs can be created well in advance of collection or submission; BioSamples allows the pre-registration of sample accession to support cross-archive data exchange and data provenance management. IDs can be created by internal pipelines as unallocated placeholders pending user submission, sometimes months in advance of the actual sample collection.