⛔ Maintenance: A BIGSdb-Pasteur maintenance is scheduled on Friday, July 04th and Saturday, July 05th. All services will be offline until late in the evening (Central European Time). During this period, the server and API will be unavailable. Please note that job submission not be available and all unfinished jobs will be killed. Sorry for any inconvenience. If any questions, contact us
Data access policy note: since January 1st, 2025, registration and authentication are mandatory to access all data curated after this date, either via the web interface or via the application programming interface (API authentication help link). Please contact us if you have any questions.
Submission guidelines for data curation
📝 Getting an account and registering to databases
If you do not have an account yet, please create a new account and register your account with the database(s) in which you wish to submit data. The steps to follow are detailed on the REGISTER page from the website banner.Submissions from users with incomplete account information will be promptly rejected.
📥 Submit data to BIGSdb-Pasteur
We encourage the submission of all isolates of your studies, so that the database would be as representative of the natural populations as possible. Thus, please do not restrict yourself to submitting only isolates that represent new sequence types: isolates with already known genotypes are also valuable.
Two separate databases are available for each pathogen: the Alleles & Profiles database and the Isolates & Genomes database.
Depending on your data (whole genomes assemblies or sanger sequences), you will have to make the required submission(s) in the corresponding database as illustrated in the scheme.
You will also find the guidelines to follow depending on the data in your possession below.
Once your submission is completed, the curators and you will automatically receive a notification.
For more information about how BIGSdb-Pasteur handles your data, please read our Policy.
Depending on your data (whole genomes assemblies or sanger sequences), you will have to make the required submission(s) in the corresponding database as illustrated in the scheme.
You will also find the guidelines to follow depending on the data in your possession below.
| Required files | Submission type | Guidelines for Submitting |
|---|---|---|
| Genome file | Genome | Whole genome assembly |
| Sanger file | Allele and Isolate | Sanger sequencing data |
Once your submission is completed, the curators and you will automatically receive a notification.
For more information about how BIGSdb-Pasteur handles your data, please read our Policy.
⏳ Curation delay & Data release
The time required to curate your submission may vary:- Whole genome assemblies : results are typically available in <48h for small batches or several days for larger batches (hundreds of genomes).
- Sanger data : this may take up to one week to complete the curation process
🔒 Data privacy options
Although we encourage the publication of provenance data and genomic sequences of your isolates as early as possible, all genome submissions (isolates metadata and assemblies) can be kept private, and submitters can at later stage make them public and associate them to PUBMED ids, at any time. Submissions without genome data are made publicly available immediately.Embargo request
If you would like to request an embargo period to keep your data private for some time (e.g., prior to your study’s publication), you can do so when submitting your data, by ticking the "Request embargo" box and selecting the desired embargo duration. The initial embargo period cannot exceed 24 months (2 years).
Once the embargo period has ended, the data will be made public automatically.
Once public, the data cannot be made private again.
Extending the Embargo Period
To extend the embargo period, please send a request by email to bigsdb@pasteur.fr at least two months before the current embargo end date. In your request, please specify the database, the list of isolate BIGSdb IDs and the requested extension duration.Each extension can last up to one year, with a maximum of three extensions. Hence, your data can remain under embargo for up to five years.
Publishing your own data at any time is possible
You can make your isolates public before the embargo date. For this, just query the isolates you wish to publish (for which you are the owner) and click on the ‘Publish’ button. Once your publication request is confirmed by a curator, your data will become public.🔄 Data updates
We kindly ask you to inform us in the case of data publication or metadata rectifications. Although we offer the possibility of data update, please make every effort to have correct metadata at submission, in order to minimize the need for updates.📰 Acknowledgments and References
Curation and maintenance of BIGSdb-Pasteur databases is performed on a voluntary basis by colleagues who dedicate their time to the community.We'd appreciate if you could acknowledge our efforts by adding the following sentence in the acknowledgments section of your publications, or any other document that might arise from curated data:
We thank the Institut Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/.
In your scientific publications or other documents, please quote the original publications on the development of nomenclature schemes, which are indicated on the references page of each organism (see example for Klebsiella references page).