Getting an account

If you do not have an account yet, please create a new account through the web site Register for a site-wide account and next register your account with the database(s) in which you wish to submit data via the automated submission system. If you already have an account associated with a database, you can reset your password, update your profile and register your account with specific databases in the site-wide account settings page.

Please ensure that you enter a valid E-mail address, as account validation details will be sent to this address. Please fill the box with your complete details using proper first letter capitalization of names and full affiliation details, i.e. department, institution, country (avoiding acronyms). This information will appear with any data that you submit.

NB. Submissions from users with incomplete account information will be promptly rejected.

Submissions

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 valuable as well.

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 following scheme.

Please submit all data (isolate’s records and sequence data) for allele and profiles definitions through your BIGSdb-Pasteur submitter account. Once your submission is completed, you and the curators will automatically receive a notification. For more information about how BIGSdb-Pasteur handles your data please read our Policy.

Whole Genome Assembly (RECOMMENDED)

Please submit one or more genome assemblies (all in the same submission batch) to the Isolates & genomes database. In this case, you will have to provide the isolate(s) metadata, and the definition of new allele(s) and MLST/cgMLST profile(s) will be performed automatically from the whole genome assembly file.

For more information on the submission procedure for whole genome assembly, please consult the Guidelines for submitting whole genome assembly data.

Sanger Sequencing (to be discontinued)

To submit Sanger sequencing data, you will have in ALL cases to make an "isolates" type submission to the Isolates & genomes database, where you will have to provide the isolate(s) metadata. In addition, an "alleles" and/or "MLST profiles" type submission in the Alleles & profiles database may be required.

The discovery of a new allele will always lead to the discovery of a new MLST profile. Therefore, when submitting a new allele, please submit the new MLST profile at the same time. This enables curators to group and process submissions more quickly. The novel allele can be marked as ‘new’ of left blank.

NB. Incomplete MLST profiles will NOT be assigned and will be promptly rejected.

For more information on the procedure for submission of Sanger data, please consult the Guidelines for submitting Sanger sequencing data.

Curation delay and data release

Depending on the type of data submitted, the time required to curate your submission may vary:

• For submissions involving whole genome assemblies, results are typically available in <24h for small batches or several days for larger batches (hundreds of genomes).
• For submissions involving Sanger data, which require more in-depth manual curation, we anticipate a delay of one week to complete the curation process.

Once the curation is complete, novel alleles and profiles are made immediately available online, as they form the basis of the public nomenclature of genotypes. You will be notified and asked to control if all data integrated in the BIGSdb database are correct.

Data privacy options

We encourage the rapid publication of provenance data and genomic sequences for your isolates. However, genome submissions (including isolate metadata and assemblies) can be kept private for some time (see below). Submitters may later choose to make them public. 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).

NB 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 before than two months prior to the current embargo end date. In your request, please specify the database and 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 appreciate if you can recognize 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).