Getting an account

Please submit all data (isolate’s information and sequence data) for allele and profiles definitions through your BIGSdb-Pasteur submitter account.

If you do not have an account yet, please create a new account thorough the site Register for a site-wide account and register your account with the database where 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. Please fill the box with your details completely with proper first letter capitalization of names and full affiliation details (avoiding acronyms). This information will appear with any data that you submit.

Register page

Once your submission is completed, you and the curators will automatically receive a notification.

Uploading data

Users are requested to submit only high-quality sequences, generated from pure cultures sequenced at a minimum coverage of 40X. Assembly files consisting of high numbers of contigs (> 500), presenting a cumulative contigs length outside the typical range of the species will not be accepted.

Once logged into the Isolates database, click on SUBMISSIONS to access the submission panel. Choose genomes to provide the isolate information (use the template available there) and assembly files (closed or draft genomes in FASTA format). A guidance note is available in the headers of the template to help you to fill-out the metadata fields. Please note that the assembly files should be named with an identifier corresponding to the isolate name. For example, if the isolate name is ATCC13883 in the isolates template, please label your assembly file as ATCC13883.fas. The suffixes .fa, .fasta or .fna are also acceptable.

Isolate homepage

MLST profiles submission:

First, submit at least one isolate record for each novel profile. Log into the Isolates database, click on SUBMISSIONS and choose isolates to provide the isolate information (use the template available there). You can submit multiple isolates in a single submission. Then, log into the Sequences and profiles database and click on ‘SUBMISSIONS’ to access the submission panel. Choose MLST profiles and paste in your profiles for assignment using the template available there. You can submit multiple MLST profiles in a single submission. Please note that the identifier id of the novel profile should correspond to the isolate name. The submitted profile should correspond to results obtained querying your sequence into BIGSdb-Pasteur Sequences and profiles database, as this database may be more up to date than external databases that download and provide our curated data on other platforms.

Alleles submission:

Once logged into the Sequences and profiles database, go to SUBMISSIONS to access the submission panel. Choose alleles to submit new alleles. You can submit any number of new sequences for a single locus as single submission. Sequences should be trimmed to the correct start/end sites for the selected locus. Please label your trace files starting with the strain code (avoiding special characters such as space, dot, slash, etc.), followed by underscore, followed by the gene name written exactly as in the database (e.g. gapA), followed by underscore, followed by any information you would like, followed by '.ab1' or '.scf'. Example: SB1_ gapA 398509385_F.ab1 and SB1 gapA _398509385_R.ab1.

SeqDef homepage

Data release

We aim to process submissions within 48h.

Once the curation is complete, allele definitions and profiles will be released immediately, as they form the basis for the public nomenclature of genotypes.

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 profiles: isolates with already known MLST types are valuable as well.

We also encourage immediate release of your isolates provenance data and genomic sequences. However, in the case you would like to ask for an embargo period (e.g. prior to publication), please specify it to the curators in the submission request mail. Data release should ideally be when your publication is accepted or no later than one year after submission to our database. Curators may automatically submit your data to the public database after this period. You will be informed about the imminent release of your data.

The proposed release date should be the same for all isolates of the submission batch. Please provide this information in the isolates submission template or via the submission confirmation mail.

You will be notified and asked to control if all data integrated in the BIGSdb database are correct. We kindly ask you to inform us in the case of metadata rectifications to allow us to keep current records updated.

Acknowledgments

Curation and maintenance of BIGSdb-Pasteur databases is performed on a voluntary basis by a handful of colleagues, who dedicate their time to the community.

We appreciate if you can recognize our efforts in the acknowledgments section of your publications:

We thank the Institut Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/.

References

Please quote the original publications on the development of nomenclature schemes from the references page.

Collaboration

For submissions of large amounts of data, or when you would like to request further analyses in addition to curation, we may ask you to add the person of the curator team in charge of analyzing your data among your co-authors.

Edit on GitLab