Nomenclature Server

The Nomenclature Server ( provides a global nomenclature for stable public cgMLST schemes, i.e. for Task Templates that were downloaded from the Task Template Sphere. If Samples are using those downloaded Task Templates they can be submitted to

Button16 Important.png Important: If no submission of any data is wanted or allowed, then only local Task Templates must be used. Samples that are using only local Task Templates will not and cannot be submitted to Local Task Templates can be defined using the cgMLST Target Definer, or by converting public Task Templates into local ones.

Allele Submission to

When Samples are processed for a downloaded Task Template, the new alleles are by default automatically submitted to and stored at The Nomenclature Server assigns new global allele type numbers to the alleles. The allelic profile is not stored at during allele submission.

The automatic allele submission can be disabled in the in the client settings, by using the menu item Options | Preferences, and selecting the the item Online Connection | Allele Submission to However, if a Sample has new alleles that are not known at, the new alleles are treated as missing data in the distance calculation (e.g., in Comparison Table).

Sample Submission to

Submission Anonymization Filter dialog for

The Sample submission to is optional (can be turned off in the assembly pipeline). It can be used to submit and store the allelic profile and optional metadata on Various options exist:

  • Store only new CT founders as anonymized samples on (default)
    Only the allelic profile and no further data (including submitter data) are stored on
  • Store only new CT founders on
    Samples that are new CT founders are stored non-anonymized on
  • Store all submitted samples on
    All Sample are stored non-anonymized on

One of the three options is required to assign to all samples a Complex Type (CT). Choosing one of these options requires a one-time registration to the nomenclature server.

The submission of a non-anonymized Sample, i.e., option 2 or 3 above is selected, requires the transfer of the following minimum data:

  • Sample ID (alternatively 'Alias ID' or 'do not submit and use ID')
  • Submitter Info (not shown public by default)
  • Submission Date (only year is shown public)
  • MLST Sequence Type (ST)
  • Core and accessory genome MLST allelic profiles
  • cgMLST Complex Type (CT, returned from
  • Percentage of Good cgMLST Targets
  • Genus
  • Species

The amount of additional metadata that should be submitted can be defined in the Submission Anonymization Filter.

Submission to is only possible if the Sample has in the cgMLST scheme at least 90% of good targets (i.e., targets passed the QC procedure and have therefore a green or yellow smiley). Allele types are only received for the good targets (green or yellow smiley). During the first submission, the user must register once with basic contact information. This information can later be modified using the menu function Options | User Settings. The submitter contact information is by default not public shown on, but it will be used to forward incoming requests about submitted Samples.

Except for the submitter information and exact submission date any submitted data is immediately made publicly available on A unique serial number is assigned to the sample, and stored back as ID in the local database. This number is also shown as link in the upper left corner of the Sample Overview. This ID link can be used to directly access the public web page of the submitted Sample and to control the data that was submitted (e.g. RID002433).

With default settings, only new CT founders will be stored as anonymized samples on the Nomenclature Server. The default settings can be changed in the general preferences settings.

The submission of Samples can be invoked manually or it can be configured in a pipeline script.

Manual Submission of a Small Number of Samples

If only a small number of samples should be submitted (e.g., around ten), it is recommended to use the following steps to see a full preview of the data that will be submitted.

Submission Preview dialog shown for manual submission to
  • Step 1: Load the Sample(s) into the workspace using the menu function File | Search Samples.
  • Step 2: Invoke the menu function Webupload16.png File | Assign or Submit new Alleles and select all Samples that should be submitted.
  • Step 3: The Submission Anonymization Filter dialog is shown to define which fields should be submitted. The last used setting is kept.
  • Step 4: Finally the Submission Preview dialog is shown with the filtered data that will be submitted. The data can now be controlled and modified just before sending it. When the dialog is confirmed, the shown data is send to

Manual Submission of a Large Number of Samples

Use the menu function Tools | Manage Submissions to or the submit button Webupload16.png in the Search Samples dialog to submit multiple Samples at once. The Submission Anonymization Filter dialog is shown to define which fields should be submitted. When the dialog is confirmed, the shown data is send to No preview of the submitted data will be shown when using this function.

Automatic Submission via Pipeline

If Samples are imported through a pipeline, it can be configured in the Submission part of the Pipeline Script that the Samples are submitted to The Submission Anonymization Filter settings are defined for each pipeline script.

In contrast to the manual submission, the pipeline submission does not show a preview dialog before the samples are submitted, because all pipeline processing runs in an automatized way. Therefore, the button Preview Epi Data can be used to show the potentially submitted epi data of the matching samples that already exist in the SeqSphere+ server database.

Resubmission of Submitted Samples

If a Sample that was already submitted is submitted again, then the data at is immediately updated. Fields that are filtered out or set to empty in the re-submission are immediately removed from

The procedure for re-submitting Samples is the same as the manual submission described above section.

Withdrawal of Submitted Samples

Submitted Samples can be withdrawn from the Nomenclature Server.

Use the menu function Tools | Manage Submissions to or the withdraw button Webwithdraw16.png in the Search Samples dialog to withdraw submitted Samples from

Filtering Metadata for Submission

The level of metadata that should be submitted can be defined in the Submission Anonymization Filter that is shown in a dialog before a manual submission is confirmed. Also in a pipeline script the Submission Anonymization Filter settings can be configured if automatic submission is selected.

New epidemiological fields that are created by the user are never submitted.

Potentially the following metadata is submitted to and shown on the public website. Unless the fields are mandatory, they can be excluded from submission (Do Not Submit). For place and time information additionally the level of detail can be set. The table shows the sample metadata fields (by default only of samples that are CT founders) that are submitted by default for a new installation of a SeqSphere+ Client.

Submission Info
Submitter Info Submit (mandatory, not public shown by default)
Submission Date Submit (mandatory, only year is public)
Sample ID Submit (generated by
Genotyping Result
MLST ST Submit (mandatory)
cgMLST/Acc. Allelic Profile Submit (mandatory)
cgMLST Complex Type Submit (mandatory)
Perc. Good cgMLST Targets Submit (mandatory)
Sequence Data
Assembly Contigs (FASTA) Submit
Epi Basic
Sample ID Submit
Alias ID Do Not Submit (alternative for Sample ID)
Collection Date Submit
Epi Source
Country of Isolation Submit
State of Isolation Submit
City of Isolation Submit
Source Type Submit
Host Submit
Host Age (years) Submit
Host Sex Submit
Host Disease Submit
Isolation Source Submit
Epi Characteristic
Genus Submit (mandatory)
Species Submit (mandatory)
Strain Submit
Genotype Submit
Serotype Submit
Pathotype Submit
Identification Method Submit
Identification Kit Vendor Submit
Culture Collection Submit
PubMed ID(s) Submit
Nuccleotide Accession(s) Submit
Experiment Accession Submit
Sample Accession Submit
StudyAccession Submit
Imported from EBI/NCBI1) Submit (mandatory)
Epi Species Specific
PFGE Pattern(s) Submit
Epi Species Specific (only for MTBC)
Spoligo Submit
MIRU 15-9 Type Submit
MIRU Lineage Submit
Gagneux Lineage Submit
Laboratory Procedure Details
Nucleic Acid Extraction Submit
Library Source Submit
Library Strategy Submit
Library Selection Submit
Library Construction Method Submit
Library Amplification Method Submit
Sequencing Protocol Submit
Library Insert Size Submit
Sequencing Length Submit
Sequencing Vendor Submit
Sequencing Platform Submit
Assembly Procedure Details
Assembly Pre-processing Submit
Assembly Type Submit
Mapping Reference Genome Submit
Assembler Submit
Assembler Version Submit
Assembler Parameters Submit
Read Statistics
Avg. Coverage (Unassembled) Submit
Avg. Read Length (Unassembled) Submit
Avg. Read Length (Processed, Unassembled) Submit
Assembly Statistics
Contig Count (Assembled) Submit
N50 (Assembled) Submit
Consensus Base Count (Assembled) Submit
Avg. Coverage (Assembled) Submit
Genome Status1) Submit (mandatory)

1) The fields Imported from EBI/NCBI and Genome Status are automatically filled if the data was imported from NCBI Genomes or SRA. Imported from EBI/NCBI can be true or false. The Genome Status can have one of the following values: Complete Genome, Chromosome, Scaffold, Contig, or SRA.