ContentsSubmitting SamplesThe cgMLST.org Nomenclature Server (www.cgMLST.org) provides a global nomenclature for stable public cgMLST schemes, i.e. for Task Template that were downloaded from the Task Template Sphere. If Samples are using those downloaded Task Templates they can be submitted to cgMLST.org. However, if a Sample has new alleles that are not known at cgMLST.org, then the Sample must be submitted with some minimum data to retrieve newly assigned allele types for them. Otherwise the new alleles are treated as missing data in distance calculation.
The submission of a Sample requires the following minimum data:
The amount of additional metadata that should be submitted can be defined in the Submission Anonymization Filter. Submission to cgMLST.org 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 not public shown on cgMLST.org, 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 cgMLST.org. A unique serial number is assigned to the sample, and stored back as Ridom ID in the local database. This number is also shown as link in the upper right corner of the Sample Overview. This Ridom 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). There are two different ways in SeqSphere+ to submit Samples to cgMLST.org: Manual Submission
Submission via PipelineIf Samples are imported through a pipeline, it can be configured in the Submission part of the Pipeline Script that the Samples are submitted to cgMLST.org. 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. Resubmitting SamplesIf a Sample that was already submitted is submitted again, then the data at cgMLST.org is immediately updated. Fields that are filtered out or set to empty in the re-submission are immediately removed from cgMLST.org. The procedure for re-submitting Samples is the same as described above in the manual submission section. Filtering Metadata for SubmissionThe 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 cgMLST.org 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 default settings for a new installation of a SeqSphere+ Client.
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. |