Submit isolates and STs

Please note that you can only get new STs assigned by also submitting corresponding isolate data. If your allelic profile contains new alleles, you will be prompted to upload trace files at the end of the submission process.

Once you have logged in, you will be presented with the option to create a new submission. Click 'Create new submission' ...

... and then from the new submission page click 'Isolate data':

You will be presented with a page that describes the isolate table fields. You need to upload data by copying and pasting from a spreadsheet with the fields in the same order as listed here. To assist in this, you can download a tab-delimited header for your spreadsheet (you may find that copying directly from the web browser to a spreadsheet results in all the headings being entered in one spreadsheet cell - if this happens, copy first to a simple text editor, like Notepad, and then copy from there to the spreadsheet). Alternatively, most databases have Excel submission templates that you can download (these may also have drop-down boxes for some fields to ensure that data are entered correctly).

Once you have your data in a spreadsheet in the right format, click 'Upload records'.

Paste the records from your spreadsheet - do not include the header line. If your isolate data contains a new allelic profile that you would like assigned, please leave the ST field blank (some databases have allele fields instead of a ST field - in that case enter your profile, leaving fields for loci that you need new alleles assigned blank) - you will be prompted later to upload allelic profiles and/or trace files. Click 'Submit Query'.

Your records are then checked against the database format. Any problems will be highlighted for you. In the example below, you can see that the species for row 2 has been omitted - this is a required field so the upload can not proceed until you go back and add the data.

When the data has been entered correctly, a 'Submit' button will appear. Click this. If all the isolates you are submitting have previously assigned STs, you will then be prompted to complete the submission. If, however, you have left the ST field blank (for databases that store ST number rather than profiles), you will next be prompted to enter new profiles for the missing STs. If there is just one or a few profiles to enter, it is easiest to enter these using the simple form. Alternatively you can upload tab-delimited profiles using a batch upload form.

If all profiles are complete you will be prompted to complete the submission. If you leave individual loci blank you will be prompted to upload trace files for them. In the example below, the aroE locus has been left blank.

Profiles are checked and the status of the submission displayed. If data are invalid (e.g. unknown allele number) they will be highlighted. Click 'Upload'.

Finally upload any missing allele trace files if prompted. The process is the same as for submitting alleles only.

Once all data have been uploaded, you will be prompted to complete the submission. At this stage you can enter any comments that you would like to send to the curator. Click 'Complete submission'. You will then be presented with a summary of your submission. This will also be E-mailed to you. The curator will be sent an E-mail to state that a submission is waiting. They should contact you once they have made your assignments.