Pre-Requisites
Before submitting inferred sequences with OGRDB, you should have run OGRDBstats on each repertoire: otherwise, please follow steps in the overall submission process before continuing. Having run OGRDBstats, you should have output files (pdf and csv) for each repertoire from which inferences have been derived. The project should be deposited in a long-term repository, and you should have an accession number for the project, and also for the subject(s) and repertoire(s) from which inferences have been derived.
You will need an account with OGRDB: register here. The institution that you provide at registration will be used in the submission. You can change this in your profile after registration if necessary.
Submission Overview
A submission is based around a single Repertoire. A Repertoire, in OGRDB, is loosely equivalent to a BioProject in Genbank or a Study in ENA. It can contain multiple Rep-Seq sequence sets (for example multiple timepoints) from multiple individuals of the same species. The Rep-Seq sequence sets must have been the subject of a published study (the publication does not need to describe the germline inference process: it provides documentation and peer review of the Rep-Seq methods used).
When providing repertoire details, please specify the repository as NCBI SRA or ENA, if possible. While IARC will, subject to its discretion, accept submissions that refer to any long-term repository, OGRDB can validate NCBI and ENA accession numbers and retrieve supporting information, which enhances the quality of the submission and guards against errors when entering the accession numbers.
Germline Inferences may have been made with one or more inference tools. Each of these may have been used with one or more settings. For example, it is possible – although by no means mandatory – that an inference was confirmed by the use of two tools, and that each tool was run more than once, with different sensitivity parameters or other adjustments. Each combination of a tool and the settings used is entered into OGRDB – hence if two different tools were each used with two settings each, there would be four tool/settings combinations.
When a tool is run against a sequence set from the repertoire, it will generate a personalised genotype. The genotype may contain both known germline sequences (from the starting database provided to the tool) and inferred sequences. The inferred genotypes are uploaded to OGRDB in a standard form: the csv file produced by OGRDBstats.
The inferred sequences to be submitted to IARC are then selected from the uploaded genotypes. Note that the same sequence may have been inferred in multiple genotypes (providing increased support). Each occurrence should be identified as an inferred sequence, selected from the genotype in which it was found.
Finally, the submitter may enter any notes that will help review – perhaps providing additional information, or explaining parts of the analysis that may not be obvious to reviewers. The pdf report produced by OGRDBstats is uploaded as an attachment to the notes.
Once all information has been entered, the submission is forwarded for review by pushing the Submit button. At this point, the submission remains visible to the submitter, but may not be edited further, unless it is passed back to the submitter by the reviewers.
It is best to complete the submission in the order listed above, as later parts of the submission depend upon information entered earlier. It is not necessary to complete submission in one sitting – it can be saved as a draft, and any part can be updated after initial entry.
Submission Workflow
New Submission
To create a new submission, log in and select Submissions from the top menu. You will see a list of submissions that you have already created under My Submissions, as well as a list of Published Submissions. Pressing the New Submission button will initiate a new submission. Once you press Create, you will be taken to the Submission Details tab of the submission entry screen.
Please note, as you use OGRDB, that you can obtain help on the fields by hovering over them. For example, if you hover over Ethnicity on the Submission Details tab, you will see an explanation of its meaning.
The submission entry tabs are set out in the order listed in the overview, and it is best to work through them in this order, starting with the Submission Details and Repertoire tabs.
Repertoire Tab
You can enter as much detail as you have at this point, and press Save Draft to save. At that point, fields are checked, and any issues will be highlighted in red.
Acknowledgements Tab
The Acknowledgements Tab is used to enter the details of anyone who should be acknowledged as contributing to the inference of the identified sequences. Please provide ORCID IDs if the individuals are listed on ORCID, as this avoids ambiguity.
Primers Tab
Please enter the primer sets used. You can create as many sets as you need for the study: please use the Notes field to describe the purpose of each set. For each set, you may upload FASTA files containing the primer names and sequences, rather than entering them individually.
Inference Tools
As described in the Overview, each combination of tool and associated settings that was used in the study should be entered here. Please provide each combination with a descriptive name (the Tool/Settings Name), for example ‘TIgGER – with full IMGT germline library’.
Genotypes
Please provide the csv files generated by OGRDBstats.
Please note that you will need to provide details of the tool and settings used with each inferred genotype – so it is best to enter these first. You will not be able to enter genotypes until you have entered details of at least one tool.
Inferred Sequences
Finally, please identify those sequences from each inferred genotype which you wish to submit for consideration. If there is a record of the inferred sequence in GenBank, enter the accession number in the Accession Number field and the version number of the record in the Version field: otherwise the fields may be left blank. Leave the Select Sets field blank, as this is currently not used in submission or review.
Notes
On the Notes tab, please upload the pdf files produced by OGRDBstats, and provide any notes that you think might be helpful for reviewers.
Simple formatting can be used when entering text, as follows:
- Words or phrases with *asterisks* will be shown in bold.
- Words or phrases with _underscores_ will be shown in italics.
- Use * as a bullet point at the start of each line to create a bulleted list.
You can also upload other files containing supplementary information.
Submission and Review
All your submissions are listed under My Submissions on the Submissions page. You can resume editing of any draft submission by clicking the pencil icon, or delete it and start over by clicking the trash icon. You can review it in read-only mode by clicking its submission ID. Once you are happy to submit, edit the submission and press Submit to IARC. Once you confirm, the submission will no longer be editable but can still be seen under My Submissions. You will receive a confirming email, and IARC will keep you updated of progress and raise any questions via email.