OGRDB Updates

[wil...@lees.org.uk]

The following updates have been made to OGRDB. Please let me know if you have questions or encounter any problems:

Gene Description Enhancements

You can hide rows that contain less than a specified number or frequency of records, or hide all except submitted inferences.

All sequences are checked against the current IMGT reference (updated once a day) and unexpected matches or mismatches are reported via icons in the right-hand column

All human sequences are checked against IGPDB (updated once a week) and matches are reported

Names of genes not contained in the IMGT reference are italicised, and shown in bold if they have been submitted as inferences.

NCBI-related Enhancements

When creating or editing a submission, the repository is now entered from a dropdown as 'NCBI SRA' or 'Other' (in which case a name must be provided).

If the repository is 'NCBI SRA', accession numbers are checked against NCBI and titles are retrieved and shown in the various tabs of the submission: for example the Inferred Sequence tab will show the title of the corresponding GenBank entry and the titles of the sequence sets pertaining to it. This makes the entry more understandable, and reduces the chance of incorrect values being submitted.

As the major repositories replicate their records, I would like to suggest that we encourage submitters to use the NCBI records as the basis of their submission wherever possible. This will save me the chore of interfacing to each repository's API!

Published Sequence Enhancements

In the Inferences tab of a Sequence, the sequence of each inference is checked against the defined sequence, and an alignment is provided. A mismatch is not necessarily an error, for example in https://ogrdb.airr-community.org/sequence/3 the trailing nucleotide of the submitted inference is omitted from the published sequence.

Additionally, for reviewers only, the Inferred Sequences tab will list matching submissions that have not as yet been included in the record for this published sequence (mismatches at the beginning or end of the sequence are permitted and will be indicated).

Minor Items

If you navigate away from a tab without saving changes, you will now be asked if you would like to save them.

The example file for a genotype had only whole numbers in the Frequency field, giving the misleading impression that decimals couldn't be used. It's now been updated to show that they can be. 

All the best

William