I know we discussed that the WSI prefix would be used for the Anon ID could it be the RVI one instead. It’s still anon enough not to distinguish location.

GSU agree that RVI prefixed Sanger Sample ID can to be used.

Team Discussion 13Nov2024

Assumption:

1. Run a script to update the IDs
2. Referencing to only RVI samples and not Heron Samples
3. Use of public name field only for RVI and not for Heron

How do we identify the samples/Study that need to be updated?

@KatyTaylor There's an attribute in sample_metadata table called sample_public_name which the manifest's PUBLIC NAME value is stored into. Is this the target for the new ID?

Outstanding questions:

• How do we determine which samples are RVI samples? Are they all under particular studies?
• If we update sanger_sample_id's that will break all RVI manifests (they will have old ids) does this matter?
• Should this be done after the manifest story so that we don't get intermediate data created after this data patch and before the manifest patch?

Quick clarifications.

• How do we determine which samples are RVI samples? Are they all under particular studies?
  Yes they will be identified by belonging to the "RVI Program - Bait Capture" study

• If we update sanger_sample_id's that will break all RVI manifests (they will have old ids) does this matter?
  We are not changing the sanger_sample_id values.
  We would like to set the sample's "Public Name" field to be identical to the sample's "Sanger Sample ID" field for these samples.

• Should this be done after the manifest story so that we don't get intermediate data created after this data patch and before the manifest patch?
  Good point. Yes.

If the sample has been accessioned whatever identifier is added to the 'name' and then added as the public name then potentially (if data is pushed to the ENA) this would expose the 'new id' as public name if is displayed as the title of the accessioned sample

@neilsycamore The issue they are trying to address is that they don't have an anonymous ID they can use for publishing data. Their sample supplier uses ids that are identifiable and they automatically transferred these over to SciOps / SequenceScape.

The accessioning logic, I believe, uses public name if present and then fails back to supplier id ?

So, by setting an anonymous id in the Public Name field they can safely publish. We thought about allocating a new id with baracoda but it seems that in this case the SequenceScape name is sufficiently anonymous.

Does that help explain things? Are there any concerns with this approach?

@TWJW-SANGER , @KatyTaylor I’ve been looking into this, and I noticed that some samples belonging to the RVI Program - Bait Capture study have their sanger_sample_id prefixed with "RandD_" (e.g., RandD_RVIxxxxxx).

I’m unsure how to handle the public names for these samples. Should we remove the "RandD_" prefix to align with the acceptance criteria, or should we leave them as they are for now?

Out of 5055 records, only 23 have their sanger_sample_id prefixed with "RandD_," which I found a bit confusing. Additionally, there doesn’t seem to be much consistency in the use of the RVI prefix—some samples are prefixed with "RVI," while others use "RVI_."
I’m not sure if this is relevant, but I thought it was worth mentioning. I also looked at the date column to try and make sense of it, but that didn’t provide any clear insights.

Good spot.

My thoughts below:

• I don't think it would be a good idea to change the sanger_sample_id, as this is likely linked to in various ways in different systems.
• I suspect that the R&D samples will not be part of the data release. So that it won't matter what their public name is as it will never be exported.
• "RVI" vs "RVI_" - is irritating, but still satisfies the requirement to be anonymous and that inconsistency will be present in other systems that feed into SequenceScape already.

I suggest that we continue as planned but I will send an email to Adrianne and Ya-Lin to cover these points and CC you both in.