GPL-895 Push cohort column to the ENA [RT 712202] (C=S, V=?)

[rl15]

User story As Management Trainee for Cellular Genetics (Charlotte B) I would like the cohort column could be pushed through to the ENA

Who are the primary contacts for this story Charlotte B

Acceptance criteria To be considered successful the solution must allow:

• [ ] TBD

Additional context

Rob B wrote (Wednesday, 17 February 2021 at 12:01)

I don't think we would need to change anything for this. Samples (apart from Heron ones) are submitted to the EBI by SequenceScape, so all the changes needed should be in your world. When we submit data, we only use the accession number already present in SequenceScape.

As Beth says, adding a cohort can be done using a sample attribute, see ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/SRA.sample.xsd and ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/SRA.common.xsd

Beth F wrote(Tuesday, 16 February 2021 at 14:17)

With fields like “cohort”, I thought they could be added as sample_attributes in the Sample submission - (https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html [ena-docs.readthedocs.io]<https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html

However, it looks like the ENA are using checklists and the Sample you provided is using the default checklist - https://www.ebi.ac.uk/ena/browser/view/ERC000011 [ebi.ac.uk]<https://www.ebi.ac.uk/ena/browser/view/ERC000011 - no cohort.

Is Rob D still looking after submitting (meta)data to the archives?

However, if you wanted to get in touch with someone from the ENA, I think Sam Holt could be a good place to start - https://www.ebi.ac.uk/about/people/sam-holt [ebi.ac.uk]<https://www.ebi.ac.uk/about/people/sam-holt

Originally raised via RT 712202 on 11th February

[JamesGlover]

Additional background

1. Still have sample accessioning in two places

• Accessionable::Sample which is the old way, does handle updates
• Accession::Sample - Updated mechanism. Doesn't handle updates

2. The old method determines which tags to send based on configuration of metadata attributes themselves. Currently for ENA this appears to be [:sample_strain_att, :sample_description], EGA adds donor, phenotype and gender. Adding fields is a case of modifying the include_tag section in `app/models/sample.rb:178)

3. The new method uses config files: config/accession/tags.yml

[neilsycamore]

Other questions (which I haven't had time to check) Does uploading manifests populate mlwh.sample table data? Is the cohort field added to iRods following update?

[rl15]

https://ssg-confluence.internal.sanger.ac.uk/x/XYjRAw (our docs) https://lucid.app/lucidchart/invitations/accept/04f21a74-46c1-493b-be89-3c61281b0f0a (for discussion on 2nd March)

[stevieing]

@stevieing speak to Cellular genetics?