make sure that the EMO BON url and the Handbook appears in the ENA entries

[isanti]

No description provided.

[kmexter]

Ioulia - in which fields should these be? (I agree they should be there!) and which URL (given that the emobon page on the embrc site has minimal content)?
On a related issue, we discussed that the SOPs (samp_mat_process) given in the logsheets should be turned into URLs in the ttl files. However, as the SOPs are all pushed together in one Handbook, we cannot "turn the SOPs into URLs". What we will do in the ttl files then is for each SOP value (e.g. SoSOP3) we will add a property "can be found in this DOI".
HOWEVER, that means I need to ask you this: when the SOPs are updated, will the Handbook update get a new DOI or will it use the old DOI? It is important that when we say "SoSOP3 can be found in [this doi]" it always refers to the handbook relevant at the time of sampling, and so if the Handbook is updated - or rather, if the SOPs in the handbook are updated - then they get a new DOI.

[cpavloud]

In https://github.com/emo-bon/sequencing-data/blob/main/shipment/batch-001/run-information-batch-001_column-descriptions.csv
there is the url_seq and the sop_seq

When the Handbook is updated, it can be updated also in OBPS (it will appear as version 2) and get a new DOI.
We didn't do it for the update we did in April, but it can be done.

However, we did update the Handbook, but basically changed only the ARMS part, so the other SOP have remained the same.

[kmexter]

Grand. Youse should check out not getting a totally new DOI but a "new version DOI" -> but that will be done via whatever OBPS can do.

what does it mean when url_seq = NA as is the case for batch1? That it is not yet available online?

[cpavloud]

url_seq = NA is in the logsheets?
I don't know, maybe it was filled in before the Handbook had a DOI?

[kmexter]

I think this was for the url to the sops for the sequences, not for the collection. Is the sequence processing protocols also in the handbook? because the column sop_seq is just a string, not a URL -> so useless from a data POV

[cpavloud]

Yes, the sequencing protocols are included in the updated (2024) Handbook.

[kmexter]

In your next update, can you give these sequencing protocols - both pages - an ID like the WaSOP3 etc have? In this way we can refer to them as a unique name and give the URL to that unique name (being the handbook DOI)

[kmexter]

FYI the handbook on OBPS is version 1 from April 2021......see https://repository.oceanbestpractices.org/handle/11329/1738
Is there a version 2 or did someone just forget to update that information on the front page of the handbook PDF?

[cpavloud]

Yes, the Handbook in OBPS is the 2021 version.
We didn't add the 2024 version in OBPS yet.
The 2024 updated Handbook at the moment is in EMBRC's website https://www.embrc.eu/sites/default/files/publications/2024.04_EMOBON%20Handbook_FINAL.pdf

[kmexter]

OK, well in order to be able to reference a DOI rather than a URL, we will point to the 2021 version (well, always to the version in OBPS). Can you tell me when you do update OBPS please?

[cpavloud]

Of course!

[cpavloud]

This is relevant to emo-bon/sequencing-crate#16 and #1