Y24-374 - [RESEARCH] As Legal we would like to ensure the Data Access Agreements actually used for Studies are synchronised with the Electronic Data Access Management (EDAM) system to avoid delays in granting access.

Description As Legal we would like to ensure the Data Access Agreements actually used for Studies are synchronised with the Electronic Data Access Management (EDAM) system to avoid delays in granting access.

Additional context or information When data has been released to the EBI, external researchers will ask to access it and then the EBI will ask the Sanger Legal team permission to grant it. Too often the data access agreement is unknown to the Legal and Governance Team resulting in delays in releasing data to external researchers.

To help mitigate this we want to create a set of user stories to achieve the following:

Add additional data access related questions/answers to the Study setup form in SequenceScape - forcing Research Managers to correctly consult with the Legal team when creating a study earlier.
Export this additional data and possibly the data access agreement document itself to the MLWH database
Work with Legal's developers to help them obtain and keep synchronised with the EDAM system.

A couple of things to note:

Studies can be created & edited at any time and samples moved between them.
The important study for EDAM is the study linked to the sequencing that produced the data specified in the sequencing submission.

Acceptance Criteria The following outputs from the research are produced:

[x] Work with the Lego & SSR team to define the required data fields and create Users Stories to implement them.
[x] Keep the Lego developers appraised of the fields and design of extension to databases.
[x] SSR team would like an additional user story to be able to bulk upload study data from a csv file generated from their Study Setup Form.
[ ] User stories should include testing with LeGo developers to ensure the correct studies are being associated with sequencing data that is released. Q: Not sure how’s best to go about this, as this I believe this is down to the MLWH sample/study association being correct, before the Data Release Team pull in the data from MLWH, as the Sample Submission/ Sequencing steps aren’t being touched in this work.

Who the primary contacts are for this work Laura B (Data Access Officer) Mugdha K (Graduate Associate) Liz C (SSR) Odion A (Senior Web Developer) - EDAM

Knowledge or Stake holders Other people that may have specific knowledge about this work or have a stake in how it is implemented. e.g. John Smith is an expert on x

Diagram

LucidChart Flowchart here

Stories

Y24-419 (To triage) Y24-420 (To triage) Y24-422 (WIP - waiting on Liz’s answers) Y24-425 (To triage)

Stakeholders

Liz Huckle, Liz Cook (SSR) Odion A (eDAM2 developer) Laura B (LeGo, Data Access Officer) Melanie Sharp (DAA) Kalia Dede/ Mugdha K (HumGen/ GenGen) Quan Lin (Data submission team) Francesca Beaton, Ali Hitchborn (CellGen)

Further reading Accessioning overview in Sequencescape Data Sharing and Data Access Agreements (FRED) Data access via eDAM* eDAM2 guidance for Research Managers Sequencescape Study creation UAT

To read HumGen Data Sharing GenGen Data Sharing eDAM2 FAQs Open Access Science eDAM2 External eDAM2 Internal

Outdated questions from stories. Move here to not clutter stories

Y24-419 Questions

Liz:

[x] eDAM Study Title; In the Sequencescape Study creation page, the field which is currently being used to pull into eDAM is “Title", which is labelled an “ENA requirement”. Should it say ENA if it required for both ENA & EGA? Maybe we should remove the “ENA requirement” label?)
[x] eDAM Study Description; same as above, but for "Study description"

Screenshot 2024-11-11 at 11 21 29

[x] Where would you like these new fields to be added, in terms of the Study page, in a new subsection? At the top, near the bottom etc? Name of section on page? Would you want to show/hide this section by default? A: If they could appears in SS in the same order as they appear in eDAM2 that would be good I think. So this would be below the study title and description sections.
[x] What would you like the toggle to be called? Maybe the in_edam eDAM question is the question we use for the toggle as to whether this eDAM section should be shown? If so, what would you like to do with the questions to show when in_edam is “No” (non_sanger_dac_notes and non_sanger_dac_details)?
[x] When viewing the Study, where would you like the eDAM fields to appear

PSD

[ ] Check when this study data is sent to the MLWH? on “activation” or when study is submitted?

Please see PSD Google Sheet with DAA fields cells in Red, for those under discussion

Answers

Re: your Qs from 2 weeks ago (sorry, I don't know how to reply directly to that message!!) For Qs 1 and 2, I want to ensure it's clear that this information will be used externally to SS, so to me "ENA/EGA requirement" sounds good, but I think Odion might have a better idea of the correct specific wording there.

Q4: yes, that toggle sounds great. Please keep those other 2 fields of "non_sanger_dac_notes" and "non_sanger_dac_details" and we will just fill them in if we have that info.

Q5: happy for the eDAM fields to appear on the main study page in whichever order they are listed when filling them in - no real preference on this at all

Y24-419 Questions

Currently in Sequencescape Study set up, there is a Study Name field. Is this linked to the eDAM field Study Title? Would you like the “Hint” for this field in eDAM adding to Sequencescape?

Regarding the Study Name field, I think so, but I can't say for sure. This is the query we run to get the studies from the MLWH: "select id_study_lims, description, accession_number, study_title, faculty_sponsor from study where data_release_strategy='managed' ", so it depends on whether the Study Name field in Sequencescape is inserted into the study table in the MLWH as study_title. Regarding the Hint, you can leave that out.

Currently in Sequencescape Study set up, under ENA specific questions there is a Title (study_study_title) and Study Description (study_description). Is the Study Description in eDAM different (not ENA specific), and if so, shall a new field for “Study Description" to the Sequencescape Study set up page? What would you like the text to show, and what would you like the field in MLWH to be?:

The Study Description in eDAM comes from the 'description' field in the study table in the MLWH. I think it's the ENA specific question, but I can't say for sure.

The same field name collabs refers to both name an institution. Should these fields be seperated to collabs_name and collabs_institution?:

No, leave as it is (see response to next question below)

There is a note in "eDAM DAA setup questions” - “Users must be able to add multiple collabs”. How would you like this to be persisted in the study table in MLWH? If there is more than one collaborator?

Might be best to save it as a json array, so something like this: [ { collabName: "", collabInstitute: "" }, { collabName: "", collabInstitute: "" } ]. We can have a call to discuss this.

Is want_pub_delay needed? For example, could this field be removed and only the publish_delay field used, and set to 12 as default?:

Yeah, it can be removed.

ega_dataset_accession_numbers What input is required for "Known EGA Dataset Accession numbers for this study”. What type is it? Is it required? It is missing from "eDAM DAA setup questions” Google Sheet below

No input is required for this because the RMs don't enter this information. These are the datasets linked to the study, eDAM pulls these datasets from the EGA archive and displays them on this question.

What is the “Hint” text for each field? Please can it be added to the Google Sheet (see eDAM fields below) Do not all fields have a “Hint”?:

Not all fields have hints.

Can we separate non_sanger_dac_notes into two serpate fields non_sanger_dac_name and non_sanger_dac_email?:

Yes this would be fine, it might make it a bit clearer and would be useful to ensure we have both the name and email address.

Could dao_send_to_giselle and dao_send_to be combined, to just be one field dao_send_to? By default the email is datasharing@sanger, or if not, input another email? Assume email requires .ac.uk? Then don't have a users name in a field.

Yeah, I'm happy with that, if Laura is happy with it as well As far as I know this should always be the datasharing mailbox, so yes it should default to this but have an option for something else just in case of odd situations.

Can ez1_to_approve be removed? And sanger_approve_by become one field? Which defaults to Sarion B email, or the manually entered email? Could ez1’s address be replaces with a non-personal / role level? (incase Sarion B ever left the institute). Also, in "eDAM DAA setup questions” doc it says Display when option 1 is selected for ez1_to_approve, is this correct, or should it display when “No” is selected for ez1_to_approve?:

Yeah, you can merge the fields, if Laura is happy with that. Regarding replacing Sarion's email with a role, we can discuss how that would work. You're right, it should be Option 2, I've updated the google sheet. As long as the approvals still go to Sarion then this is fine. If she left then I guess we would just update this to the email address of whoever took over doing approvals from her.

In "eDAM DAA setup questions” doc it says Display when option 1 is selected for in_edam, is this correct, or should it display when “No” is selected for in_edam?

It should display when "No" is selected, I've updated the google sheet.

Is approved_by_lego okay? A “yes”/ “No” input? Is the text description okay, or would you like anything adding? e.g. “Confirm this study has been approved by LeGo and added to eDAM2 internal”. Would you like this to be nearer the start of the form? If “No”, can the user still submit the Study in Sequencescape?.

Could you clarify what role this question plays when answered?

Would you like all these questions to be in their own group, within the Study setup page? Where exactly would you like them to go on the form (at the bottom/ top etc?):

If they could appears in SS in the same order as they appear in eDAM2 that would be good I think. So this would be below the study title and description sections.

Are all these questions only required if the Studies release strategy is EGA, or ENA, or Both (ie would these questions only want to appear if EGA/ENA checkbox is selected in Sequencescape set up form?):

These questions are only needed for managed access data held in EGA (not ENA), and only those using the standard WSI DAA (so if they’re using a different DAA like the DDD or CGP ones for example, then the questions aren’t needed).

Y24-420 Questions

Odion:

[x] How is best to put a story in to the eDAMs dev cycle, requesting the ability for eDAM to pull in data from MLWH UAT DB? A: You don't need to put a story in, once we are ready to pull from the MLWH UAT DB, i'll implement this on the eDAM2 dev
[x] In Sequencescape's Study edit page, we are going to add a note saying something like: “If you would like to update any of the eDAM required fields, please update these in eDAM directly.” Have you a URL for a Test and Production environment we can link to from this page, to make it easier for the users to update the fields in eDAM? A: Internal eDAM2 dev: (https://edam-internal.dev.sanger.ac.uk/#/). Internal eDAM2 live: (https://edam-admin.sanger.ac.uk/#/)

Y24-422 Questions

Liz:

Where would you like this to appear? e.g. as a Link on the right pane “Bulk Study upload from CSV”, which opens to a new page?
How's best to keep Sequencescape Study headers in sync with SSR Google Study Set Up Form?

Answers

HI Harriet - in answer to your Qs for me above: Q1 - yes, a button on the right hand side to allow "Bulk study upload from csv" would be perfect. Note that we still want to be able to do a study creation as we do at the moment by filling in each individual box - this would be an additional feature. We also still want to be able to edit individual fields for a study like we can at the moment Q2 - good Q!! If there are changes that we need to make to the info we collect for studies, we will ensure we let psd know (I assume raise a new story for new fields that we need). Do we need to do any more than that?

sanger / sequencescape