Peng he - Fetal organoids

[ESapenaVentura]

Project short name:

FetalOrganoids

Primary Wrangler:

@ESapenaVentura

Secondary Wrangler:

TBD

Associated files:

• Google Drive: TBD (Brokered directly to arrayexpress)
• Accession: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11267?accession=E-MTAB-11267

Key Events

• [x] Send initial instructions about contributing, including questionnaire and T&Cs
• [x] Receive project questionnaire
• [x] Assign the Primary Wrangler
• [x] Receive T&C form filled out by at least 1 representative of group/project
• [ ] Send custom metadata template spreadsheet, how-to guide and directions for submitting data, matrix and cell annotation files.
• [ ] Receive spreadsheet (to a sufficient standard to submit dataset)
• [ ] Receive data, matrix and cell annotation files (to a sufficient standard to submit dataset)
• [ ] Curate metadata spreadsheet with ontologies
• [ ] Upload sheet to validate metadata
• [ ] Run graph validator & Check linking
• [ ] Validate data files
• [ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Get final approval of submission from the contributor including release date, metadata spreadsheet and data files
• [ ] Submit to production and inform ingest-devs the project is ready for archiving
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

Please track the below as well as the key events:

1. Track date first spreadsheet received and final spreadsheet sent by editing ticket to include date next to event.
2. Track spreadsheet iterations by placing asterisks next to receive spreadsheet event.
3. Track any metadata issues/tickets made for dataset with a bulleted list of links under received spreadsheet event. Links should be to the ticket in the metadata repo.

[ESapenaVentura]

Current status:

Can't broker to DCP yet. Data is still private.

[ofanobilbao]

@ESapenaVentura do we have any data or metadata yet? Or have we progressed? Or we have only been told it's coming?

[ofanobilbao]

@ESapenaVentura Is this even in Ingest? The ticket was opened nearly 2 years ago. And no movement. Should we simply close the ticket?

[ESapenaVentura]

This was release some time ago, but we weren't notified - https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11267?accession=E-MTAB-11267

[ofanobilbao]

This now is published on peer-reviewed journal. https://doi.org/10.1016/j.cell.2022.11.005

[ofanobilbao]

@ESapenaVentura and @Wkt8 I believe Wei pushed the pre-print to DCP. And we did not maybe connect the two together. If that's the case, I believe we can close this one. We could potentially add the peer-reviewed version of the paper to the DCP submitted project for completeness (tbd)