Skin Atlas Bionetwork

[idazucchi]

Context: Following the general HCA meetings in June 2022 (see here) we decided to work directly with the organ Bionetworks to support them as they assemble the first drafts of organ atlases. Gabs first got in touch with the skin bionetwork and this will be an opportunity to figure out how we can work with the bionetworks, figure out what they need and how we can help.

Description of the task: to be expanded / make tickets as we take on the tasks

1. figure out how many projects need to be wrangled #850
2. define our priorities - in line with Maria (head of the skin bionetwork?)
   • is there a more important dataset?
   • do we want to work with the contributor who still need to deposit their data first? do they need archiving?
   • prioritise more complex/larger datasets?
3. discuss a timeline with Maria?
4. discuss with Maria the need for skin specific schema fields
5. discuss with Maria their needs for metadata format -
   • converting from HCA spreadsheet to a flattened version
   • do they need to have something more similar to cellxgene? so metadata by barcode?
6. start wrangling
7. start discussion on how to display and curate the atlas draft

Link to spreadsheet here.

Acceptance criteria for the task:

• [x] all the tasks have been discussed
• [x] each dataset has a ticket
• [ ] all the datasets have been wrangled

[idazucchi]

We are setting up a follow up meeting with the skin atlas team and possibly one with Hao to discuss the metadata format

[idazucchi]

I'm sending the metadata spreadsheets that are ready to Maria so that she can start working on them and use as starting point to request additional metadata from the authors

We should have another 2 ready in the next few days hopefully - ami's and mine

[arschat]

Based on the paper A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization, an update on the publication list and the metadata can be done.

Metadata in Supplementary Table 2 (download) are identical to ES comparisson done here with only difference being:

• study_ID is added with the DOI of the publication
• skin_disorders renamed to skin_disorder and skin_disorder_type is removed
• In Validation tab all fields now have NA (not available) option.
• On Notes tab, skin_disorders is mentioned as know_skin_disease

Out of the 40 publications listed, there are 13 already in DCP, and 8 in ingest.

[arschat]

Bionetwork Spreadsheet Updated with the new projects from Roadmap Atlas paper. https://docs.google.com/spreadsheets/d/129T_QsKKCqJmPiwuK9qLl7uxASUplI84At6ewu2vwLA/edit#gid=1334414990

All projects are on ingest, and for some we need to contact the authors (i.e. 1, 2, 3)

Status	Count
Published in DCP	15
Submitted	1
In Progress	0
Stalled	3
Eligible	21
TOTAL	40

There is one lattice project that on ingest is labeled as submitted but there is no submission at all (on dcp, in import request form, or on ingest).

[arschat]

Updated table here (wave 2 projects)