CPmicroEnvironment update

[arschat]

Project was published in DCP but donor metadata is inconsistent between DCP vs publication/GEO (34 vs 12 donor).

Project short name:

CPmicroEnvironment

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder, previous spreadsheet, updated spreadsheet

Published study links

• Paper: 10.1136/gutjnl-2021-324546

• Accessioned data: GSE165045

• ingest: c5ca43aa-3b2b-4216-8eb3-f57adcbc99a1

Key Events

• [ ] Convert published metadata to HCA spreadsheet
• [ ] Manually curate dataset to meet HCA metadata standard
• [ ] Collect any matrix and cell-type annotation files
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [ ] Upload sheet to validate metadata
• [ ] Transfer raw files to ingest to validate data files
• [ ] Check linking using ingest graph validator
• [ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Submit dataset to Production
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[arschat]

Donor information of original submission seem to be incorrect.

The number of donors according to Table 1 is 3+9=12 while in the original DCP submission is 34. It seems that each library listed in GEO had it's own donor while for each donor there were 3 different library protocols (scRNA-seq, CITE-seq, TCR-seq) with the exception of donors BL12, Idio4 and BL10, Idio2 who did not have CITE-seq (3 * 12 - 2 = 34 GSM accession).

It is now modelled with 12 entities in donor, specimen, cell_suspension.

[arschat]

New submission is now in graph valid. We need to decide if we want to keep file & protocol uuids or not:

1. new file & protocol uuids
   • new submission & clear staging area before re-submit
2. old file & protocol uuids
   • edit initial submission with enrique's script. clear staging area as well?

[arschat]

will proceed with solution number 2. @arschat to create a spreadsheet with updates and uuids, run first part of script and once good, share with @ESapenaVentura

[arschat]

hca-util-upload-area uuid: 7292c116-0ada-457f-8fa7-833c817674f2

[arschat]

I created a spreadsheet using the updated biomaterial metadata but all the existing uuids (biomaterials, processes, protocols, files).

[arschat]

Enrique fixed a typo I made in cell_suspensions uuids, we roll back the files schema version to the last version using data: prefix since EDAM: prefix does not yet work in prod

sequence_file: from 10.0.0 to 9.6.0 analysis_file: from 8.0.0 to 7.0.0

Fixed some graph invalid errors (specimen to file instead of cell suspension to file), fixed project title to match publication, cleaned staging area from previous submission and exported and import form sent.