EGAS00001004653 - PancreasTopographiesTosti10x

arschat commented 2 months ago

Project short name:

~~SPAN~~ PancreasTopographiesTosti10x

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

Google Drive: folder
ingest: b3938158-4e8d-4fdb-9e13-9e94270dde16

Published study links

Paper: 10.1053/j.gastro.2020.11.010
Accessioned data: EGAS00001004653 supl_link

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 commented 2 months ago

Dataset has been partially wrangled, but it contains invalid metadata. Should be revised and resubmitted as is part of Pancreas bionetwork list.

arschat commented 2 months ago

Seems that project was partially wrangled by Ami, but abandoned because no sequence or analysis files were available at that time #827 Now analysis files are available at http://singlecell.charite.de/pancreas, I've downloaded them and start wrangling dataset again.

arschat commented 2 months ago

Removing previous submission since it had not being published before. Spreadsheet saved here.

arschat commented 2 months ago

hca-util area 39d07165-5711-4c82-870a-7496214fde73

I added the schema tab in the spreadsheeet to specify the version of the files that allows the validation (until EDAM update is completed).

arschat commented 2 months ago

Graph valid and ready for sec review!

idazucchi commented 2 months ago

Hi! Nice job on this dataset, I have only a couple of small comments

Donor / Specimen

I think the disease for TUM_13_donor could be pancreatic neuroendocrine neoplasm since the tumor is reported as a pancreatic disease
for donor TUM_C1_donor : From this paper it sounds like Mixed Muellerian Tumor is a malignant tumor affecting the uterus that can rarely develop metastasis in the pancreas. I would suggest carcinosarcoma in place of adenofibroma because adenofibroma has benign mixed Muellerian tumor as synonym.

Collection protocol

shouldn't Standford_protocol be collecting specimen from organ postmortem? the donors are dead at collection time

Cell suspension

very minor -but- should we change the description to Nuclei suspension?

Analysis file

input CS for chronic_* files should be TUM_CP1_nuc and TUM_CP2_nuc

arschat commented 2 months ago

Nice catch on the wrong CS for the chronic_* files! Thank you for the review. I applied all changes to the submission, and is now exported!

[x] import form sent

arschat commented 2 months ago

Noticed a flip of diseases for donors TUM_25_donor and TUM_C1_donor. Replaced that in staging area's metadata jsons.

Copied contents of the json files

gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json
gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json

Created locally the files and flipped the diseases field with text editor

Uploaded edited files to staging area

gsutil cp 2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json
gsutil cp 0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json

I updated both biomaterials in ingest as well TUM_25_donor, and TUM_C1_donor
change status to exported

it was indeed a mistake:
- TUM_C1_donor has to have pancreatic ductal adenocarcinoma and it had carcinosarcoma -> Mixed Muellerian Tumor
- TUM_25_donor has to have carcinosarcoma -> Mixed Muellerian Tumor and it had pancreatic ductal adenocarcinoma

arschat commented 4 weeks ago

verified in browser

ebi-ait / hca-ebi-wrangler-central