The Human and Mouse Enteric Nervous System at Single-Cell Resolution

ebi-ait / hca-ebi-wrangler-central

This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.

https://ebi-ait.github.io/hca-ebi-wrangler-central/

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The Human and Mouse Enteric Nervous System at Single-Cell Resolution #784

Closed idazucchi closed 2 years ago

idazucchi commented 2 years ago

Project short name:

HumanMouseEntericNervousSystem

Primary Wrangler:

Ami

Secondary Wrangler:

Wei

Associated files

Published study links

Paper: The Human and Mouse Enteric Nervous System at Single-Cell Resolution
Accessioned data: single cell portal

Ingest

Key Events

[ ] Convert published metadata to HCA spreadsheet
[ ] Manually curate dataset to meet HCA metadata standard
[ ] Collect any matrix and cell-type annotation files
[ ] Upload sheet to validate metadata
[ ] Check linking using ingest graph validator
[ ] Transfer raw files to ingest to 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
[ ] Submit dataset to Production
[ ] Complete the Export SOP
[ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

ami-day commented 2 years ago

Need information from the authors. Sent them an email.

Wkt8 commented 2 years ago

Have had a look and made some changes and comments! See (https://docs.google.com/spreadsheets/d/11D-IBFeG0JTyXMUyFvLO6we9lZoa9d8u/edit?usp=sharing&ouid=114069941208994528669&rtpof=true&sd=true) Donor Organism Tab:

There were multiple duplicate mice in the donor_organism tab (e.g. M1_colon_plate and M1_colon_droplet). Whilst these are separate cell suspensions, there is only 1 donor_organism (Mouse with ID M1). I removed the duplicate mice and changed the donor_organism IDs
I also changed the strains of the mice to the strain mentioned in the publication
I also changed the Input Donor Organism ID column in the specimen_from_organism tab

ami-day commented 2 years ago

Thanks @Wkt8 !

The publication wasn't clear so I asked the authors about their donor-sample linkings. They said that the mouse donors with identical mouse IDs in the different tabs are actually different mice for the plate vs droplet and colon vs ileum samples, and linked to different donor metadata (sex and age for example). So, there are multiple M1 mice, for example. They are not duplicates.

I will have a look at the mice strains you added and add them, if it makes sense based on the mouse donors given they are not duplicated.

ami-day commented 2 years ago

Waiting to hear back about SCP bulk data download. The SCP team said thy would change our data quote for today so we can download all the bam files.

ami-day commented 2 years ago

Validated in ingest staging.

Wkt8 commented 2 years ago

Issues with downloading sequence files from the SCP (they have a daily quota on downloads). They have raised Ami's download quota to facilitate downloading.

ami-day commented 2 years ago

bam files are converting to fastq files.

ami-day commented 2 years ago

Exported.

Wkt8 commented 2 years ago

The supplementary links for this project (https://data.humancellatlas.org/explore/projects/7be05025-9972-493a-856f-3342a8d1b183?catalog=dcp17) are not formatted correctly. They are showing up all as one big link rather than three separate links.

The project information description is not the same as the project abstract.

There was also an existing project for this in Ingest from the import-from-valentin's script which had most of the appropriate project information - it would be good to use these projects instead of creating new ones!

ami-day commented 2 years ago

The supplementary links for this project (https://data.humancellatlas.org/explore/projects/7be05025-9972-493a-856f-3342a8d1b183?catalog=dcp17) are not formatted correctly. They are showing up all as one big link rather than three separate links.

The project information description is not the same as the project abstract.

There was also an existing project for this in Ingest from the import-from-valentin's script which had most of the appropriate project information - it would be good to use these projects instead of creating new ones!

Thanks for checking @Wkt8 ! I will fix the supplementary links now and keep in mind using the existing projects for next time. For now I have updated the project form with the initial relevant project metdata.

I think we didn't ever have a rule that the project description should be the same as the project abstract. I prefer to provide a shorter overview for the project description, as opposed to copy and pasting the abstract.

ami-day commented 2 years ago

Update done (https://contribute.data.humancellatlas.org/submissions/detail?uuid=c3e29a85-51e5-4a96-89a5-37e9b9a9593b&project=7be05025-9972-493a-856f-3342a8d1b183). The project is now in Complete status, have asked the devs to push it back to metadata valid status, so it can be re-graph validated and re-exported.

ESapenaVentura commented 2 years ago

Pushed to valid, should be able to re-validate graph and submit now

ESapenaVentura commented 2 years ago

Please update on status - Did you do the updates? the project was exported as part of 809

ami-day commented 2 years ago

Yes the updates were done and it was exported.

ESapenaVentura commented 2 years ago

Re-opening as the updates need to be checked in the browser once they go live

gabsie commented 2 years ago

This is exported, needs an import form for release 20. @ami-day

ami-day commented 2 years ago

Submitted the import form