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brain-bican / metadata-schemas

A repository for BICAN metadata schemas and their development.
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New Metadata Schema Request: Image-based Spatial Transcriptomics #49

Open rightbower opened 1 month ago

rightbower commented 1 month ago

Contact Details

pamela.baker@alleninstitute.org

Schema Name

Image-based Spatial Transcriptomics Metadata

Oranizational Usage

BICAN

General Description

This is a metadata schema that describes the metadata requirements for sample registration and data submission for image-based spatial transcriptomics experiments, from tissue processing to imaging. There are separate sheets for donor/specimne metadata at NIMP and BIL, bench chemistry and imaging metadata, and gene panel metadata.

Suggested Reviewers

@djarecka @MariahKenney @rightbower

What format are you submitting your schema in?

.xlsx or .csv or .tsv

Completed README

patrick-lloyd-ray commented 1 month ago

@ucscbrianlee would also be a good reviewer here.

ucscbrianlee commented 1 month ago

@ucscbrianlee would also be a good reviewer here.

Thanks!

This all looks great, thank you for giving me the opportunity to be a reviewer.

For the chemistry and imaging metadata, I was curious about the "light treatment time" field. This isn't one that I've seen in other groups (HuBMAP/HTAN), and also was not considering for our SSPsyGene schema, the consortium I am working on where we also have spatial transcriptomics and MERFISH data. I am guessing that light treatment came up when gathering input from BICAN generating labs? I see that this field is "if applied" and so it looks great for BICAN. I am more asking in case SSPsyGene should consider this field, or how it was decided it add it.

I shared on Gene Panel Metadata.csv that for SSPsyGene we landed on HGNC identifiers for gene symbol, while also planning to use Ensembl for IDs. I would be curious if there was any input/feedback to SSPsyGene about using HGNC versus NCBI/Ensembl for gene name/symbol.

patrick-lloyd-ray commented 1 month ago

@djarecka @MariahKenney @rightbower @ucscbrianlee

Would you be able to discuss progress on this at the WG meeting next week?

ucscbrianlee commented 1 month ago

Thank you again for the opportunity to participate with the metadata schema. I would be happy to share comments from the perspective of my SSPsyGene spatial transcriptomics attempts to build a version1 of metadata (our group likely will not be receiving CODEX/CosMx data until Q2 of 2025 it looks like currently; we currently do have some MERFISH).

patrick-lloyd-ray commented 1 month ago

Great! If the other reviewers are prepared to push this schema forward for discussion, I think that would be a good addition.

djarecka commented 1 month ago

I left the comments in the PR, but I'm also happy to discuss during the meeting

patrick-lloyd-ray commented 1 month ago

I left the comments in the PR, but I'm also happy to discuss during the meeting

Will you be able to fix what is wrong with the schema before the meeting?

djarecka commented 1 month ago

I left the comments in the PR, but I'm also happy to discuss during the meeting

Will you be able to fix what is wrong with the schema before the meeting?

Sorry, but I mostly had questions, and pointed to some parts that seem inconsistent to me, I'm not sure how to fix it