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MBC metadata not correct #600

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leexgh opened this issue Mar 12, 2024 · 1 comment
Open

MBC metadata not correct #600

leexgh opened this issue Mar 12, 2024 · 1 comment

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@leexgh
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leexgh commented Mar 12, 2024

MBC metadata is not correct, especially for cvs files.
E.g. Looking at the codex data, in htan portal for HTA1_213_6752303, the data file id is HTA1_213_6752303111.
https://humantumoratlas.org/explore?selectedFilters=%5B%7B%22group%22%3A%22AtlasName%22%2C%22value%22%3A%22HTAN+HTAPP%22%7D%2C%7B%22value%22%3A%22CODEX%22%2C%22group%22%3A%22assayName%22%2C%22count%22%3A13%2C%22isSelected%22%3Afalse%7D%5D&tab=file#
image
But for HTA1_213_6752 there are codex_level2 and codex_level3 available, the parent Id should not point to biospecimen id

@clarisse-lau
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Hi @leexgh - these are integrated h5ad files for which we are releasing under OtherAssay with the understanding that upstream CODEX level 2&3 data remains unreleased (I don't see codex_level2 and codex_level3 for HTA1_213_6752 on the portal, nor any CSVs for codex. Can you let me know where you're seeing these?)

As the integrated data files are annotated under the minimal template, only HTAN Parent Biospecimen ID is provided. We can use this as the link to biospecimen/clinical data.

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