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10X Visium model integration #135

Merged
merged 26 commits into from
Aug 29, 2024
Merged

10X Visium model integration #135

merged 26 commits into from
Aug 29, 2024

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Bankso
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@Bankso Bankso commented Aug 2, 2024

Fixes #134

Changelog

  • Added attributes, valid values, mappings, and schema definitions for 10X Visium Level 1, 2, 3, 4, and Auxiliary Files
  • Updated 'dependsOn Component' fields throughout the model, to prep the model for visualization

A separate branch and PR will be used to add the documentation updates at a later date.

Google sheet links to models:
10X Visium RNA Spatial Profiling Level 1
10X Visium RNA Spatial Profiling Level 2
10X Visium RNA Spatial Profiling Level 3
10X Visium RNA Spatial Profiling Level 4
10X Visium Spatial Profiling Auxiliary Files

@Bankso Bankso added the major PR label for a major update label Aug 2, 2024
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@aditigopalan aditigopalan left a comment

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@Bankso is the empty column at the end expected for all these files? The rest looks good to me!

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Bankso commented Aug 16, 2024

@Bankso is the empty column at the end expected for all these files?

That's a good question - which files do you mean?

The final columns for the annotationProperty and valid value CSVs are Validation Rules and nonpreferred_values, respectively. In a lot of situations, we don't end up having values in those columns.

For the google sheet templates, I think the empty right-hand columns are ignored when the CSV gets downloaded

@aditigopalan
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@Bankso is the empty column at the end expected for all these files?

That's a good question - which files do you mean?

The final columns for the annotationProperty and valid value CSVs are Validation Rules and nonpreferred_values, respectively. In a lot of situations, we don't end up having values in those columns.

For the google sheet templates, I think the empty right-hand columns are ignored when the CSV gets downloaded

Ah that clarifies it, makes sense!

@aditigopalan aditigopalan merged commit aee7c84 into main Aug 29, 2024
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@aditigopalan aditigopalan deleted the visium-model branch August 29, 2024 13:43
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Integrate the HTAN 10X Visium Data Model
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