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Map blueprint ontology to CL names#983

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allyhawkins merged 5 commits intoAlexsLemonade:mainfrom
allyhawkins:allyhawkins/map-blueprint-ontology-name
Jan 14, 2025
Merged

Map blueprint ontology to CL names#983
allyhawkins merged 5 commits intoAlexsLemonade:mainfrom
allyhawkins:allyhawkins/map-blueprint-ontology-name

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Purpose/implementation Section

Please link to the GitHub issue that this pull request addresses.

Closes #979

What is the goal of this pull request?

Here I am adding a column that maps the ontology ID in BlueprintEncodeData to the CL name found in the cell type ontology.

Briefly describe the general approach you took to achieve this goal.

  • I updated the script that creates the consensus reference table to include a column for the mapped name blueprint_annotation_cl. This also means a huge diff for this file since it includes a new column.
  • Since the reference that we have doesn't have every combination of assignments (due to size constraints), I also map the IDs in the script to combine all tables and add consensus labels. Ultimately, I chose to remove the blueprint_annotation_fine column altogether and just use the blueprint_annotation_cl column.
  • I then updated the readme to reflect this change.

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Analysis module and review

Reproducibility checklist

  • Code in this pull request has been added to the GitHub Action workflow that runs this module.
  • The dependencies required to run the code in this pull request have been added to the analysis module Dockerfile.
  • If applicable, the dependencies required to run the code in this pull request have been added to the analysis module conda environment.yml file.
  • If applicable, R package dependencies required to run the code in this pull request have been added to the analysis module renv.lock file.

@allyhawkins allyhawkins requested review from jashapiro and removed request for jaclyn-taroni January 13, 2025 21:40
@allyhawkins allyhawkins changed the title Allyhawkins/map blueprint ontology name Map blueprint ontology to CL names Jan 13, 2025
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LGTM

@allyhawkins
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I'm going to cancel the workflow run for this module since the changes I just had to merge in from main aren't relevant.

@allyhawkins allyhawkins merged commit b870a08 into AlexsLemonade:main Jan 14, 2025
@allyhawkins allyhawkins deleted the allyhawkins/map-blueprint-ontology-name branch January 14, 2025 21:00
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Successfully merging this pull request may close these issues.

Use names from cell type ontology (CL) instead of blueprint names in consensus reference

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