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Bulk datasets from eQTL Catalogue are classified as single cell #3589

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ireneisdoomed opened this issue Oct 21, 2024 · 0 comments · May be fixed by opentargets/gentropy#894
Open
4 tasks

Bulk datasets from eQTL Catalogue are classified as single cell #3589

ireneisdoomed opened this issue Oct 21, 2024 · 0 comments · May be fixed by opentargets/gentropy#894
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Genetics Relates to Open Targets genetics team

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@ireneisdoomed
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Describe the bug
The distinction between bulk and single cell datasets from eQTL Catalogue is based on the ontology of the measured trait, which is not accurate.

Observed behaviour
In the step that processes eQTL Catalogue SuSIE results to generate credible sets and a study index we infer what type of data was analysed (bulk / single cell results) based on the ontology of the mapped trait.

Because this inference is not accurate (there are many bulk datasets mapped to an UBERON), we have contacted the eQTL Catalogue to include this metadata as part of their study table.
https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/blob/master/data_tables/dataset_metadata_upcoming.tsv

Expected behaviour
To correctly distinguish between single cell and bulk datasets based on the studyType.

To Reproduce
Steps to reproduce the behaviour:

  • To update raw_studies_metadata_path to point to the latest study table
  • To update raw_studies_metadata_schema to add the new column
  • To update _identify_study_type to represent single cell study types
  • Because we take the study table as a template to which studies to ingest, we want to make sure that updating this table doesn't break the process. Are we ingesting more studies with the update?
@ireneisdoomed ireneisdoomed added the Genetics Relates to Open Targets genetics team label Oct 21, 2024
@Tobi1kenobi Tobi1kenobi self-assigned this Oct 28, 2024
@Tobi1kenobi Tobi1kenobi linked a pull request Nov 4, 2024 that will close this issue
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