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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.
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?
The text was updated successfully, but these errors were encountered:
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:
raw_studies_metadata_path
to point to the latest study tableraw_studies_metadata_schema
to add the new column_identify_study_type
to represent single cell study typesThe text was updated successfully, but these errors were encountered: