Datasets:

OpenMed
/

pgc-mdd

Error code:   InfoError
Exception:    DataFilesNotFoundError
Message:      No (supported) data files found in OpenMed/pgc-mdd
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 223, in compute_first_rows_from_streaming_response
                  info = get_dataset_config_info(path=dataset, config_name=config, token=hf_token)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 268, in get_dataset_config_info
                  builder = load_dataset_builder(
                            ^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1315, in load_dataset_builder
                  dataset_module = dataset_module_factory(
                                   ^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1201, in dataset_module_factory
                  raise e1 from None
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1182, in dataset_module_factory
                  ).get_module()
                    ^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 645, in get_module
                  module_name, default_builder_kwargs = infer_module_for_data_files(
                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 306, in infer_module_for_data_files
                  raise DataFilesNotFoundError("No (supported) data files found" + (f" in {path}" if path else ""))
              datasets.exceptions.DataFilesNotFoundError: No (supported) data files found in OpenMed/pgc-mdd

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PGC Major Depressive Disorder — GWAS Summary Statistics

Dataset Description

Genome-wide association study (GWAS) summary statistics for Major Depressive Disorder phenotypes from the Psychiatric Genomics Consortium (PGC).

Each publication is available as a separate subset (config) and can be loaded independently.

Usage

from datasets import load_dataset

# Load a specific GWAS
ds = load_dataset("OpenMed/pgc-mdd", "AntiDepResponse2021")
print(ds)

List all available subsets

from datasets import get_dataset_config_names
print(get_dataset_config_names("OpenMed/pgc-mdd"))

Subsets

Config	Phenotype	Journal	Year	PubMed
`AntiDepResponse2021`	Antidepressant Response	Biol Psychiatry: Global Open Science	2021	Pending
`mdd2013`	Major Depression	Molecular Psychiatry	2013	22472876
`mdd2018`	Major Depression	Nature Genetics	2018	29700475
`mdd2018_noUKBB`	Major Depression (no UK Biobank)	Nature Genetics	2018	29700475
`mdd2021asi`	Major Depression (East Asian)	JAMA Psychiatry	2021	34586374
`mdd2023diverse`	Major Depression (Multi-Ancestry)	Nature Genetics	2023	38177345
`mdd2025`	Major Depression	Cell	2025	39814019
`ppd2023`	Peripartum Depression	American Journal of Psychiatry	2023	37849304

Data Format

All data is stored as Apache Parquet shards (10,000 rows each). Common columns:

Column	Description
`SNP` / `ID`	SNP rsID or variant identifier
`CHR`	Chromosome
`BP` / `POS`	Base-pair position (typically GRCh37/hg19)
`A1`	Effect allele
`A2`	Non-effect allele
`OR` / `BETA`	Odds ratio or effect size
`SE`	Standard error
`P`	P-value
`_source_file`	Original source filename