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Datasets:
OpenMed
/
pgc-other

Tasks:
Tabular Regression
Tabular Classification
Modalities:
Tabular
Text
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
gwas
summary-statistics
psychiatric-genomics
pgc
other
mental-health
Libraries:
Datasets
Dask
Polars
License:
Dataset card Data Studio Files
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MaziyarPanahi commited on
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Add PGC Other Psychiatric Conditions GWAS summary statistics (parquet, 10k-row shards)

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  1. .gitattributes +1 -0
  2. README.md +107 -0
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.gitattributes CHANGED
@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
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+ supplementary/ciac/ciac.readme.docx filter=lfs diff=lfs merge=lfs -text
README.md ADDED
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+ ---
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+ license: cc-by-4.0
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+ task_categories:
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+ - tabular-regression
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+ - tabular-classification
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+ tags:
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+ - gwas
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+ - summary-statistics
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+ - psychiatric-genomics
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+ - pgc
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+ - other
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+ - mental-health
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+ - genetics
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+ - genomics
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+ pretty_name: >-
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+ PGC Other Psychiatric Conditions GWAS Summary Statistics
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+ size_categories:
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+ - 1M-10M
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+ configs:
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+ - config_name: "bpd2025"
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+ data_files:
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+ - split: train
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+ path: "data/bpd2025/*.parquet"
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+ - config_name: "ciac"
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+ data_files:
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+ - split: train
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+ path: "data/ciac/*.parquet"
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+ ---
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+
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+ # PGC Other Psychiatric Conditions — GWAS Summary Statistics
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+
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+ [![License: CC BY 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey)](https://creativecommons.org/licenses/by/4.0/)
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+
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+ ## Dataset Description
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+
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+ Genome-wide association study (GWAS) summary statistics for **Other Psychiatric Conditions** phenotypes from the [Psychiatric Genomics Consortium (PGC)](https://pgc.unc.edu/).
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+
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+ This dataset contains multiple GWAS publications as separate subsets (configs). Each can be loaded independently.
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+
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+ ## Usage
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+
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+ ```python
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+ from datasets import load_dataset
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+
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+ # Load a specific GWAS (e.g., bpd2025)
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+ ds = load_dataset("OpenMed/pgc-other", "bpd2025")
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+ print(ds)
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+ ```
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+
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+ ### Available Configs
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+
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+ ```python
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+ from datasets import get_dataset_config_names
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+ configs = get_dataset_config_names("OpenMed/pgc-other")
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+ print(configs)
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+ ```
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+
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+ ## Subsets (Publications)
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+
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+ | Config | Phenotype | Journal | Year | PubMed | Rows | License |
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+ |--------|-----------|---------|------|--------|------|---------|
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+ | `bpd2025` | Borderline Personality Disorder | Nature Genetics | 2025 | Pending | 30,901,961 | CC BY 4.0 |
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+ | `ciac` | Clozapine-Induced Agranulocytosis | Nature Communications | 2014 | [25187353](https://pubmed.ncbi.nlm.nih.gov/25187353/) | — | CC BY 4.0 |
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+
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+ ## Data Format
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+
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+ All data has been converted to **Apache Parquet** format with shards of 10,000 rows. Common columns include:
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+
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+ | Column | Description |
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+ |--------|-------------|
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+ | `SNP` / `ID` | SNP rsID or variant identifier |
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+ | `CHR` | Chromosome |
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+ | `BP` / `POS` | Base-pair position (typically GRCh37/hg19) |
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+ | `A1` / `ALT` | Effect allele |
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+ | `A2` / `REF` | Non-effect (reference) allele |
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+ | `OR` / `BETA` | Odds ratio or effect size |
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+ | `SE` | Standard error |
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+ | `P` | P-value |
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+ | `INFO` | Imputation quality score |
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+ | `FRQ` / `MAF` | Allele frequency |
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+ | `_source_file` | Original source filename |
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+
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+ > **Note:** Column names vary between publications. The `_source_file` column tracks the original file each row came from.
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+
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+ ## Citation
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+
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+ When using any subset, please cite:
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+
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+ 1. The **original publication** (see PubMed links above)
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+ 2. The **data DOI** from Figshare (see supplementary metadata)
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+ 3. **Acknowledge the PGC:**
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+ > "Data were obtained from the Psychiatric Genomics Consortium — https://pgc.unc.edu/"
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+
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+ ## Terms of Use
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+
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+ This dataset is released under the **[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)** license.
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+
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+ By using PGC summary statistics you agree to:
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+
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+ 1. Cite the original publication(s)
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+ 2. Not attempt to re-identify individual participants
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+ 3. Comply with the PGC's [data use policies](https://pgc.unc.edu/for-researchers/data-access/)
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+
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+ ## Source
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+
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+ - **Consortium:** [Psychiatric Genomics Consortium (PGC)](https://pgc.unc.edu/)
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+ - **PGC Downloads:** [pgc.unc.edu/for-researchers/download-results/](https://pgc.unc.edu/for-researchers/download-results/)
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