Data Download
You can get all data from Open Targets Genetics via:
EMBL-EBI FTP, database Open Targets Genetics
Google BigQuery, project open-targets-genetics:genetics
Google Cloud Storage (GCS) paywalled public bucket
Please note that if you download this data using Google Cloud Storage, all charges to bucket open-targets-genetics-releases
will be billed to the requester.
Please refer to the Requester Pays feature for Google Cloud Storage for more detail.
Data Schema
The list of datasets with each corresponding data schema
Please change the URL tags to their corresponding tables, stated above, as required.
Folder name | Format | Spark Schema | SQL Schema (Clickhouse Dialect) |
---|---|---|---|
variant-index | parquet | - | - |
v2g | jsonl | ||
v2d | jsonl | ||
d2v2g | jsonl | - | |
lut/genes-index | jsonl | - | |
lut/overlap-index | jsonl | - | |
lut/study-index | jsonl | - | |
lut/variant-index | jsonl | - |
Some Tips
Previewing datasets from the GCS bucket
The gsutil
command can be used to preview datasets prior to downloading:
Loading data into a ClickHouse instance
There is an initial bash script you can use in order to load all data into a ClickHouse instance. In that script, you will find lines like this
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