Data Download

You can get all data from Open Targets Genetics via:

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.

Versioning Table

Data

19.03.03

10.05.05

Backend scripts

19.03.08

19.05.28

Spark pipeline

19.03.10

19.05.15

GraphQL API

19.03.11

19.05.26

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

schema link

schema link

v2d

jsonl

schema link

schema link

d2v2g

jsonl

-

schema link

lut/genes-index

jsonl

-

schema link

lut/overlap-index

jsonl

-

schema link

lut/study-index

jsonl

-

schema link

lut/variant-index

jsonl

-

schema link

Some Tips

Checking some lines from the GCS Bucket

You can potentially stream the content directly from a Google Cloud Bucket using gsutil command

gsutil cat 'gs://open-targets-genetics-releases/19.03.04/lut/variant-index/part-*' | head -1 | jq .
{
"chr_id": "1",
"position": 55545,
"ref_allele": "C",
"alt_allele": "T",
"rs_id": "rs28396308",
"most_severe_consequence": "downstream_gene_variant",
"gene_id_any_distance": 13546,
"gene_id_any": "ENSG00000186092",
"gene_id_prot_coding_distance": 13546,
"gene_id_prot_coding": "ENSG00000186092",
"raw": 0.028059,
"phred": 3.065,
"gnomad_afr": 0.3264216148287779,
"gnomad_amr": 0.4533582089552239,
"gnomad_asj": 0.26666666666666666,
"gnomad_eas": 0.35822021116138764,
"gnomad_fin": 0.31313131313131315,
"gnomad_nfe": 0.26266330506532204,
"gnomad_nfe_est": 0.3397858319604613,
"gnomad_nfe_nwe": 0.23609443777511005,
"gnomad_nfe_onf": 0.2256,
"gnomad_nfe_seu": 0.1,
"gnomad_oth": 0.27403846153846156
}

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

echo create studies tables
clickhouse-client -m -n < studies_log.sql
gsutil cat "${base_path}/lut/study-index/part-*" | clickhouse-client -h 127.0.0.1 --query="insert into ot.studies_log format JSONEachRow "
clickhouse-client -m -n < studies.sql
clickhouse-client -m -n -q "drop table ot.studies_log;"