Open Targets - Data Lakehouse Ready

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/opentargets-dataset")

fs.listdir("s3://aws-roda-hcls-datalake/opentargets_latest/")

Description:

This a Parquet representation of the Open Targets Platform's latest export. The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification. The Open Targets Platform (https://www.targetvalidation.org) is a freely available resource for the integration of genetics, genomics, and chemical data to aid systematic drug target identification and prioritisation. This dataset is 'Lakehouse Ready'. Meaning, you can query this data in-place straight out of the Registry of Open Data S3 bucket. Deploy this dataset's corresponding CloudFormation template to create the AWS Glue catalog entries into your account in about 30 seconds. That one step will enable you to write SQL with AWS Athena, build dashboards and charts with Amazon Quicksight, perform HPC with AWS EMR, or join into your AWS Redshift clusters. More detail in (the documentation)[https://github.com/aws-samples/data-lake-as-code/blob/roda/README.md.

Contact:

This a Parquet representation of the Open Targets Platform's latest export. The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification. The Open Targets Platform (https://www.targetvalidation.org) is a freely available resource for the integration of genetics, genomics, and chemical data to aid systematic drug target identification and prioritisation. This dataset is 'Lakehouse Ready'. Meaning, you can query this data in-place straight out of the Registry of Open Data S3 bucket. Deploy this dataset's corresponding CloudFormation template to create the AWS Glue catalog entries into your account in about 30 seconds. That one step will enable you to write SQL with AWS Athena, build dashboards and charts with Amazon Quicksight, perform HPC with AWS EMR, or join into your AWS Redshift clusters. More detail in (the documentation)[https://github.com/aws-samples/data-lake-as-code/blob/roda/README.md.

Update Frequency:

Within two weeks of new Open Targets releases

Managed By:

https://aws.amazon.com/

Resources:

1. resource:

   • Description: Latest Open Targets release. Updates within two weeks of new Open Targets version. Information on Open Targets releases can be found here.
   • ARN: arn:aws:s3:::aws-roda-hcls-datalake/opentargets_latest/
   • Region: us-east-1
   • Type: S3 Bucket

2. resource:

   • Description: Open Targets v20.06. Does not update.
   • ARN: arn:aws:s3:::aws-roda-hcls-datalake/opentargets_20_06/
   • Region: us-east-1
   • Type: S3 Bucket

3. resource:

   • Description: Open Targets v19.11. Does not update
   • ARN: arn:aws:s3:::aws-roda-hcls-datalake/opentargets_1911/
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

chemistry, genetic, genomic, molecule, life sciences, biotech blueprint, parquet

Tutorials:

1. tutorial:
   • Title: Data Lake as Code Deployment Guide
   • URL: https://github.com/aws-samples/data-lake-as-code/blob/roda/docs/roda_install.md
   • AuthorName: AWS Biotech Blueprints Team
   • Services: Athena, Glue, Lake Formation

Publication:

1. publication:
   • Title: Data Lake as Code, Featuring ChEMBL and Open Targets
   • URL: https://aws.amazon.com/blogs/startups/a-data-lake-as-code-featuring-chembl-and-opentargets/
   • AuthorName: Paul Underwood