opentargets/clinical_evidence

OpenTargets Clinical Evidence Dataset

This OpenTargets clinical evidence dataset represents a comprehensive collection of clinical trial data linking genetic targets to diseases, containing 32 structured columns that capture the complete lifecycle of clinical studies. The dataset is annotated with clinical trials' predicted stop reason and genetic evidence when available and was referenced in the Why Clinical Trials Stop: The Role of Genetics. The study analyzed 28,842 stopped clinical trials and demonstrated that genetic evidence significantly influences trial efficacy.

This dataset was generated with the 22.04 Open Targets Data with this script.

Tutorial

To access the dataset, you can use HF datasets:

from datasets import load_dataset

ds = load_dataset("opentargets/clinical_evidence")

# see first record
next(ds.iter(1))

Features

The dataset contains a lot of genetic and clinical features which can be used for ML modelling.

The features are summarized in the table below:

Column Name	Data Type	Description	Example Values
targetId	string	Ensembl gene identifier representing the target gene	ENSG00000004468, ENSG00000065518
diseaseId	string	Disease ontology identifier using EFO or MONDO terms	EFO_0000203, MONDO_0005148
nctid	string	ClinicalTrials.gov identifier for the clinical trial	NCT03236428, NCT01089192
clinicalStatus	string	Current status of the clinical trial	Active, not recruiting, Completed, Withdrawn, Terminated, Suspended
clinicalPhase	int64	Numeric representation of the clinical trial phase	1, 2, 3, 4
studyStartDate	string	Date when the clinical trial began (YYYY-MM-DD format)	2017-11-24, 2016-11-30
stopStatus	string	Reason for trial discontinuation (null if ongoing/completed normally)	null, Withdrawn, Terminated, Suspended
isStopped	string	Boolean indicator if the trial was stopped	stopped, null
phase4	string	Indicates if this is a Phase IV (post-marketing) trial	Phase IV, null
phase3	string	Indicates if this is a Phase III trial	Phase III+, null
phase2	string	Indicates if this is a Phase II trial	Various phase indicators, null
id	int64	Internal record identifier	Numeric identifiers
why_stopped	string	Detailed reason why a trial was discontinued	Trial-specific discontinuation reasons
phase	string	String representation of the trial phase	Phase descriptors
status	string	Trial status information	Status descriptions
last_update_posted_date	string	Most recent update to the trial record	Date strings
completion_date	string	Date when the trial was completed (if applicable)	Date strings
prediction	string	Computational prediction about the target-disease association	Prediction values
metaprediction	string	Meta-analysis prediction combining multiple evidence sources	Meta-prediction values
max_l2g	double	Maximum locus-to-gene (L2G) score indicating genetic evidence strength	Floating point scores
l2g_075	string	L2G score threshold at 0.75 confidence level	Threshold indicators
l2g_05	string	L2G score threshold at 0.5 confidence level	Threshold indicators
l2g_025	string	L2G score threshold at 0.25 confidence level	Threshold indicators
l2g_01	string	L2G score threshold at 0.1 confidence level	Threshold indicators
l2g_005	string	L2G score threshold at 0.05 confidence level	Threshold indicators
taId	string	Therapeutic area identifier	Therapeutic area codes
taLabel	string	Full therapeutic area label	Therapeutic area names
taLabelSimple	string	Simplified therapeutic area label	Simplified area names
gc	double	Gene constraint score	Floating point constraint scores
lof_tolerance	string	Loss-of-function tolerance classification	Tolerance classifications
rnaDistribution	string	RNA expression distribution pattern	Distribution patterns
rnaSpecificity	string	RNA expression specificity	Specificity measures
partnersBin	string	Protein interaction partners classification	Partner classifications
datasourceId	string	Identifier for the data source	Data source identifiers
datatypeId	string	Type of evidence data	Evidence type identifiers
total	int64	Total count or score for the evidence	Numeric totals

Citation

@article{razuvayevskaya2023clinical,
  title={Why Clinical Trials Stop: The Role of Genetics},
  author={Razuvayevskaya, Olesya and Lopez, Irene and Dunham, Ian and Ochoa, David},
  journal={medRxiv},
  pages={2023--02},
  year={2023},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2023.02.07.23285407}
}

OpenTargets

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Reproduction

Dataset was generated with the 22.04 Open Targets Data with this script.