data/README.md

metadata

license: cc-by-sa-4.0
language:
  - en
tags:
  - drug-target-interaction
  - clinical-trials
  - protein-protein-interaction
  - negative-results
  - benchmark
  - bioinformatics
task_categories:
  - text-classification
  - question-answering
  - text-generation
size_categories:
  - 10M<n<100M

NegBioDB: A Negative Results Database for Biomedical Sciences

NegBioDB is a large-scale database of experimentally confirmed negative results across three biomedical domains, paired with dual ML/LLM benchmarks for evaluating how well computational methods handle negative evidence.

Overview

Domain	Negative Results	Entities	Benchmark Tasks
DTI (Drug-Target Interaction)	24,965,618 pairs	919K compounds, 3.7K targets	ML (M1) + LLM (L1-L4)
CT (Clinical Trial Failure)	102,850 results	216K trials, 176K interventions	ML (M1-M2) + LLM (L1-L4)
PPI (Protein-Protein Interaction)	2,220,786 pairs	18.4K proteins	ML (M1)

Data Sources

DTI Domain

Source	License	Contribution
ChEMBL 34	CC BY-SA 3.0	Curated bioactivity data
PubChem BioAssay	Public domain	HTS screening results
BindingDB	CC BY-SA 3.0	Binding measurements
DAVIS	CC BY 4.0	Kinase selectivity panel

CT Domain

Source	License	Contribution
AACT (ClinicalTrials.gov)	Public domain	Trial metadata
Open Targets	Apache 2.0	Drug-target mappings
CTO	MIT	Clinical trial outcomes
Shi & Du 2024	CC BY 4.0	Safety/efficacy data

PPI Domain

Source	License	Contribution
IntAct	CC BY 4.0	Curated non-interactions
HuRI	CC BY 4.0	Y2H systematic negatives
hu.MAP 3.0	CC BY 4.0	Complex-derived negatives
STRING v12.0	CC BY 4.0	Zero-score protein pairs

File Structure

DTI Files

File	Size	Rows	Description
negbiodb_dti_pairs.parquet	139.4 MB	24,965,618	All negative DTI pairs with metadata
negbiodb_m1_balanced.parquet	270.2 MB	1,725,446	M1 balanced dataset (1:1 pos:neg)
negbiodb_m1_realistic.parquet	753.3 MB	9,489,953	M1 realistic dataset (1:10 pos:neg)
negbiodb_m1_uniform_random.parquet	467.3 MB	1,767,380	Control: uniform random negatives
negbiodb_m1_degree_matched.parquet	274.9 MB	1,767,380	Control: degree-matched negatives
negbiodb_m1_balanced_ddb.parquet	1.0 GB	1,725,446	M1 balanced with degree-balanced split

CT Files

File	Size	Rows	Description
ct/negbiodb_ct_pairs.parquet	1.7 MB	102,850	All CT failure pairs
ct/negbiodb_ct_m1_balanced.parquet	308.7 KB	11,222	CT-M1 balanced (success vs failure)
ct/negbiodb_ct_m1_realistic.parquet	896.4 KB	36,957	CT-M1 realistic ratio
ct/negbiodb_ct_m2.parquet	2.2 MB	112,298	CT-M2 multiclass failure category

PPI Files

File	Size	Rows	Description
ppi/negbiodb_ppi_pairs.parquet	685.2 MB	2,220,786	All negative PPI pairs
ppi/ppi_m1_balanced.parquet	120.5 MB	123,456	PPI-M1 balanced (1:1 pos:neg)
ppi/ppi_m1_realistic.parquet	744.8 MB	679,008	PPI-M1 realistic (1:10 ratio)

LLM Benchmark Files (DTI)

File	Items	Description
llm_benchmarks/l1_mcq.jsonl	1,942	L1: 4-class activity MCQ
llm_benchmarks/l3_reasoning_pilot.jsonl	50	L3: Scientific reasoning (pilot)
llm_benchmarks/l4_tested_untested.jsonl	500	L4: Tested vs untested discrimination

Benchmark Tasks

ML Benchmarks

Task	Domain	Type	Splits
M1	DTI	Binary (active/inactive)	random, cold_compound, cold_target, degree_balanced
CT-M1	CT	Binary (success/failure)	random, cold_drug, cold_condition, temporal, scaffold, cold_both
CT-M2	CT	7-way failure category	Same as CT-M1
PPI-M1	PPI	Binary (interact/non-interact)	random, cold_protein, cold_both, degree_balanced

LLM Benchmarks (DTI)

Task	Type	Size	Description
L1	MCQ classification	1,600	4-class activity level
L2	Structured extraction	~100	Extract results from abstracts
L3	Reasoning	50	Explain compound-target inactivity
L4	Discrimination	400	Tested vs untested pair

License

This dataset is released under CC BY-SA 4.0, due to the viral clause of ChEMBL's CC BY-SA 3.0 license. See the LICENSE file for details.

Citation

@dataset{negbiodb2026,
  title={NegBioDB: A Negative Results Database for Biomedical Sciences},
  author={Jang, Jungwon},
  year={2026},
  url={https://github.com/jang1563/NegBioDB}
}