Datasets:

jang1563
/

NegBioDB

pair_id int64	intervention_id int64	condition_id int64	smiles string	inchikey string	inchikey_connectivity string	chembl_id string	molecular_type string	intervention_type string	condition_name string	mesh_id string	confidence_tier string	primary_failure_category string	num_trials int64	num_sources int64	highest_phase_reached string	intervention_degree int64	condition_degree int64	earliest_completion_year float64	split_random string	split_cold_drug string	split_cold_condition string	split_temporal string	split_scaffold string	split_degree_balanced string
189,153	3	4	null	null	null	null	null	drug	Healthy Participants	Arbovirus Infections	gold	safety	12	2	phase_3	4,088	44	2,012	train	train	train	train	null	train
189,154	3	5	null	null	null	null	null	drug	Heart Failure	Cardiovascular Diseases	gold	efficacy	62	2	phase_4	4,088	185	2,006	train	train	train	train	null	train
189,155	3	6	null	null	null	null	null	drug	Plaque Psoriasis	null	gold	efficacy	22	1	phase_4	4,088	71	2,015	test	train	train	train	null	train
189,156	3	7	null	null	null	null	null	drug	Bladder Cancer	Carcinoma	gold	efficacy	8	1	phase_3	4,088	136	2,011	train	train	test	train	null	train
189,157	3	8	null	null	null	null	null	drug	Healthy	null	gold	efficacy	91	2	phase_4	4,088	457	2,008	train	train	val	train	null	train
189,158	3	10	null	null	null	null	null	drug	Cardiovascular Disease	Cardiovascular Diseases	gold	efficacy	22	1	phase_4	4,088	55	2,007	test	train	train	train	null	train
189,159	3	19	null	null	null	null	null	drug	Exercise	Behavior	gold	efficacy	1	1	phase_4	4,088	3	null	train	train	train	train	null	train
189,160	3	20	null	null	null	null	null	drug	Sleep	Behavior	gold	efficacy	5	2	phase_4	4,088	19	2,013	train	train	train	train	null	test
189,161	3	21	null	null	null	null	null	drug	Cicatrix	Cicatrix	copper	other	1	1	phase_2	4,088	7	2,022	train	train	train	test	null	train
189,162	3	22	null	null	null	null	null	drug	Pruritus	Pathological Conditions, Signs and Symptoms	gold	efficacy	6	2	phase_4	4,088	34	2,014	train	train	train	train	null	train
189,163	3	24	null	null	null	null	null	drug	Pulmonary Hypertension	Cardiovascular Diseases	gold	efficacy	22	2	phase_4	4,088	64	2,009	train	train	train	train	null	train
189,164	3	25	null	null	null	null	null	drug	Leukemia	Burkitt Lymphoma	gold	efficacy	8	1	phase_3	4,088	260	2,009	train	train	train	train	null	train
189,165	3	26	null	null	null	null	null	drug	Lymphoma	Burkitt Lymphoma	gold	efficacy	11	1	phase_3	4,088	361	2,009	train	train	train	train	null	train
189,166	3	27	null	null	null	null	null	drug	Epilepsy	Brain Diseases	gold	efficacy	15	2	phase_4	4,088	62	2,003	train	train	train	train	null	train
189,167	3	30	null	null	null	null	null	drug	Adenocarcinoma of the Pancreas	Actinomycetales Infections	bronze	efficacy	1	1	phase_2	4,088	17	2,012	val	train	test	train	null	train
189,168	3	31	null	null	null	null	null	drug	Cognition	Breast Diseases	gold	efficacy	1	1	phase_4	4,088	4	2,010	test	train	train	train	null	train
189,169	3	32	null	null	null	null	null	drug	Aging	Breast Diseases	gold	enrollment	8	1	phase_3	4,088	29	2,015	val	train	train	train	null	train
189,170	3	35	null	null	null	null	null	drug	Ischemia	Arterial Occlusive Diseases	gold	enrollment	2	1	phase_4	4,088	11	2,011	train	train	val	train	null	test
189,171	3	36	null	null	null	null	null	drug	Prostate Cancer	Genital Diseases	gold	efficacy	27	2	phase_4	4,088	418	2,004	test	train	train	train	null	test
189,172	3	37	null	null	null	null	null	drug	Metastatic Colorectal Cancer	Colonic Diseases	gold	efficacy	9	1	phase_3	4,088	132	2,010	train	train	train	train	null	train
189,173	3	38	null	null	null	null	null	drug	Rosacea	Rosacea	gold	efficacy	2	1	phase_3	4,088	18	2,008	test	train	val	train	null	train
189,174	3	39	null	null	null	null	null	drug	Advanced Hepatocellular Carcinoma	Adenocarcinoma	silver	safety	2	1	phase_2	4,088	18	2,009	train	train	test	train	null	train
189,175	3	41	null	null	null	null	null	drug	Bipolar Disorder	Bipolar Disorder	gold	efficacy	43	2	phase_4	4,088	102	2,007	test	train	train	train	null	train
189,176	3	43	null	null	null	null	null	drug	NAFLD	Digestive System Diseases	silver	efficacy	4	1	phase_2	4,088	12	2,017	train	train	train	train	null	train
189,177	3	46	null	null	null	null	null	drug	Pyoderma Gangrenosum	Colitis	bronze	efficacy	1	1	phase_3	4,088	7	2,025	train	train	train	test	null	train
189,178	3	47	null	null	null	null	null	drug	Crohn's Disease	Colitis	gold	efficacy	46	2	phase_4	4,088	141	2,008	train	train	train	train	null	train
189,179	3	48	null	null	null	null	null	drug	Ulcerative Colitis	Colitis	gold	efficacy	61	2	phase_4	4,088	168	2,009	test	train	train	train	null	train
189,180	3	49	null	null	null	null	null	drug	Inflammatory Bowel Disease	Colitis	bronze	enrollment	4	2	phase_3	4,088	21	2,014	train	train	train	train	null	train
189,181	3	50	null	null	null	null	null	drug	HIV Infections	Blood-Borne Infections	gold	efficacy	38	2	phase_4	4,088	368	1,996	test	train	test	train	null	train
189,182	3	51	null	null	null	null	null	drug	Healthy Volunteer	null	copper	other	3	1	phase_1	4,088	14	2,020	val	train	test	test	null	train
189,183	3	52	null	null	null	null	null	drug	Myeloma	Blood Protein Disorders	silver	efficacy	1	1	phase_2	4,088	53	2,022	train	train	test	test	null	test
189,184	3	53	null	null	null	null	null	drug	Stem Cell Transplantation	Blood Protein Disorders	bronze	enrollment	1	1	phase_1_2	4,088	25	2,011	train	train	test	train	null	train
189,185	3	54	null	null	null	null	null	drug	Acute Myeloid Leukemia	Hematologic Diseases	gold	efficacy	7	2	phase_3	4,088	286	2,017	train	train	train	train	null	test
189,186	3	56	null	null	null	null	null	drug	Graft vs Host Disease	Graft vs Host Disease	bronze	enrollment	1	1	phase_2	4,088	41	2,021	train	train	train	test	null	train
189,187	3	58	null	null	null	null	null	drug	Pulmonary Disease, Chronic Obstructive	Chronic Disease	gold	efficacy	51	2	phase_4	4,088	212	2,008	train	train	train	train	null	train
189,188	3	60	null	null	null	null	null	drug	Hypertension	Cardiovascular Diseases	gold	efficacy	44	2	phase_4	4,088	326	2,006	train	train	train	train	null	train
189,189	3	63	null	null	null	null	null	drug	Chronic Hepatitis C	Blood-Borne Infections	silver	other	6	2	phase_3	4,088	55	2,008	test	train	test	train	null	test
189,190	3	64	null	null	null	null	null	drug	Schizophrenia	Behavior	gold	efficacy	97	2	phase_4	4,088	279	2,007	test	train	train	train	null	train
189,191	3	65	null	null	null	null	null	drug	Healthy Volunteers	Autoimmune Diseases	gold	other	46	2	phase_4	4,088	205	2,008	train	train	train	train	null	val
189,192	3	66	null	null	null	null	null	drug	Diabetes Mellitus, Type 1	Autoimmune Diseases	gold	efficacy	16	1	phase_3	4,088	113	2,009	train	train	train	train	null	train
189,193	3	67	null	null	null	null	null	drug	Immune Thrombocytopenia	Autoimmune Diseases	gold	efficacy	2	1	phase_3	4,088	8	2,015	train	train	train	train	null	train
189,194	3	68	null	null	null	null	null	drug	Metastatic Breast Cancer	Breast Diseases	gold	efficacy	10	1	phase_3	4,088	142	2,017	train	train	train	train	null	test
189,195	3	70	null	null	null	null	null	drug	Myelodysplastic Syndromes	Bone Marrow Diseases	gold	efficacy	16	2	phase_3	4,088	196	2,010	test	train	test	train	null	train
189,196	3	71	null	null	null	null	null	drug	Seasonal Allergic Rhinitis	Asthma	gold	efficacy	18	1	phase_4	4,088	39	1,993	train	train	train	train	null	test
189,197	3	72	null	null	null	null	null	drug	Asthma	Asthma	gold	efficacy	146	2	phase_4	4,088	589	2,003	train	train	train	train	null	test
189,198	3	73	null	null	null	null	null	drug	Metastatic Hormone-Sensitive Prostate Cancer	null	gold	efficacy	2	1	phase_3	4,088	8	2,023	test	train	train	test	null	test
189,199	3	74	null	null	null	null	null	drug	Acute Graft Versus Host Disease	Bronchial Diseases	copper	other	1	1	phase_3	4,088	10	2,021	val	train	train	test	null	train
189,200	3	75	null	null	null	null	null	drug	Erectile Dysfunction	Dyslipidemias	gold	efficacy	7	1	phase_4	4,088	41	2,008	train	train	train	train	null	train
189,201	3	79	null	null	null	null	null	drug	Alzheimer's Disease	Alzheimer Disease	gold	efficacy	78	2	phase_4	4,088	157	2,007	test	train	val	train	null	val
189,202	3	80	null	null	null	null	null	drug	Hepatitis C	Blood Protein Disorders	gold	efficacy	14	2	phase_4	4,088	105	2,010	train	train	test	train	null	train
189,203	3	81	null	null	null	null	null	drug	Cryoglobulinemia	Blood Protein Disorders	bronze	enrollment	1	1	phase_2	4,088	3	2,018	test	train	test	val	null	train
189,204	3	82	null	null	null	null	null	drug	Dengue	Arbovirus Infections	silver	efficacy	3	2	phase_2	4,088	7	2,020	test	train	train	test	null	train
189,205	3	83	null	null	null	null	null	drug	Hypersensitivity	Asthma	gold	efficacy	2	1	phase_3	4,088	14	2,020	train	train	train	test	null	train
189,206	3	85	null	null	null	null	null	drug	Lung Cancer	Bronchial Neoplasms	gold	efficacy	29	1	phase_3	4,088	250	2,008	train	train	train	train	null	test
189,207	3	88	null	null	null	null	null	drug	Glucose Metabolism Disorders	Brain Diseases	gold	efficacy	5	2	phase_4	4,088	18	2,007	train	train	train	train	null	train
189,208	3	92	null	null	null	null	null	drug	Xerostomia	Head and Neck Neoplasms	bronze	strategic	1	1	phase_2	4,088	12	2,012	test	train	val	train	null	train
189,209	3	95	null	null	null	null	null	drug	Atrial Fibrillation New Onset	Arrhythmias, Cardiac	bronze	enrollment	1	1	null	4,088	4	2,015	test	train	train	train	null	train
189,210	3	97	null	null	null	null	null	drug	COVID-19	COVID-19	gold	efficacy	150	2	phase_4	4,088	527	2,020	val	train	train	test	null	train
189,211	3	98	null	null	null	null	null	drug	SARS-CoV 2	COVID-19	bronze	other	5	2	phase_3	4,088	41	2,020	test	train	train	test	null	train
189,212	3	102	null	null	null	null	null	drug	Multiple Sclerosis	Autoimmune Diseases	gold	efficacy	63	2	phase_4	4,088	172	2,002	val	train	train	train	null	train
189,213	3	103	null	null	null	null	null	drug	Hepatocellular Carcinoma	Adenocarcinoma	gold	efficacy	13	2	phase_3	4,088	179	2,008	test	train	test	train	null	train
189,214	3	104	null	null	null	null	null	drug	Infertility	Adnexal Diseases	gold	enrollment	4	1	phase_4	4,088	99	2,011	train	train	train	train	null	train
189,215	3	107	null	null	null	null	null	drug	Postoperative Pain	Neurologic Manifestations	gold	efficacy	15	1	phase_4	4,088	128	2,008	train	train	train	train	null	val
189,216	3	108	null	null	null	null	null	drug	Non-Small Cell Lung Cancer	Bronchial Neoplasms	gold	efficacy	33	2	phase_3	4,088	317	2,008	val	train	train	train	null	train
189,217	3	111	null	null	null	null	null	drug	Cerebral Infarction	Brain Diseases	gold	efficacy	2	1	phase_4	4,088	8	2,008	test	train	train	train	null	train
189,218	3	113	null	null	null	null	null	drug	Acute Stroke	Brain Diseases	bronze	other	3	2	phase_3	4,088	9	2,012	train	train	train	train	null	train
189,219	3	114	null	null	null	null	null	drug	Brain Infarction	Brain Diseases	bronze	efficacy	2	1	phase_3	4,088	4	2,008	test	train	train	train	null	train
189,220	3	117	null	null	null	null	null	drug	Constipation	Basal Ganglia Diseases	gold	efficacy	11	1	phase_4	4,088	50	2,006	train	train	train	train	null	train
189,221	3	118	null	null	null	null	null	drug	Parkinson Disease	Basal Ganglia Diseases	gold	efficacy	29	2	phase_4	4,088	133	2,008	val	train	train	train	null	train
189,222	3	120	null	null	null	null	null	drug	Deep Vein Thrombosis	Cardiovascular Diseases	bronze	other	3	1	phase_4	4,088	24	2,003	train	train	train	train	null	val
189,223	3	121	null	null	null	null	null	drug	Pulmonary Embolism	Cardiovascular Diseases	bronze	other	5	2	phase_4	4,088	39	2,017	train	train	train	train	null	train
189,224	3	122	null	null	null	null	null	drug	Traumatic Brain Injury	Brain Damage, Chronic	gold	efficacy	13	2	phase_4	4,088	65	2,010	train	train	train	train	null	train
189,225	3	123	null	null	null	null	null	drug	Diabetes Mellitus	Cardiovascular Diseases	gold	efficacy	25	2	phase_4	4,088	170	2,004	train	train	train	train	null	train
189,226	3	124	null	null	null	null	null	drug	Essential Hypertension	Cardiovascular Diseases	silver	efficacy	2	1	phase_2_3	4,088	30	2,017	train	train	train	train	null	train
189,227	3	125	null	null	null	null	null	drug	Vomiting	Abdominal Pain	gold	efficacy	6	1	phase_3	4,088	47	2,010	test	train	train	train	null	train
189,228	3	126	null	null	null	null	null	drug	Nausea	Abdominal Pain	gold	efficacy	8	1	phase_4	4,088	58	2,010	train	train	train	train	null	val
189,229	3	127	null	null	null	null	null	drug	Abdominal Pain	Abdominal Pain	gold	efficacy	4	1	phase_3	4,088	12	2,008	val	train	train	train	null	val
189,230	3	128	null	null	null	null	null	drug	Cannabis Use	Abdominal Pain	copper	other	1	1	phase_3	4,088	3	2,023	test	train	train	test	null	train
189,231	3	129	null	null	null	null	null	drug	Melanoma	Melanoma	gold	efficacy	14	1	phase_3	4,088	265	2,008	train	train	val	train	null	train
189,232	3	133	null	null	null	null	null	drug	Autoimmune Diseases	Autoimmune Diseases	silver	efficacy	3	2	phase_4	4,088	12	2,024	test	train	train	test	null	train
189,233	3	135	null	null	null	null	null	drug	Acute Myeloid Leukemia (AML)	Hematologic Diseases	gold	efficacy	2	1	phase_3	4,088	84	2,024	train	train	train	test	null	train
189,234	3	138	null	null	null	null	null	drug	IgA Nephropathy	Autoimmune Diseases	silver	other	4	2	phase_3	4,088	19	2,018	train	train	train	val	null	train
189,235	3	140	null	null	null	null	null	drug	Menopause	Anxiety Disorders	gold	efficacy	19	2	phase_4	4,088	45	2,006	train	train	train	train	null	train
189,236	3	141	null	null	null	null	null	drug	Perimenopause	Anxiety Disorders	silver	efficacy	1	1	phase_1_2	4,088	2	2,024	train	train	train	test	null	train
189,237	3	142	null	null	null	null	null	drug	Generalized Myasthenia Gravis	Autoimmune Diseases	gold	efficacy	5	2	phase_3	4,088	9	2,020	val	train	train	test	null	train
189,238	3	143	null	null	null	null	null	drug	Type 1 Diabetes Mellitus	Autoimmune Diseases	gold	efficacy	15	1	phase_3	4,088	86	2,011	train	train	train	train	null	train
189,239	3	144	null	null	null	null	null	drug	T1D	Autoimmune Diseases	silver	efficacy	1	1	phase_2	4,088	3	2,020	train	train	train	test	null	train
189,240	3	145	null	null	null	null	null	drug	T1DM	Autoimmune Diseases	silver	efficacy	1	1	phase_2	4,088	3	2,020	train	train	train	test	null	train
189,241	3	150	null	null	null	null	null	drug	Type 1 Diabetes	Autoimmune Diseases	gold	efficacy	13	1	phase_4	4,088	86	2,010	train	train	train	train	null	train
189,242	3	153	null	null	null	null	null	drug	Clostridium Difficile	Bacterial Infections	gold	enrollment	4	1	phase_4	4,088	16	2,012	train	train	train	train	null	train
189,243	3	155	null	null	null	null	null	drug	Clostridium Difficile Infection Recurrence	Bacterial Infections	bronze	other	2	2	phase_4	4,088	3	2,019	train	train	train	val	null	val
189,244	3	158	null	null	null	null	null	drug	CDI	Bacterial Infections	silver	efficacy	1	1	phase_2	4,088	3	2,023	train	train	train	test	null	train
189,245	3	160	null	null	null	null	null	drug	Recurrent Clostridium Difficile Infection	Bacterial Infections	silver	efficacy	1	1	phase_2	4,088	7	2,023	train	train	train	test	null	train
189,246	3	161	null	null	null	null	null	drug	C.Difficile Diarrhea	Bacterial Infections	silver	efficacy	1	1	phase_2	4,088	2	2,023	val	train	train	test	null	val
189,247	3	164	null	null	null	null	null	drug	Chronic Hepatitis B	Blood-Borne Infections	gold	efficacy	11	2	phase_3	4,088	56	2,012	test	train	test	train	null	test
189,248	3	166	null	null	null	null	null	drug	Eye Infections, Bacterial	Bacterial Infections	gold	efficacy	1	1	phase_4	4,088	3	2,012	train	train	train	train	null	train
189,249	3	169	null	null	null	null	null	drug	Ocular Hypertension	Eye Diseases	silver	other	2	2	phase_4	4,088	82	2,020	train	train	train	test	null	train
189,250	3	170	null	null	null	null	null	drug	Esophageal Squamous Cell Carcinoma	Carcinoma	silver	efficacy	1	1	phase_2	4,088	30	2,023	train	train	test	test	null	train
189,251	3	173	null	null	null	null	null	drug	HIV	null	gold	efficacy	20	2	phase_4	4,088	114	2,009	train	train	test	train	null	train
189,252	3	175	null	null	null	null	null	drug	Myasthenia Gravis, Generalized	Autoimmune Diseases	gold	efficacy	1	1	phase_3	4,088	4	2,021	train	train	train	test	null	train

End of preview. Expand in Data Studio

NegBioDB

Negative Results Database & Dual ML/LLM Benchmark for Biomedical Sciences

Approximately 90% of scientific experiments produce null or inconclusive results, yet the vast majority remain unpublished. NegBioDB systematically collects experimentally confirmed negative results across four biomedical domains and provides dual-track ML + LLM benchmarks to quantify the impact of this publication bias on AI models.

Quick Start

# Load any domain with the datasets library
from datasets import load_dataset

# DTI pairs (30.5M negative compound-target interactions)
dti = load_dataset("jang1563/NegBioDB", "dti_pairs", split="train")

# Clinical trial failures (102K intervention-condition pairs)
ct = load_dataset("jang1563/NegBioDB", "ct_pairs", split="train")

# PPI negatives (2.2M confirmed non-interactions)
ppi = load_dataset("jang1563/NegBioDB", "ppi_pairs", split="train")

# Gene essentiality (22.5M gene-cell-line pairs)
ge = load_dataset("jang1563/NegBioDB", "ge_pairs", split="train")

Or load directly with pandas:

import pandas as pd
from huggingface_hub import hf_hub_download

# Download a specific file
path = hf_hub_download("jang1563/NegBioDB", "data/negbiodb_dti_pairs.parquet", repo_type="dataset")
df = pd.read_parquet(path)
print(df.shape)  # (1_725_446, ~20 columns)

Database Statistics

Domain	Negative Results	Key Entities	Sources	DB Size
DTI	30,459,583	919K compounds, 3.7K targets	ChEMBL, PubChem, BindingDB, DAVIS	~21 GB
CT	132,925	177K interventions, 56K conditions	AACT, CTO, Open Targets, Shi & Du	~500 MB
PPI	2,229,670	18.4K proteins	IntAct, HuRI, hu.MAP, STRING	849 MB
GE	28,759,256	19,554 genes, 2,132 cell lines	DepMap (CRISPR, RNAi)	~16 GB
Total	~61.6M		14 sources	~38 GB

Key Findings

ML: Negative Source Matters

DTI -- Degree-matched negatives inflate LogAUC by +0.112 on average. Cold-target splits cause catastrophic failure:

DTI Model	Random (NegBioDB)	Random (Degree-Matched)	Cold-Target
DeepDTA	0.833	0.919	0.325
GraphDTA	0.843	0.967	0.241
DrugBAN	0.830	0.955	0.151

PPI -- PIPR cold_both AUROC drops to 0.409 (below random); MLPFeatures remains robust at 0.950.

CT -- NegBioDB negatives are trivially separable (AUROC ~1.0); M2 7-way classification is challenging (best macro-F1 = 0.51).

GE -- Cold-gene splits reveal severe generalization gaps; degree-balanced negatives modestly improve ranking metrics.

LLM: L4 Discrimination Reveals Domain Differences

Domain	L4 MCC Range	Interpretation	Contamination
DTI	≤ 0.18	Near random	Not detected
PPI	0.33--0.44	Moderate	Yes (temporal gap)
CT	0.48--0.56	Meaningful	Not detected
GE	Pending	--	--

Exported Datasets

DTI

File	Description
`negbiodb_dti_pairs.parquet`	1.7M compound-target pairs with 5 split columns
`negbiodb_m1_balanced.parquet`	M1: 1.73M rows (1:1 active:inactive)
`negbiodb_m1_realistic.parquet`	M1: 9.49M rows (1:10 ratio)
`negbiodb_m1_balanced_ddb.parquet`	Degree-balanced split
`negbiodb_m1_uniform_random.parquet`	Uniform random negatives (control)
`negbiodb_m1_degree_matched.parquet`	Degree-matched negatives (control)

CT

File	Description
`ct/negbiodb_ct_pairs.parquet`	102,850 failure pairs, 6 splits
`ct/negbiodb_ct_m1_balanced.parquet`	Binary: 11,222 rows (5,611 pos + 5,611 neg)
`ct/negbiodb_ct_m2.parquet`	7-way category: 112,298 rows

PPI

File	Description
`ppi/negbiodb_ppi_pairs.parquet`	2,220,786 negative pairs with split columns
`ppi/ppi_m1_balanced.parquet`	M1: 123,456 rows (1:1 pos:neg)
`ppi/ppi_m1_realistic.parquet`	M1: 679,008 rows (1:10 ratio)

GE

File	Description
`ge/negbiodb_ge_pairs.parquet`	22.5M gene-cell-line pairs with 5 split columns

LLM Benchmarks

File	Description
`llm_benchmarks/l1_mcq.jsonl`	L1: Multiple-choice classification
`llm_benchmarks/l4_tested_untested.jsonl`	L4: Tested vs. untested discrimination
`ct_llm/ct_l*_dataset.jsonl`	CT domain LLM datasets (L1-L4)
`ppi_llm/ppi_l*_dataset.jsonl`	PPI domain LLM datasets (L1-L4)
`ge_llm/ge_l*_dataset.jsonl`	GE domain LLM datasets (L1-L4)

Data Sources

Source	Records	License
ChEMBL v36	371K	CC BY-SA 3.0
PubChem BioAssay	29.6M	Public Domain
BindingDB	404K	CC BY
DAVIS	20K	Public
AACT (ClinicalTrials.gov)	216,987 trials	Public Domain
CTO	20,627	MIT
Open Targets	32,782 targets	Apache 2.0
Shi & Du 2024	119K + 803K rows	CC BY 4.0
IntAct	779 pairs	CC BY 4.0
HuRI	500,000 pairs	CC BY 4.0
hu.MAP 3.0	1,228,891 pairs	MIT
STRING v12.0	500,000 pairs	CC BY 4.0
DepMap CRISPR	28.7M gene-cell pairs	CC BY 4.0
DepMap RNAi	Integrated	CC BY 4.0

Reproducing from Source

Full pipeline code is available at GitHub.

git clone https://github.com/jang1563/NegBioDB.git
cd NegBioDB
make setup          # Create venv and install dependencies
make db             # Initialize SQLite database
make download       # Download all sources
make load-all       # Run ETL pipelines

Citation

@misc{negbiodb2026,
  title={NegBioDB: A Negative Results Database and Dual ML/LLM Benchmark for Biomedical Sciences},
  author={Kim, JangKeun},
  year={2026},
  url={https://github.com/jang1563/NegBioDB}
}

License & Contact

License: CC BY-SA 4.0 (required by ChEMBL's CC BY-SA 3.0 viral clause)

Contact: JangKeun Kim (jak4013@med.cornell.edu) -- Weill Cornell Medicine

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