Stage: Target ID
19 benchmarks, ranked by composite score. ← All stages
| # | Benchmark | Description | Modalities | Score | Flags |
|---|---|---|---|---|---|
| 1 | Open Targets Platform | Integrates genetic, genomic, pharmacological evidence to score targets for 20k+ diseases. | cross-modality | 100.0 | |
| 2 | DepMap (Cancer Dependency Map) | Genome-scale CRISPR/RNAi essentiality across 1150 cancer cell lines + omics. | cross-modality | 100.0 | |
| 3 | ProteinGym | 217 DMS substitution assays + indel + clinical variants — de facto standard for VEPs. | protein-general | 97.5 | |
| 4 | STRING | Protein-protein interaction & functional association network across 12k organisms. | protein-general | 94.9 | |
| 5 | CASP15 | CASP15 blind structure prediction including multimer and ligand-bound categories. | protein-general | 94.9 | |
| 6 | PrimeKG | Precision medicine knowledge graph integrating 20 sources for 17k diseases. | cross-modality | 91.9 | |
| 7 | Longevity Benchmark (Insilico) | 19 aging/longevity benchmarks on ScienceAIBench/InsilicoBench/DDB — NHANES mortality, TCGA survival, methylation age, GTEx, Olink proteomic, longevity synergy. | cross-modality | 90.6 | |
| 8 | LINCS L1000 / CMap | 1.3M transcriptional profiles across 978 landmark genes after genetic or chemical perturbations. | small-moleculecross-modality | 89.9 | |
| 9 | canSAR | Cancer translational knowledge base integrating pharmacology, bioactivity, structure, druggability. | small-moleculeprotein-general | 89.4 | |
| 10 | scPerturb | Harmonized single-cell perturbation datasets (genetic + chemical) with standardized metadata. | cross-modality | 88.9 | |
| 11 | CZ Virtual Cell Challenge | Open challenge to predict transcriptomic responses to genetic & chemical perturbations across cell types, hosted by CZ Biohub. | cross-modality | 88.1 | |
| 12 | TargetBench (Insilico) | 10 disease-area target identification benchmarks on ScienceAIBench/DDB (cancer, cardiovascular, endocrine/metabolic, fibrotic, inflammation/immunology, neuro, etc.). | cross-modality | 84.6 | |
| 13 | CAFA5 | CAFA 5th edition — blind GO annotation eval (142k targets; Kaggle 2023, 1625 teams). | protein-general | 84.3 | |
| 14 | DisGeNET | Large collection of gene-disease associations (text-mining + curation + repositories). | cross-modality | 81.0 | license-gated-commercial |
| 15 | FLIP | Fitness landscape inference benchmarks with realistic train/test splits (AAV, GB1, Meltome, SCL, Bind). | protein-general | 80.8 | |
| 16 | CPTAC Proteogenomic Benchmarks | Proteogenomic benchmarks across 10 tumor types — drives DREAM proteogenomic challenges. | cross-modality | 80.8 | |
| 17 | TAPE | Tasks Assessing Protein Embeddings — 5 tasks (secondary structure, contact, fluorescence, stability, homology). | protein-general | 74.9 | deprecated-recommend-replace |
| 18 | PEER | PEER — 14 protein property prediction tasks across structure/function/interaction. | protein-general | 74.4 | |
| 19 | ClawBio Skill Correctness Bench | Third-party (Biostochastics LLC) benchmark of bio-analysis skills on safety / correctness / honesty. 10 skills × 182 tests. | cross-modality | 74.2 |