Tox21
Molecular toxicity dataset across 12 nuclear receptor and stress response pathway assays. Each molecule is represented by its atom and bond structure; the learning task is to predict whether a molecule is active (toxic) in a given assay.
Tasks: 12 tasks (in <task>/train/)
| Task | Description |
|---|---|
nr_ahr |
Aryl hydrocarbon receptor activation |
nr_ar |
Androgen receptor activation |
nr_ar_lbd |
Androgen receptor ligand-binding domain activation |
nr_aromatase |
Aromatase enzyme inhibition |
nr_er |
Estrogen receptor activation |
nr_er_lbd |
Estrogen receptor ligand-binding domain activation |
nr_ppar_gamma |
PPAR-gamma (peroxisome proliferator-activated receptor gamma) activation |
sr_are |
Antioxidant response element pathway activation |
sr_atad5 |
ATAD5 genotoxicity stress response |
sr_hse |
Heat shock response element pathway activation |
sr_mmp |
Mitochondrial membrane potential disruption |
sr_p53 |
p53 tumour suppressor pathway activation |
Head relation: f(Mol) — true if molecule Mol is active (positive) in the assay.
Background relations:
| Relation | Arity | Description |
|---|---|---|
atom(Mol, Atom, Element) |
3 | Atom Atom in molecule Mol has element symbol Element |
bond(Mol, Atom1, Atom2, BondType) |
4 | Atoms Atom1 and Atom2 in molecule Mol are connected by a bond of type BondType |
bond_type_single(BondType) |
1 | BondType is a single bond |
bond_type_double(BondType) |
1 | BondType is a double bond |
bond_type_triple(BondType) |
1 | BondType is a triple bond |
bond_type_aromatic(BondType) |
1 | BondType is an aromatic bond |
element_c(Element) |
1 | Element is carbon (C) |
element_n(Element) |
1 | Element is nitrogen (N) |
element_o(Element) |
1 | Element is oxygen (O) |
element_s(Element) |
1 | Element is sulfur (S) |
element_* |
1 | One relation per element; 51 element types total (Ag, Al, As, Au, B, Ba, Be, Bi, Br, C, Ca, Cd, Cl, Co, Cr, Cu, Dy, F, Fe, Gd, Ge, H, Hg, I, In, K, Li, Mg, Mn, Mo, N, Na, Nd, Ni, O, P, Pb, Pd, Pt, S, Sb, Se, Si, Sn, Sr, Ti, Tl, V, Yb, Zn, Zr) |
Dataset statistics: 7,831 molecules total; each task directory contains only molecules that were tested in that assay (many molecules have no label for a given assay). Positive (active) counts range from 186 (nr_ppar_gamma) to 942 (sr_are).
Task statistics
| task_name | num_bk_facts | num_bk_relations | num_pos_examples | num_neg_examples |
|---|---|---|---|---|
nr_ahr |
240887 | 57 | 768 | 5781 |
nr_ar |
272913 | 57 | 309 | 6956 |
nr_ar_lbd |
245942 | 57 | 237 | 6521 |
nr_aromatase |
208008 | 57 | 300 | 5521 |
nr_er |
221474 | 57 | 793 | 5400 |
nr_er_lbd |
256146 | 57 | 350 | 6605 |
nr_ppar_gamma |
228033 | 57 | 186 | 6264 |
sr_are |
194501 | 57 | 942 | 4890 |
sr_atad5 |
259036 | 57 | 264 | 6808 |
sr_hse |
222174 | 57 | 372 | 6095 |
sr_mmp |
207909 | 57 | 918 | 4892 |
sr_p53 |
247030 | 57 | 423 | 6351 |
Source: Tox21 Data Challenge (2014). OGB dataset ogbg-moltox21. Hu, Z. et al. "Open Graph Benchmark: Datasets for Machine Learning on Graphs." NeurIPS, 2020. https://ogb.stanford.edu/