Extracting NCATS LD50 datasets

Extraction steps

• Download the original raw dataset from here, which include 80,081 compounds measured against a total of 59 endpoints;
• Use RDKit to transform the SMILES to their canonical forms;
• Endpoints with the most measurements:

Endpoint	Compounds
mouse_intraperitoneal_LD50_(?log(mol/kg))_(?log(mol/kg))	36295
mouse_oral_LD50_(?log(mol/kg))	23373
mouse_intravenous_LD50_(?log(mol/kg))	16978
rat_oral_LD50_(?log(mol/kg))	10190
mouse_subcutaneous_LD50_(?log(mol/kg))	6769
rat_intraperitoneal_LD50_(?log(mol/kg))	5021
rat_intravenous_LD50_(?log(mol/kg))	2472
rat_subcutaneous_LD50_(?log(mol/kg))	1896
mouse_unreported_LD50_(?log(mol/kg))	1739
rabbit_skin_LD50_(?log(mol/kg))	1495
mammal (species unspecified)_unreported_LD50_(?log(mol/kg))	1129
rabbit_oral_LD50_(?log(mol/kg))	894
rat_skin_LD50_(?log(mol/kg))	835

• Focus on the first eight endpoints and for each endpoint, drop compounds with fewer than 4 atoms;

mouse_intraperitoneal_LD50_(?log(mol/kg))_(?log(mol/kg))	canonical_smiles
3.193687	CNN
1.940775	CCO
0.473706	CO
2.916573	CI
1.888338	CNC
1.582446	CCBr
2.444842	CCI
2.370307	CC#N
1.945005	CC=O
2.288595	ClCCl
2.758550	ICI
1.264442	NC=O
0.890260	CSC
2.400937	C1CO1
4.399809	C[Hg]Cl
1.689866	O=CO
4.000071	N#C[Na]
4.036188	N#C[K]
2.473158	N#CN
2.040894	N#CS
1.237392	CCN
2.188689	N#CO
1.157720	CN
1.782274	C[Se]C
3.627308	N#C[SeH]
1.059158	C
2.518576	C=C
4.032669	C[Hg+]

mouse_oral_LD50_(?log(mol/kg))	canonical_smiles
2.854248	C=O
3.046821	CNN
1.125590	CCO
0.642397	CO
3.863580	C#N
1.478412	ClCBr
2.183593	CC#N
1.689733	CC=O
1.988062	ClCCl
1.155297	NC=O
1.437597	S=C=S
1.225149	CSC
3.639386	C[Hg]Cl
3.884269	N#C[K]
2.067384	N#CN
3.227576	C1CS1
2.070692	N#CS
1.708925	N#CO
1.435486	C[Se]C
3.896719	C[Te]C
2.831173	C[As]=S
3.627308	N#C[SeH]
0.205286	C

mouse_intravenous_LD50_(?log(mol/kg))	canonical_smiles
3.017451	CNN
1.368282	CCO
0.832699	CO
4.436147	C#N
1.826593	CC#N
2.181577	C1CO1
2.298970	O=CO
4.398714	N#C[K]
2.173424	N#CN
2.579609	N#CS
1.561833	C

mouse_subcutaneous_LD50_(?log(mol/kg))	canonical_smiles
2.000376	C=O
3.265506	CNN
0.745116	CCO
0.514494	CO
3.110709	CI
1.353002	CNC
1.667498	BrCBr
2.193030	CCI
0.962067	CC#N
1.895787	CC=O
1.118844	ClCCl
2.508789	ICI
4.133964	N#C[Na]
4.000774	N#C[K]
3.259723	C[As]=S

rat_oral_LD50_(?log(mol/kg))	canonical_smiles
2.477497	C=O
3.029158	CNN
0.814604	CCO
0.902487	CO
2.647031	CBr
1.447916	CCl
3.271288	CI
3.206713	BrCBr
1.906957	CCBr
1.412911	ClCBr
2.096903	C=CCl
1.222410	CC#N
1.959566	CCS
1.724956	ClCCl
0.907207	NC=O
1.802460	S=C=S
1.274836	CSC
2.786643	C1CO1
3.923920	C[Hg]Cl
1.621601	O=CO
3.881381	N#C[Na]
4.114718	N#C[K]
3.458074	C1CN1
2.528606	C1CS1
3.036830	N#C[Ag]
1.872310	N#CS
1.850043	N#C[Cu]
2.051972	CCN
1.457630	N#CO
2.330211	C=CBr
1.366993	CC=N
1.715327	C[Se]C
4.322688	C[Te]C
3.086445	C[As]=S
4.025249	N#C[SeH]
3.176487	C=NO
0.945439	CCC
0.017765	C
3.697211	C[Hg+]

rat_intraperitoneal_LD50_(?log(mol/kg))	canonical_smiles
3.120623	CNN
4.107106	CCO
0.628982	CO
3.147780	CI
3.062967	CNC
1.794253	CCBr
2.674516	CCI
1.683926	CC#N
2.439242	CCS
1.967181	ClCCl
2.822562	ICI
0.897733	NC=O
4.358416	C[Hg]Cl
4.056799	N#C[Na]
4.211628	N#C[K]
4.090097	C1CN1
3.155777	C1CS1
3.416980	O=C=S
2.039142	N#CS
1.695123	C[Se]C

rat_intravenous_LD50_(?log(mol/kg))	canonical_smiles
2.537978	C=O
3.162796	CNN
1.505046	CCO
1.177136	CO
4.523297	C#N
1.388036	CC#N
4.257385	N#C[K]
2.701124	N#CN

rat_subcutaneous_LD50_(?log(mol/kg))	canonical_smiles
1.854248	C=O
3.119378	CNN
2.847111	CBr
3.110709	CI
1.069277	CC#N
1.837796	CC=O
1.051548	NC=O
2.372134	C1CO1
3.920814	N#C[K]
2.824784	C1CS1