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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 9 new columns ({'std', 'Unnamed: 0', '50%', 'min', '75%', 'count', 'mean', 'max', '25%'}) and 9 missing columns ({'definition', 'parents_count', 'parents', 'xrefs', 'all_positive_examples_count', 'id', 'name', 'all_positive_examples', 'xrefs_count'}).
This happened while the csv dataset builder was generating data using
hf://datasets/MonarchInit/C3PO/classes_slim_summary.csv (at revision 72e3b2dfb2b576ffb9ff13dec8d9f8a9bcc9371c)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1870, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
Unnamed: 0: string
count: double
mean: double
std: double
min: double
25%: double
50%: double
75%: double
max: double
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1241
to
{'id': Value(dtype='string', id=None), 'name': Value(dtype='string', id=None), 'definition': Value(dtype='string', id=None), 'parents': Value(dtype='string', id=None), 'xrefs': Value(dtype='string', id=None), 'all_positive_examples': Value(dtype='string', id=None), 'parents_count': Value(dtype='int64', id=None), 'xrefs_count': Value(dtype='float64', id=None), 'all_positive_examples_count': Value(dtype='int64', id=None)}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1417, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1049, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 924, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1000, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1872, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 9 new columns ({'std', 'Unnamed: 0', '50%', 'min', '75%', 'count', 'mean', 'max', '25%'}) and 9 missing columns ({'definition', 'parents_count', 'parents', 'xrefs', 'all_positive_examples_count', 'id', 'name', 'all_positive_examples', 'xrefs_count'}).
This happened while the csv dataset builder was generating data using
hf://datasets/MonarchInit/C3PO/classes_slim_summary.csv (at revision 72e3b2dfb2b576ffb9ff13dec8d9f8a9bcc9371c)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
id string | name string | definition string | parents string | xrefs string | all_positive_examples string | parents_count int64 | xrefs_count float64 | all_positive_examples_count int64 |
|---|---|---|---|---|---|---|---|---|
CHEBI:10036 | wax ester | A fatty acid ester resulting from the condensation of the carboxy group of a fatty acid with the alcoholic hydroxy group of a fatty alcohol. | ['CHEBI:35748', 'CHEBI:73702'] | ['KEGG:C01629', 'MetaCyc:Wax-Esters', 'PMID:12831900', 'PMID:17750349', 'PMID:18821728', 'PMID:21247555', 'PMID:21256496', 'PMID:21961954', 'PMID:22058425', 'PMID:22685145', 'PMID:22878160', 'PMID:23087036', 'PMID:23109878', 'PMID:23196873', 'PMID:23272127', 'Wikipedia:Wax_ester'] | ['C(CCCCCCCC)CCCCC(OCCCCCCCCCCCCCC)=O', 'O(CCCCCCCCCCCCCCCCCCCC)C(=O)CCCCCCC/C=C\\C/C=C\\CCCCC', 'O(CCCCCCCCCCCCCCCCCCCC)C(=O)CCCCCCC/C=C\\C/C=C\\C/C=C\\CC', 'O(CCCCCCCCCCCCCCCCCCCC)C(=O)CCCCCCC/C=C\\CCCC', 'O(CCCCCCCCCCCCCCCCCCCCCC)C(=O)CCCCCCC/C=C\\C/C=C\\CCCCC', 'O(CCCCCCCCCCCCCCCCCCCCCC)C(=O)CCCCCCC/C=C\\C/C=C\\C/C... | 2 | 16 | 116 |
CHEBI:10283 | 2-hydroxy fatty acid | Any fatty acid with a hydroxy functional group in the alpha- or 2-position. | ['CHEBI:24654', 'CHEBI:49302'] | ['KEGG:C05102', 'PMID:6423633', 'PMID:9826358'] | ['OC(=O)C(\\O)=C/C=C', 'OC(C(CC)C)C(O)=O', 'C(CCCCCC)CC(C(=O)O)O', 'C(=C\\C/C=C\\CCCCC)\\CCCCCCC(C(=O)O)O', 'C(CCCCCCC=C(C(=O)O)O)CC', 'C(C(CCCCCC/C=C\\CCCCCC)O)(=O)O', 'C(C)CCCCCC/C=C\\CCCCCCCCCCC(C(=O)O)O', 'C(\\CCCCCCC(C(=O)O)O)=C\\CCCCCCCC', 'C(=O)(C(CCCCCCCC/C=C\\CCCCCCCC)O)O', 'C(CCCCCCCC)CCCCCCC[C@H](C(O)=O)O', ... | 2 | 3 | 59 |
CHEBI:10615 | omega-hydroxy fatty acid | Any member of the class of naturally-occurring straight-chain fatty acids n carbon atoms long with a carboxyl group at position 1 and a hydroxyl at position n (omega). | ['CHEBI:15734', 'CHEBI:24654'] | ['KEGG:C03547', 'PMID:13771448', 'PMID:16660004'] | ['OC(CCCCCCCCCCC(CCCCCCO)O)=O', 'C(\\CCO)=C\\C/C=C\\C/C=C\\C\\C=C/C=C/C(CCCC(=O)O)O', 'C(CCC(O)=O)/C=C\\C/C=C\\C/C=C\\CCCCCCCCO', 'C(=C\\C/C=C\\CCCCCO)\\CCCCCCCC(=O)O', 'C(C(C(CCCCCCCCO)O)O)CCCCCCC(=O)O', 'C1(CCCCCCCC(=O)O)C(CCCCCCCCO)O1', 'C(C(O)=O)C/C=C\\C/C=C\\C/C=C\\C=C\\[C@H](C/C=C\\C/C=C\\CCO)O', 'C(C(O)=O)C/C=C\... | 2 | 3 | 89 |
CHEBI:11750 | 3-sn-phosphatidyl-L-serine | A 3-sn-glycerophosphoserine compound having acyl substituents at the 1- and 2-hydroxy positions. | ['CHEBI:18303'] | ['KEGG:C02737', 'LIPID_MAPS_instance:LMGP03010000', 'PMID:16341241'] | ['O(C[C@H](COP(=O)(OC[C@@H](C(O)=O)N)O)OC(CCCCCCC/C=C/CCCCCCCC)=O)C(CCCCCCC/C=C/CCCCCCCC)=O', 'C([C@](COP(O)(=O)OC[C@@](COC(=O)CCCCCCCCCCCCCCCCC)(OC(=O)CCCCCCCCCCCCCCCCCC)[H])(N)[H])(=O)O', 'C([C@](COP(O)(=O)OC[C@@](COC(=O)CCCCCCCCCCCCCCCCC)(OC(=O)CCCCCCCCCCCCCCCCCCC)[H])(N)[H])(=O)O', 'C([C@](COP(O)(=O)OC[C@@](COC(=O)... | 1 | 3 | 29 |
CHEBI:131565 | steroid aldehyde | Any steroid substituted by a formyl group. | ['CHEBI:17478', 'CHEBI:35341'] | null | ['CC12CCC3C(C1CCC2(C)O)CCC4C3(CC(C(=O)C4)C=O)C', 'CC12CCC3C(C1(CCC2C4=CC(=O)OC4)O)CCC5(C3(CCC(C5)O)C=O)O', 'C[C@@]12[C@@]3([C@]([C@]4([C@@](C[C@H]3O)(C)[C@@](CC4)(C)O)[H])(CCC1=CC(C(=C2)C=O)=O)[H])[H]', 'C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC[C@]2(CC(C1)=O)[H])[H])(CC[C@@H]4O)[H])C)[H])C=O', 'C1C[C@@H](C([C@@]2([C@@]1([... | 2 | null | 66 |
CHEBI:131619 | C27-steroid | A steroid compound with a structure based on a 27-carbon (cholestane) skeleton. | ['CHEBI:35341'] | null | ['C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC=C2C[C@H](C1)O)[H])(CC[C@@]4([C@H](C)CC/C=C(\\CO)/C)[H])[H])C)[H])C', 'C1[C@@]2([C@]3(CC[C@]4([C@](C3=CC=C2C[C@H](C1)O)(CC[C@@]4([C@@H](CCCC(C)(C)O)C)[H])[H])C)[H])C', 'C1[C@@]2([C@]3(CC[C@]4([C@](C3=CC=C2C[C@H](C1)O)(CC[C@@]4([C@@H](CC[C@@H](C(C)C)O)C)[H])[H])C)[H])C', '[H][C@@]1... | 1 | null | 40 |
CHEBI:131622 | steroidal acyl-CoA(4-) | An acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of any steroidal acyl-CoA; major species at pH 7.3. | ['CHEBI:58342'] | null | ['C(CC[C@]([C@@]1([C@]2([C@H](C[C@@]3([C@]4(CCC(C=C4C[C@H]([C@]3([C@@]2(CC1)[H])[H])O)=O)C)[H])O)C)[H])(C)[H])(=O)SCCNC(CCNC(=O)[C@@H](C(COP(OP(OC[C@H]5O[C@@H](N6C7=C(C(=NC=N7)N)N=C6)[C@@H]([C@@H]5OP([O-])([O-])=O)O)(=O)[O-])(=O)[O-])(C)C)O)=O', 'C(CC[C@]([C@@]1([C@]2([C@H](C[C@@]3([C@]4(CCC(C=C4C=C[C@]3([C@@]2(CC1)[H]... | 1 | null | 51 |
CHEBI:131860 | octadecanoid anion | An unsaturated fatty acid anion obtained by the deprotonation of the carboxy group of any octadecanoid. | ['CHEBI:2580', 'CHEBI:57560'] | null | ['C(CCCCCCC/C=C\\C([C@H]1[C@H](CCCCC)O1)O)(=O)[O-]', 'CCCCCC(O)\\C=C\\C=C/CCCCCCCC([O-])=O', 'CCCCC\\C=C/C=C/C(O)CCCCCCCC([O-])=O', 'C(=C/C=C/C(CCCCCCCC([O-])=O)=O)/CCCCC', 'C(CCCCCCC\\C=C/C=C/[C@@H](CCCCC)OO)(=O)[O-]', 'C(/C=C\\CCCCCCCC(=O)[O-])=C\\[C@@H](C/C=C\\CC)OO', 'C(CCCCCCC/C=C\\[C@H](/C=C\\C/C=C\\CC)OO)(=O)[O-... | 2 | null | 80 |
CHEBI:131863 | docosanoid | Any oxygenated derivative of C22 polyunsaturated fatty acids, such as docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA). | ['CHEBI:15904', 'CHEBI:26208'] | null | ['C(C(O)=O)C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C(C)O', 'OC(CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C=C\\[C@H](C/C=C\\CC)OO)=O', 'OC(CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C=C\\[C@H](CCCCC)OO)=O', 'OC(CCCCC/C=C\\C/C=C\\C/C=C\\C=C\\C(C/C=C\\CC)OO)=O', 'OC(CCCCC/C=C\\C/C=C\\C=C\\C(C/C=C\\C/C=C\\CC)OO)=O', 'OC(CC/C=C\\C/C=C\\C/C=C\\C=C\\... | 2 | null | 102 |
CHEBI:131864 | docosanoid anion | A polyunsaturated fatty acid anion obtained by the deprotonation of the carboxy group of any docosanoid. | ['CHEBI:57560'] | null | ['C(\\C=C\\C=C\\[C@H]1[C@@H](O1)C/C=C\\C/C=C\\CC)=C\\C/C=C\\CCC([O-])=O', 'C(C([O-])=O)C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C(C)O', 'C(C/C=C\\C[C@@H](/C=C/C=C\\C=C\\C=C\\[C@H]([C@H](C/C=C\\CC)O)O)O)C([O-])=O', '[O-]C(CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C=C\\[C@H](C/C=C\\CC)OO)=O', '[O-]C(CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C=C\... | 1 | null | 94 |
CHEBI:131869 | hydroxy monounsaturated fatty acid | Any monounsaturated fatty acid carrying one or more hydroxy substituents. | ['CHEBI:24654', 'CHEBI:25413'] | null | ['C(CCCCCCCC(C=C)O)(O)=O', 'C(=C/CCCCCCCC(O)C)\\C(=O)O', 'C(CCCCCCC=C(C(=O)O)O)CC', 'C(C(CCCCCC/C=C\\CCCCCC)O)(=O)O', 'C(C)CCCCCC/C=C\\CCCCCCCCCCC(C(=O)O)O', 'C(\\CCCCCCC(C(=O)O)O)=C\\CCCCCCCC', 'C(=O)(C(CCCCCCCC/C=C\\CCCCCCCC)O)O', 'OC(CCCCCCCC(O)=O)C(=O)C/C=C/CCCCC', 'O[C@H](CCC(=O)O)C/C=C\\CCCCC', 'O=C(CC(=O)O)CC/C=... | 2 | null | 54 |
CHEBI:131871 | hydroxy polyunsaturated fatty acid anion | Any polyunsaturated fatty acid anion carrying one or more hydroxy substituents. | ['CHEBI:59835', 'CHEBI:76567'] | null | ['C(CCC)C[C@@H](\\C=C\\C=C/C\\C=C/C=C/[C@H](CCCC([O-])=O)OO)O', 'C(CCC)(C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCCC([O-])=O)O', 'O=C(CCC/C=C\\C/C=C\\C/C=C\\C/C=C\\C(CCCC)O)[O-]', 'C(CCC([O-])=O)/C=C\\C/C=C\\C/C=C\\CCCCCCC(C)O', 'C(C([O-])=O)C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C(C)O', 'C(CCC([O-])=O)/C=C\\C/C=C\\C/C=C\\CCCCC... | 2 | null | 119 |
CHEBI:131872 | hydroxy saturated fatty acid anion | Any saturated fatty acid anion carrying one or more hydroxy substituents. | ['CHEBI:58953', 'CHEBI:59835'] | null | ['C(CC(CCCCCCC)O)(=O)[O-]', 'OC(CCCC(=O)[O-])C', 'OC(CCCCCCCCC)CCCCCCCC(=O)[O-]', '[O-]C(CCCCCCCCCCCC(CCCCC)O)=O', 'C(CCCCCCCCCC)CCC(CCCC([O-])=O)O', 'C(CCCCCCCCCCCCCCC([O-])=O)CCC(C)O', '[O-]C(=O)CCCCCCCCC(CCCCCCCC)O', 'C(CCCCCCCC[C@@H](CCCCCCCC)O)([O-])=O', 'CCCCCC(O)CCCCCCCC([O-])=O', 'CCCCC(O)CCCCCCCCC([O-])=O', 'C... | 2 | null | 30 |
CHEBI:131903 | pyranopyrazole | An organic heterobicyclic compound whose skeleton consists of a pyran ring which is ortho-fused to a pyrazole ring. | ['CHEBI:27171', 'CHEBI:38101'] | null | ['CC1=C2C(C(=C(OC2=NN1)N)C#N)C3=C(N(N=C3C)C4=CC=CC=C4)C', 'COC1=CC=CC(=C1)C2=C3C(C(=C(OC3=NN2)N)C#N)C4=CSC=C4', 'CCC1=CC=C(C=C1)C2C(=C(OC3=NNC(=C23)CC(=O)OC)N)C#N', 'CC1=NN(C2=C1C(C(=C(O2)N)C#N)C3=CC(=CC=C3)Cl)CC4=CC=CC=C4', 'CC1=C2C(C(=C(OC2=NN1)N)C#N)CC(C)C', 'COC1=CC=C(C=C1)C2=C3C(C(=C(OC3=NN2)N)C#N)C4=COC=C4', 'CCC... | 2 | null | 32 |
CHEBI:131927 | dicarboxylic acids and O-substituted derivatives | A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. | ['CHEBI:36586'] | null | ['N[C@@H]([C@H](O)C(O)=O)C(O)=O', 'COC(=O)C1=CC(=C(C=C1)C(=O)OC)NC(=O)OC2=CC=CC=C2', 'O=C(O)C(C(O)=O)(C)C', 'CCOC(=O)C1=CC(=C(C=C1)C(=O)OCC)NC(=S)NC2=C(C=C(C=C2)[N+](=O)[O-])OC', 'OC(=O)C\\C=C\\C=C(/O)C(O)=O', 'OC1C=CC=C(C1C(O)=O)C(=O)CCC(O)=O', 'CN1CCN(CC1)C(=S)NC2=C(C=CC(=C2)C(=O)OC)C(=O)OC', 'OC(=O)CC(=O)\\C=C/C(O)=... | 1 | null | 904 |
CHEBI:13209 | long-chain fatty acid ethyl ester | A fatty acid ethyl ester resulting from the formal condensation of the carboxy group of a long-chain fatty acid with the hydroxy group of ethanol. | ['CHEBI:78206'] | null | ['O(C(=O)CCCC/C=C\\C/C=C\\C/C=C\\CCCCC)CC', 'CCCCC\\C=C/C\\C=C/CCCCCCCC(=O)OCC', 'CCCCCCCCCCCCCC(=O)OCC', 'CCOC(=O)CCCCCCC\\C=C/C\\C=C/C\\C=C/CC', 'CCOC(=O)CCCC\\C=C/C\\C=C/C\\C=C/C\\C=C/CC', 'CCCCCCCCCCCCCCCCCCCC(=O)OCC', 'CCCCCCCC\\C=C/CCCCCCCCCC(=O)OCC', 'CCCCCCCCCC\\C=C/CCCCCCCC(=O)OCC', 'CCCCCC\\C=C/CCCCCCCCCCCC(=... | 1 | null | 26 |
CHEBI:132120 | resolvin | Hydroxy fatty acids that are di- or trihydroxy metabolites of the polyunsaturated omega-3 fatty acids, particularly icosapentaenoic acid, docosahexaenoic acid and docosapentaenoic acid. | ['CHEBI:15904', 'CHEBI:24654', 'CHEBI:26191'] | ['PMID:25359497', 'PMID:26546247', 'PMID:26986653', 'Wikipedia:Resolvin'] | ['C(\\CCC(O)=O)=C\\C[C@@H](C(/C=C/C=C/C=C\\C=C\\[C@H](C/C=C\\CC)O)=O)O', 'C(\\CCC(O)=O)=C\\C[C@@H]([C@@H](\\C=C\\C=C\\C=C/C=C/C(C/C=C\\CC)=O)O)O', 'OC(CCCC(\\C=C/C=C/C=C/C(C\\C=C/C=C/[C@@H](CC)O)O)O)=O', 'CCC(\\C=C\\C=C/C=C/C(C\\C=C/C=C/C(CCCCCC(=O)O)O)O)O', 'CC/C=C\\C/C=C\\C=C\\C(C(/C=C/C=C\\C(CCCCCC(O)=O)O)O)O', 'CC/... | 3 | 4 | 27 |
CHEBI:132124 | 1,4-benzoquinones | Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives. | ['CHEBI:22729', 'CHEBI:25830'] | null | ['CC(C)C1=CC(=O)C(C)=CC1=O', 'C1=C(C(C(=C(C1=O)OC)O)=O)C', 'C1(C=C(C(C(=C1)Cl)=O)Cl)=O', 'O(C=1C(=O)C(C\\C=C(\\CC\\C=C(\\CC\\C=C(\\CCC=C(C)C)/C)/C)/C)=C(C(=O)C1OC)C)C', 'C1(C(=C(C(C(=C1C2=CC=C(C=C2)O)O)=O)C3=CC=C(C=C3)O)O)=O', 'C1(C=C(C(C(=C1)Cl)=O)O)=O', '[H][C@@]12CC(=O)O[C@]1([H])C1=C(C(=O)C3=C(C=CC=C3O)C1=O)[C@]1(O... | 2 | null | 108 |
CHEBI:132130 | hydroxyquinone | Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group. | ['CHEBI:33822', 'CHEBI:36141'] | null | ['C1(=C(C(C(=C(C1=O)O)O)=O)O)O', '[C@H](C)([C@@H]([C@@H]([C@H](\\C=C\\O[C@]1(OC=2C(C1=O)=C3C(C(C(C=C3[O-])=O)=O)=C(C2C)[O-])C)OC)C)OC(=O)C)[C@H](O)[C@@H]([C@@H](O)[C@@H](C)/C=C/C=C(/C)\\C(N)=O)C', '[C@H](C)([C@@H]([C@@H]([C@H](\\C=C\\O[C@]1(OC=2C(C1=O)=C3C(C(C(=CC3=O)[O-])=O)=C(C2C)[O-])C)OC)C)OC(=O)C)[C@H](O)[C@@H]([C... | 2 | null | 74 |
CHEBI:132142 | 1,4-naphthoquinones | A naphthoquinone in which the oxo groups of the quinone moiety are at positions 1 and 4 of the parent naphthalene ring. | ['CHEBI:25481', 'CHEBI:25830'] | null | ['C1COCCN1C2=C(C(=O)C3=CC=CC=C3C2=O)NC4=CC=CC(=C4)C(=O)O', 'CCOC1=CC=C(C=C1)NC2=C(C(=O)C3=CC=CC=C3C2=O)OC', 'CN(C1=CC=CC=C1)C2=C(C(=O)C3=CC=CC=C3C2=O)NC(=O)C4=CC=C(C=C4)Cl', 'CC1CCN(CC1)C2=C(C(=O)C3=CC=CC=C3C2=O)NS(=O)(=O)C4=CC=CC=C4', 'C=CCNC1=C(C(=O)C2=CC=CC=C2C1=O)Cl', 'CC1CCCN(C1)C2=C(C(=O)C3=CC=CC=C3C2=O)NS(=O)(=O... | 2 | null | 93 |
CHEBI:132155 | hydroxynaphthoquinone | Any naphthoquinone in which the naphthaoquinone moiety is substituted by at least one hydroxy group. | ['CHEBI:132130', 'CHEBI:25481'] | ['Wikipedia:Hydroxynaphthoquinone'] | ['[C@H](C)([C@@H]([C@@H]([C@H](\\C=C\\O[C@]1(OC=2C(C1=O)=C3C(C(C(C=C3[O-])=O)=O)=C(C2C)[O-])C)OC)C)OC(=O)C)[C@H](O)[C@@H]([C@@H](O)[C@@H](C)/C=C/C=C(/C)\\C(N)=O)C', '[C@H](C)([C@@H]([C@@H]([C@H](\\C=C\\O[C@]1(OC=2C(C1=O)=C3C(C(C(=CC3=O)[O-])=O)=C(C2C)[O-])C)OC)C)OC(=O)C)[C@H](O)[C@@H]([C@@H](O)[C@@H](C)/C=C/C=C(/C)\\C(... | 2 | 1 | 41 |
CHEBI:132157 | hydroxy-1,4-naphthoquinone | Any member of the class of 1,4-naphthoquinones in which the naphthoquinone moiety is substituted by at least one hydroxy group. | ['CHEBI:132142', 'CHEBI:132155'] | null | ['Oc1cccc2C(=O)C=CC(=O)c12', 'C1=CC=C(C2=C1C(C=C(C2=O)O)=O)O', 'CC(C)=CC[C@H](O)C1=CC(=O)c2c(O)ccc(O)c2C1=O', 'CC(C)=CC[C@H](OC(=O)C=C(C)C)C1=CC(=O)c2c(O)ccc(O)c2C1=O', 'Cc1ccc(O)c2C(=O)C(C)=C(O)C(=O)c12', 'Oc1ccc(O)c2C(=O)C=CC(=O)c12', 'Oc1cc(O)c2C(=O)C=C(O)C(=O)c2c1', 'OC1=CC(=O)c2ccccc2C1=O', 'Cc1cc(O)c2C(=O)C=C(C(=... | 2 | null | 35 |
CHEBI:132367 | beta-D-glucuronoside(1-) | A carbohydrate acid derivative anion obtained by deprotonation of the carboxy group of any beta-D-glucuronoside. | ['CHEBI:63551'] | null | ['C=1C(=CC=C(C1)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C([O-])=O)O)O)O)NC(=O)C', 'C=1(O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C([O-])=O)O)O)O)C=CC(=C(C1)OC)NC(C)=O', 'C1[C@]2([C@]3([C@@](C4=C(C=C(O[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)C(=O)[O-])O)O)O)C=C4)CC3)(CC[C@@]2(C(=O)C1)C)[H])[H])[H]', 'C1[C@]2([C@]3([C@@](C4=C(CC3)C=C(C=... | 1 | null | 56 |
CHEBI:13248 | anilide | Any aromatic amide obtained by acylation of aniline. | ['CHEBI:22712', 'CHEBI:62733'] | ['KEGG:C01402', 'PMID:23535982', 'PMID:23968552', 'PMID:24273122', 'PMID:6205897'] | ['C1=CC=C(C=C1)NC(=O)C[C@@H]2C=C[C@@H]([C@H](O2)CO)NC(=O)CC3=CN=CC=C3', 'CCC(=O)NC1=CC2=C(C=C1)OC[C@@H]3[C@H](CC[C@@H](O3)CC(=O)NC4=C(C=CC=C4F)F)N(C2=O)C', 'CN1[C@H]2CC[C@H](O[C@@H]2COC3=C(C1=O)C=C(C=C3)NC(=O)C4CCOCC4)CC(=O)NC5=CC(=CC=C5)OC', 'CN1[C@@H]2CC[C@H](O[C@H]2COC3=C(C1=O)C=C(C=C3)NC(=O)C4CCOCC4)CC(=O)NC5=CC(=C... | 2 | 5 | 326 |
CHEBI:132502 | fatty acid 18:3 | Any trienoic fatty acid containing 18 carbons. | ['CHEBI:73155'] | null | ['CCCC\\C=C\\C=C\\C=C/CCCCCCCC(O)=O', 'OC(CCCCCCCC(O)=O)/C=C/C=C/C=C/C(=O)CC', 'C(CCCCCC(=O)O)C/C=C/CC(/C=C(/C=C/CCO)\\O)=O', 'OC(=O)CCCCCCCC/C=C/C=C/C/C=C/CC', 'OC(=O)CCCCCCC/C=C/C/C=C/C=C/CCC', 'OC(=O)CCCCCCC/C=C/C/C=C\\C/C=C\\CC', 'OC(=O)CCCCCCC/C=C/C/C=C/C/C=C/CC', 'O[C@@H](CCCCCC(O)=O)[C@@H](O)/C=C\\C/C=C\\C/C=C\\... | 1 | null | 70 |
CHEBI:132742 | lysophosphatidic acid | A member of the class of lysophosphatidic acids obtained by hydrolytic removal of one of the two acyl groups of any phosphatidic acid. A 'closed' class. | ['CHEBI:32957'] | null | ['C([C@@](CO)(OC(CCCCCCCCCCCCCCCCC)=O)[H])OP(O)(=O)O', 'CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(O)(O)=O', 'P(OC[C@H](O)COC(=O)CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC)(O)(O)=O', 'P(OC[C@H](O)COC(=O)CCCCCCCCCCCCCCCCCCCC)(O)(O)=O', 'P(OC[C@H](O)COC(=O)CCCCCCCCCCC/C=C\\C/C=C\\CCCCC)(O)(O)=O', 'P(OC[C@H](O)COC(=O)CCCCCCCCC... | 1 | null | 60 |
CHEBI:133004 | bisbenzylisoquinoline alkaloid | A type of benzylisoquinoline alkaloid whose structures are built up of two benzylisoquinoline units linked by ether bridges. Various structural patterns resulting from additional bridging between the two units by direct carbon-carbon bridging or by methylenedioxy groups are common. | ['CHEBI:22750'] | ['PMID:1955879', 'PMID:2191354', 'PMID:3323421'] | ['COc1cc2CCN(C)[C@H]3Cc4ccc(Oc5cc(C[C@@H]6N(C)CCc7cc(OC)c(O)c(Oc1cc23)c67)ccc5O)cc4', 'COc1cc2CCN(C)[C@H]3Cc4ccc(Oc5c(O)c(OC)cc6CCN(C)[C@@H](Cc7ccc(O)c(Oc1cc23)c7)c56)cc4', 'O1C=2C=C3C(=CC2OC)CCN([C@H]3CC4=CC=C(OC=5C=C(C[C@@]6(N(CCC=7C6=C1C(O)=C(OC)C7)C)[H])C=CC5OC)C=C4)C', 'O1C=2C=C3C(=CC2OC)C=CN=C3C(=O)C4=CC=C(OC=5C=... | 1 | 3 | 35 |
CHEBI:133131 | spiro-epoxide | An oxaspiro compound in which a carbon atom of an epoxide ring is the only common member of two rings. | ['CHEBI:32955', 'CHEBI:37948'] | null | ['[C@@]12([C@]([C@]3(C(O[C@@](C1)([C@]3(C(O)(C)C)[H])[H])=O)[H])([C@@H]4[C@H]([C@@]25OC5)O4)O)C', '[C@@]12([C@H](C)O1)C(O[C@H]3[C@@]4([N+](CC=C4COC([C@]([C@@H](C2)C)(C)O)=O)(CC3)[O-])[H])=O', '[C@@]12([C@H](C)O1)C(O[C@H]3[C@@]4(N(CC=C4COC([C@](C(C2)=C)(C)O)=O)CC3)[H])=O', '[C@@]12([C@H](C)O1)C(O[C@H]3[C@@]4([N+](CC=C4C... | 2 | null | 57 |
CHEBI:133135 | chromenochromene | Any organic heteroolycyclic compound whose skeleton two ortho-fused chromene rings, and their derivatives. | ['CHEBI:38166'] | null | ['CC(=C)C1CC2=C(O1)C=CC3=C2OC4=C(C3=O)C5=CC(=C(C=C5OC4)OC)OC', 'CC(C)=CCC=1C(=CC(=C2C(C=3C(C=C(C)C)OC=4C=C(C=CC4C3OC12)O)=O)O)O', 'O1[C@@]2([C@](C(=O)C3=C1C=4C[C@H](OC4C=C3)C(C)C)(C=5C(OC2)=CC(OC)=C(OC)C5)[H])[H]', 'O1C2C(O)(C=3C(OC2)=CC(OC)=C(OC)C3)C(=O)C=4C1=C5C(OC(C=C5)(C)C)=C(OC)C4', 'O1C2C(C=3C(OC2)=CC(O)=C(OC)C3)... | 1 | null | 46 |
End of preview.
CHEBI Chemical Classification Program Ontology (C3PO) Benchmark
Name: C3PO-v237
A benchmark for chemical classification, derived from v237 of the CHEBI ontology.
The benchmark consists of
- 177,875 Structures, each represented by a SMILES string
- 1364 Classes, each of which classify (directly or indirectly) between 25 and 5000 Structures
The CHEBI smiles property (obo:chebi/smiles) is used to derive
structures. Only SMILES strings that lacked a * wildcard are
used. If multiple CHEBI entries have the same SMILES, they are
collapsed.
The benchmark can be further partitioned based on different properties.
C3PO-Slim is the subset of structures that have at least one xref (mapping), representing the set of classes that are more commonly used in the biological literature and in other databases.
20% of the structures are designated as being for validation purposes. The remaining 80% can be used for training and testing.
The benchmark can be downloaded as either a single JSON file, or separate CSVs for classes and structures. Summary stats files are also provided:
- dataset.json - the complete benchmark
- classes.csv - all classes
- classes_slim.csv - slim classes (any with an xref)
- structures.csv - all structures
- classes_summary.csv - summary statistics for classes
- classes_slim_summary.csv - summary statistics for classes
- structures_summary.csv - summary statistics for structures
- metadata.csv - metadata about how this was derived.
For a description of all fields, see:
For the code that extracts the benchmark from CHEBI, see:
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