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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type struct<component_id: int64, component_type: string, description: string, organism: string, sequence: string, tax_id: int64> to null
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2013, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, 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 2302, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2261, in cast_table_to_schema
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2261, in <listcomp>
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1802, in wrapper
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1802, in <listcomp>
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2020, in cast_array_to_feature
arrays = [_c(array.field(name), subfeature) for name, subfeature in feature.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2020, in <listcomp>
arrays = [_c(array.field(name), subfeature) for name, subfeature in feature.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2020, in cast_array_to_feature
arrays = [_c(array.field(name), subfeature) for name, subfeature in feature.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2020, in <listcomp>
arrays = [_c(array.field(name), subfeature) for name, subfeature in feature.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2020, in cast_array_to_feature
arrays = [_c(array.field(name), subfeature) for name, subfeature in feature.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2020, in <listcomp>
arrays = [_c(array.field(name), subfeature) for name, subfeature in feature.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2075, in cast_array_to_feature
casted_array_values = _c(array.values, feature.feature)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2116, in cast_array_to_feature
return array_cast(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1964, in array_cast
raise TypeError(f"Couldn't cast array of type {_short_str(array.type)} to {_short_str(pa_type)}")
TypeError: Couldn't cast array of type struct<component_id: int64, component_type: string, description: string, organism: string, sequence: string, tax_id: int64> to null
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1529, 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 1154, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1029, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1124, 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 1884, 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 2040, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
chembl dict | zinc null | surechembl null | uci string | nikkaji null | actor null | mcule null | comptox null | probes_and_drugs null | molport null | fdasrs null | drugbank null | pdb null | chebi null | chemicalbook null | dailymed null | fda null | pharmgkb null | lincs null | metabolights null | clinicaltrials null | rxnorm null | MedChemExpress null | hmdb null | kegg_ligand null | atlas null | recon null | lipidmaps null | selleck null | nih_ncc null | swisslipids null |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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{
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"availability_type": {
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"biotherapeutic": {
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"black_box_warning": {
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"chebi_par_id": {
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"chirality": {
"0": -1
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"cross_references": {
"0": []
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"dosed_ingredient": {
"0": fal... | null | null | 31 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
{
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"chirality": {
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{
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"dosed_ingredient": {
"0": fal... | null | null | 33 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
null | null | null | 34 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
{
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"dosed_ingredient": {
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{
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"dosed_ingredient": {
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{
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"chirality": {
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"cross_references": {
"0": []
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"dosed_ingredient": {
"0": fal... | null | null | 37 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
End of preview.
YAML Metadata Warning:empty or missing yaml metadata in repo card
Check out the documentation for more information.
Definición de campos
- uci_id: UniChEM identifier.
- chembl_id: ChEMBL identifier.
- molecule_type: Type of molecule (Small molecule, Protein, Antibody, Oligosaccharide, Oligonucleotide, Cell, Unknown).⁶
- alogp: Calculated ALogP. Ghose-Crippen-Viswanadhan octanol-water partition coefficient (ALogP).¹ ²
- aromatic_rings: number of aromatic rings. Aromatic rings are common structural components of polymers.
- cx_logd: The calculated octanol/water distribution coefficient at pH7.4 using ChemAxon v17.29.0.³
- cx_logp: The calculated octanol/water partition coefficient using ChemAxon v17.29.0.³
- cx_most_apka: The most acidic pKa calculated using ChemAxon v17.29.0.³
- cx_most_bpka: The most basic pKa calculated using ChemAxon v17.29.0.³
- full_molformula: Molecular formula for the full compound (including any salt).⁴
- full_mwt: Molecular weight of the full compound including any salts.⁴
- hba: Number hydrogen bond acceptors.⁴
- hba_lipinski: Number of hydrogen bond acceptors calculated according to Lipinski's original rules (i.e., N + O count)).⁴
- hbd: Number hydrogen bond donors.⁴
- hbd_lipinski: Number of hydrogen bond donors calculated according to Lipinski's original rules (i.e., NH + OH count).⁴
- heavy_atoms: Number of heavy (non-hydrogen) atoms.⁴
- molecular_species: Indicates whether the compound is an acid/base/neutral.⁵
- mw_freebase: Molecular weight of parent compound.⁴
- mw_monoisotopic: Monoisotopic parent molecular weight.⁴
- num_lipinski_ro5_violations: Number of violations of Lipinski's rule of five using HBA_LIPINSKI and HBD_LIPINSKI counts.⁵
- num_ro5_violations: Number of violations of Lipinski's rule-of-five, using HBA and HBD definitions.⁵
- psa: Polar surface area.⁴
- qed_weighted: Weighted quantitative estimate of drug likeness (as defined by Bickerton et al., Nature Chem 2012).⁴
- ro3_pass: Indicates whether the compound passes the rule-of-three (mw < 300, logP < 3 etc).⁵
- rtb: Number rotatable bonds.⁴
- canonical_smiles: Canonical smiles, with no stereochemistry information. Generated using pipeline pilot.⁵
- standard_inchi: IUPAC standard InChI for the compound.⁵
- standard_inchi_key: IUPAC standard InChI key for the compound.⁵
- natural_product: Indicates whether the compound is natural product-derived (currently curated only for drugs).⁶
- inorganic_flag: Indicates whether the molecule is inorganic (i.e., containing only metal atoms and <2 carbon atoms).⁶
- therapeutic_flag: Indicates that a drug has a therapeutic application (as opposed to e.g., an imaging agent, additive etc).⁶
- biotherapeutic: A single related resource. Can be either a URI or set of nested resource data.⁶
- polymer_flag: Indicates whether a molecule is a small molecule polymer (e.g., polistyrex).⁶
- prodrug: Indicates that the molecule is a pro-drug (see molecule hierarchy for active component, where known).⁶
- kegg_id: KEGG identifier.
- formula: Molecular formula for the full compound.
- exact_mass: Mass of the compound (from KEGG).
- mol_weight: mass of a molecule of a substance, based on 12 as the atomic weight of carbon-12.⁸
- atom: An ATOM entry represents KEGG Atom Type .¹⁰
- bond: A BOND entry is defined as a pair of ATOM entries that form a chemical bond in a molecule, corresponding to many named bonds in organic chemistry and biochemistry. ¹⁰
- chebi_id: ChEBI identifier.
- definition: A simple definition of this compound.
- mass: Returns the average mass. The relative masses are calculated from tables of relative atomic masses (atomic weights) published by IUPAC. (from CheBI).⁷
- mol: ChEBI stores the two-dimensional or three-dimensional structural diagrams as connection tables in MDL molfile format.⁷
- smiles: The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings.
- inchi: The International Chemical Identifier (InChI) is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web.
- inchi_key: The InChIKey, sometimes referred to as a hashed InChI, is a fixed length (27 character) condensed digital representation of the InChI that is not human-understandable.
- cas_id: CAS Registry Number. A CAS Registry Number is a unique and unambiguous identifier for a specific substance that allows clear communication and, with the help of CAS scientists, links together all available data and research about that substance.
- substance: Full substance name as recognized by CFSAN (FDA). ⁹
- regs: Code of Federal Regulations associated numbers of this compound (FDA). ⁹
- syns: Synonyms of the compound (FDA).
- used_for: The physical or technical effect(s) the substance has in or on food; see 21 CFR 170.3(o) for definitions. (FDA). ⁹
¹ http://chemgps.bmc.uu.se/help/dragonx/GhoseCrippenViswanadhanAlogP.html
² http://www.talete.mi.it/help/dproperties_help/index.html?molecular_properties.htm
³ http://chembl.blogspot.com/2020/03/chembl-26-released.html
⁴ https://micha-protocol.org/glossary/index
⁵ https://www.ebi.ac.uk/chembl/api/data/drug/schema
⁶ https://www.ebi.ac.uk/chembl/api/data/molecule/schema
⁷ http://libchebi.github.io/libChEBI%20API.pdf
⁸ https://www.britannica.com/science/molecular-weight
¹⁰ https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-S6-S2
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