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The dataset generation failed
Error code: DatasetGenerationError
Exception: CastError
Message: Couldn't cast
extensions: struct<bindingnorm:bindingdb: struct<article_doi: string, chembl_id: string, curation_source: string (... 525 chars omitted)
child 0, bindingnorm:bindingdb: struct<article_doi: string, chembl_id: string, curation_source: string, date_curated: string, date_p (... 441 chars omitted)
child 0, article_doi: string
child 1, chembl_id: string
child 2, curation_source: string
child 3, date_curated: string
child 4, date_publication: string
child 5, license_tier: string
child 6, ligand_het_id: string
child 7, ligand_inchikey: string
child 8, n_target_chains: string
child 9, patent_number: string
child 10, pdb_complex_ids: list<item: string>
child 0, item: string
child 11, pdb_target_chain_ids: list<item: string>
child 0, item: string
child 12, ph: string
child 13, pmid: string
child 14, pubchem_cid: string
child 15, target_organism: string
child 16, target_seq_lengths: list<item: int64>
child 0, item: int64
child 17, target_seq_sha256s: list<item: string>
child 0, item: string
child 18, target_sequences: list<item: string>
child 0, item: string
child 19, temp_c: string
child 20, uniprot_id: string
child 1, bindingnorm:source: struct<training_eligible: bool>
child 0, training_eligible: bool
id: string
license_reference: string
license_status: string
media_type: string
missing_reasons: struct<
...
ot (TrEMBL) Submitted Name of Target Chain 38: string
child 618, UniProt (TrEMBL) Submitted Name of Target Chain 39: string
child 619, UniProt (TrEMBL) Submitted Name of Target Chain 4: string
child 620, UniProt (TrEMBL) Submitted Name of Target Chain 40: string
child 621, UniProt (TrEMBL) Submitted Name of Target Chain 41: string
child 622, UniProt (TrEMBL) Submitted Name of Target Chain 42: string
child 623, UniProt (TrEMBL) Submitted Name of Target Chain 43: string
child 624, UniProt (TrEMBL) Submitted Name of Target Chain 44: string
child 625, UniProt (TrEMBL) Submitted Name of Target Chain 45: string
child 626, UniProt (TrEMBL) Submitted Name of Target Chain 46: string
child 627, UniProt (TrEMBL) Submitted Name of Target Chain 47: string
child 628, UniProt (TrEMBL) Submitted Name of Target Chain 48: string
child 629, UniProt (TrEMBL) Submitted Name of Target Chain 49: string
child 630, UniProt (TrEMBL) Submitted Name of Target Chain 5: string
child 631, UniProt (TrEMBL) Submitted Name of Target Chain 50: string
child 632, UniProt (TrEMBL) Submitted Name of Target Chain 6: string
child 633, UniProt (TrEMBL) Submitted Name of Target Chain 7: string
child 634, UniProt (TrEMBL) Submitted Name of Target Chain 8: string
child 635, UniProt (TrEMBL) Submitted Name of Target Chain 9: string
child 636, ZINC ID of Ligand: string
child 637, koff (s-1): string
child 638, kon (M-1-s-1): string
child 639, pH: string
reason: string
line: int64
to
{'line': Value('int64'), 'raw': {'Article DOI': Value('string'), 'Authors': Value('string'), 'BindingDB Entry DOI': Value('string'), 'BindingDB Ligand Name': Value('string'), 'BindingDB MonomerID': Value('string'), 'BindingDB Reactant_set_id': Value('string'), 'BindingDB Target Chain Sequence 1': Value('string'), 'BindingDB Target Chain Sequence 10': Value('string'), 'BindingDB Target Chain Sequence 11': Value('string'), 'BindingDB Target Chain Sequence 12': Value('string'), 'BindingDB Target Chain Sequence 13': Value('string'), 'BindingDB Target Chain Sequence 14': Value('string'), 'BindingDB Target Chain Sequence 15': Value('string'), 'BindingDB Target Chain Sequence 16': Value('string'), 'BindingDB Target Chain Sequence 17': Value('string'), 'BindingDB Target Chain Sequence 18': Value('string'), 'BindingDB Target Chain Sequence 19': Value('string'), 'BindingDB Target Chain Sequence 2': Value('string'), 'BindingDB Target Chain Sequence 20': Value('string'), 'BindingDB Target Chain Sequence 21': Value('string'), 'BindingDB Target Chain Sequence 22': Value('string'), 'BindingDB Target Chain Sequence 23': Value('string'), 'BindingDB Target Chain Sequence 24': Value('string'), 'BindingDB Target Chain Sequence 25': Value('string'), 'BindingDB Target Chain Sequence 26': Value('string'), 'BindingDB Target Chain Sequence 27': Value('string'), 'BindingDB Target Chain Sequence 28': Value('string'), 'BindingDB Target Chain Sequence 29': Value('string'), 'BindingDB Target Chain Sequenc
...
'), 'UniProt (TrEMBL) Submitted Name of Target Chain 38': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 39': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 4': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 40': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 41': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 42': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 43': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 44': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 45': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 46': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 47': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 48': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 49': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 5': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 50': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 6': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 7': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 8': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 9': Value('string'), 'ZINC ID of Ligand': Value('string'), 'koff (s-1)': Value('string'), 'kon (M-1-s-1)': Value('string'), 'pH': Value('string')}, 'reason': Value('string')}
because column names don't match
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1827, in _prepare_split_single
for key, table in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 343, in _generate_tables
self._cast_table(pa_table, json_field_paths=json_field_paths),
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 132, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
extensions: struct<bindingnorm:bindingdb: struct<article_doi: string, chembl_id: string, curation_source: string (... 525 chars omitted)
child 0, bindingnorm:bindingdb: struct<article_doi: string, chembl_id: string, curation_source: string, date_curated: string, date_p (... 441 chars omitted)
child 0, article_doi: string
child 1, chembl_id: string
child 2, curation_source: string
child 3, date_curated: string
child 4, date_publication: string
child 5, license_tier: string
child 6, ligand_het_id: string
child 7, ligand_inchikey: string
child 8, n_target_chains: string
child 9, patent_number: string
child 10, pdb_complex_ids: list<item: string>
child 0, item: string
child 11, pdb_target_chain_ids: list<item: string>
child 0, item: string
child 12, ph: string
child 13, pmid: string
child 14, pubchem_cid: string
child 15, target_organism: string
child 16, target_seq_lengths: list<item: int64>
child 0, item: int64
child 17, target_seq_sha256s: list<item: string>
child 0, item: string
child 18, target_sequences: list<item: string>
child 0, item: string
child 19, temp_c: string
child 20, uniprot_id: string
child 1, bindingnorm:source: struct<training_eligible: bool>
child 0, training_eligible: bool
id: string
license_reference: string
license_status: string
media_type: string
missing_reasons: struct<
...
ot (TrEMBL) Submitted Name of Target Chain 38: string
child 618, UniProt (TrEMBL) Submitted Name of Target Chain 39: string
child 619, UniProt (TrEMBL) Submitted Name of Target Chain 4: string
child 620, UniProt (TrEMBL) Submitted Name of Target Chain 40: string
child 621, UniProt (TrEMBL) Submitted Name of Target Chain 41: string
child 622, UniProt (TrEMBL) Submitted Name of Target Chain 42: string
child 623, UniProt (TrEMBL) Submitted Name of Target Chain 43: string
child 624, UniProt (TrEMBL) Submitted Name of Target Chain 44: string
child 625, UniProt (TrEMBL) Submitted Name of Target Chain 45: string
child 626, UniProt (TrEMBL) Submitted Name of Target Chain 46: string
child 627, UniProt (TrEMBL) Submitted Name of Target Chain 47: string
child 628, UniProt (TrEMBL) Submitted Name of Target Chain 48: string
child 629, UniProt (TrEMBL) Submitted Name of Target Chain 49: string
child 630, UniProt (TrEMBL) Submitted Name of Target Chain 5: string
child 631, UniProt (TrEMBL) Submitted Name of Target Chain 50: string
child 632, UniProt (TrEMBL) Submitted Name of Target Chain 6: string
child 633, UniProt (TrEMBL) Submitted Name of Target Chain 7: string
child 634, UniProt (TrEMBL) Submitted Name of Target Chain 8: string
child 635, UniProt (TrEMBL) Submitted Name of Target Chain 9: string
child 636, ZINC ID of Ligand: string
child 637, koff (s-1): string
child 638, kon (M-1-s-1): string
child 639, pH: string
reason: string
line: int64
to
{'line': Value('int64'), 'raw': {'Article DOI': Value('string'), 'Authors': Value('string'), 'BindingDB Entry DOI': Value('string'), 'BindingDB Ligand Name': Value('string'), 'BindingDB MonomerID': Value('string'), 'BindingDB Reactant_set_id': Value('string'), 'BindingDB Target Chain Sequence 1': Value('string'), 'BindingDB Target Chain Sequence 10': Value('string'), 'BindingDB Target Chain Sequence 11': Value('string'), 'BindingDB Target Chain Sequence 12': Value('string'), 'BindingDB Target Chain Sequence 13': Value('string'), 'BindingDB Target Chain Sequence 14': Value('string'), 'BindingDB Target Chain Sequence 15': Value('string'), 'BindingDB Target Chain Sequence 16': Value('string'), 'BindingDB Target Chain Sequence 17': Value('string'), 'BindingDB Target Chain Sequence 18': Value('string'), 'BindingDB Target Chain Sequence 19': Value('string'), 'BindingDB Target Chain Sequence 2': Value('string'), 'BindingDB Target Chain Sequence 20': Value('string'), 'BindingDB Target Chain Sequence 21': Value('string'), 'BindingDB Target Chain Sequence 22': Value('string'), 'BindingDB Target Chain Sequence 23': Value('string'), 'BindingDB Target Chain Sequence 24': Value('string'), 'BindingDB Target Chain Sequence 25': Value('string'), 'BindingDB Target Chain Sequence 26': Value('string'), 'BindingDB Target Chain Sequence 27': Value('string'), 'BindingDB Target Chain Sequence 28': Value('string'), 'BindingDB Target Chain Sequence 29': Value('string'), 'BindingDB Target Chain Sequenc
...
'), 'UniProt (TrEMBL) Submitted Name of Target Chain 38': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 39': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 4': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 40': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 41': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 42': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 43': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 44': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 45': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 46': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 47': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 48': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 49': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 5': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 50': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 6': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 7': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 8': Value('string'), 'UniProt (TrEMBL) Submitted Name of Target Chain 9': Value('string'), 'ZINC ID of Ligand': Value('string'), 'koff (s-1)': Value('string'), 'kon (M-1-s-1)': Value('string'), 'pH': Value('string')}, 'reason': Value('string')}
because column names don't match
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 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1880, 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.
line int64 | raw dict | reason string |
|---|---|---|
2 | {
"Article DOI": "Article DOI",
"Authors": "Authors",
"BindingDB Entry DOI": "BindingDB Entry DOI",
"BindingDB Ligand Name": "BindingDB Ligand Name",
"BindingDB MonomerID": "BindingDB MonomerID",
"BindingDB Reactant_set_id": "BindingDB Reactant_set_id",
"BindingDB Target Chain Sequence 1": "BindingDB Targ... | unparseable affinity; preserve raw record for review |
2 | {
"Article DOI": "Article DOI",
"Authors": "Authors",
"BindingDB Entry DOI": "BindingDB Entry DOI",
"BindingDB Ligand Name": "BindingDB Ligand Name",
"BindingDB MonomerID": "BindingDB MonomerID",
"BindingDB Reactant_set_id": "BindingDB Reactant_set_id",
"BindingDB Target Chain Sequence 1": "BindingDB Targ... | unparseable affinity; preserve raw record for review |
2 | {"Article DOI":"Article DOI","Authors":"Authors","BindingDB Entry DOI":"BindingDB Entry DOI","Bindin(...TRUNCATED) | unparseable affinity; preserve raw record for review |
2 | {"Article DOI":"Article DOI","Authors":"Authors","BindingDB Entry DOI":"BindingDB Entry DOI","Bindin(...TRUNCATED) | unparseable affinity; preserve raw record for review |
199 | {"Article DOI":"10.1021/jm00164a002","Authors":"Krantz, A; Spencer, RW; Tam, TF; Liak, TJ; Copp, LJ;(...TRUNCATED) | no supported endpoint value |
577 | {"Article DOI":"10.1021/jm0208370","Authors":"Markgren, PO; Schaal, W; Hamalainen, M; Karlen, A; Hal(...TRUNCATED) | no supported endpoint value |
579 | {"Article DOI":"10.1021/jm0208370","Authors":"Markgren, PO; Schaal, W; Hamalainen, M; Karlen, A; Hal(...TRUNCATED) | no supported endpoint value |
580 | {"Article DOI":"10.1021/jm0208370","Authors":"Markgren, PO; Schaal, W; Hamalainen, M; Karlen, A; Hal(...TRUNCATED) | no supported endpoint value |
581 | {"Article DOI":"10.1021/jm0208370","Authors":"Markgren, PO; Schaal, W; Hamalainen, M; Karlen, A; Hal(...TRUNCATED) | no supported endpoint value |
582 | {"Article DOI":"10.1021/jm0208370","Authors":"Markgren, PO; Schaal, W; Hamalainen, M; Karlen, A; Hal(...TRUNCATED) | no supported endpoint value |
End of preview.
BindingDB ChEMBL-Sourced Slice — Normalized Dataset
Normalized binding-affinity measurements for the ChEMBL-derived portion of BindingDB (BindingDB's re-exported ChEMBL records).
License and attribution
The underlying measurement data derives from BindingDB's ChEMBL-sourced slice and is redistributed here under CC BY-SA 3.0, following BindingDB's license terms for this portion of its data:
- BindingDB: https://www.bindingdb.org — The BindingDB project, University of California, San Diego / Skaggs School of Pharmacy.
- ChEMBL: https://www.ebi.ac.uk/chembl/ — EMBL-EBI. The original bioactivity data originate in ChEMBL (itself CC BY-SA 3.0).
If you use this dataset, please cite BindingDB and ChEMBL per their respective citation requirements, and distribute derivatives under CC BY-SA 3.0.
Contents
parts/part-*/records.jsonl.gz— normalized evidence records (measurements + source records with assay/provenance metadata, pH/temperature where present)parts/part-*/measurements.csv/measurements.parquet— compact tablesparts/part-*/quarantine.jsonl— source rows quarantined during normalizationparts/part-*/raw/— preserved raw source evidence
Scope note
This package is BindingDB's representation of ChEMBL-derived measurements — not a native ChEMBL database dump. Assay context is limited to what BindingDB re-exports; richer assay entities live in native ChEMBL releases.
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