Datasets:
PDBEurope
/
protein_structure_NER_model_v1.2

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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 2 new columns ({'Biochemical', 'B-experimental_method'}) and 2 missing columns ({'Molecular', 'O'}).

This happened while the csv dataset builder was generating data using

hf://datasets/PDBEurope/protein_structure_NER_model_v1.2/annotation_IOB/dev.tsv (at revision 5c9db0f0e8dc3d605c264a4fd0b2bf74de904358)

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 2011, 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 2256, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Biochemical: string
              B-experimental_method: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 527
              to
              {'Molecular': Value(dtype='string', id=None), 'O': Value(dtype='string', 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 1321, 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 935, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, 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 1882, 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 2013, 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 2 new columns ({'Biochemical', 'B-experimental_method'}) and 2 missing columns ({'Molecular', 'O'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/PDBEurope/protein_structure_NER_model_v1.2/annotation_IOB/dev.tsv (at revision 5c9db0f0e8dc3d605c264a4fd0b2bf74de904358)
              
              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)

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Molecular
string
O
string
Dissection
O
of
O
Xyloglucan
B-chemical
Recognition
O
in
O
a
O
Prominent
O
Human
B-species
Gut
O
Symbiont
O
Polysaccharide
B-gene
utilization
I-gene
loci
I-gene
(
O
PUL
B-gene
)
O
within
O
the
O
genomes
O
of
O
resident
O
human
B-species
gut
O
Bacteroidetes
B-taxonomy_domain
are
O
central
O
to
O
the
O
metabolism
O
of
O
the
O
otherwise
O
indigestible
O
complex
O
carbohydrates
B-chemical
known
O
as
O
“
O
dietary
O
fiber
O
.”
O
However
O
,
O
functional
O
characterization
O
of
O
PUL
B-gene
lags
O
significantly
O
behind
O
sequencing
O
efforts
O
,
O
which
O
limits
O
physiological
O
understanding
O
of
O
the
O
human
B-species
-
O
bacterial
B-taxonomy_domain
symbiosis
O
.
O
Here
O
,
O
we
O
present
O
the
O
biochemical
B-experimental_method
,
I-experimental_method
structural
I-experimental_method
,
I-experimental_method
and
I-experimental_method
reverse
I-experimental_method
genetic
I-experimental_method
characterization
I-experimental_method
of
O
two
O
unique
O
cell
B-protein_type
surface
I-protein_type
glycan
I-protein_type
-
I-protein_type
binding
I-protein_type
proteins
I-protein_type
(
O
SGBPs
B-protein_type
)
O
encoded
O
by
O
a
O
xyloglucan
B-gene
utilization
I-gene
locus
I-gene
(
O
XyGUL
B-gene
)
O
from
O
Bacteroides
B-species
End of preview.