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tsantosh7
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COVID-19_Annotations

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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 1 new columns ({'RNA'}) and 1 missing columns ({'ABSTRACT'}).

This happened while the csv dataset builder was generating data using

hf://datasets/tsantosh7/COVID-19_Annotations/dev.tsv (at revision b31afad97a9fada96522cc2f5b080338d4a3f7cd)

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
              RNA: string
              O: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 471
              to
              {'ABSTRACT': 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 1 new columns ({'RNA'}) and 1 missing columns ({'ABSTRACT'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/tsantosh7/COVID-19_Annotations/dev.tsv (at revision b31afad97a9fada96522cc2f5b080338d4a3f7cd)
              
              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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ABSTRACT
string
O
string
:
O
A
O
region
O
of
O
the
O
bovine
B-SPEC
coronavirus
B-SPEC
(
O
BCV
B-SPEC
)
O
genome
O
that
O
functions
O
as
O
a
O
packaging
O
signal
O
has
O
been
O
cloned
O
.
O
The
O
291
O
-
O
nucleotide
B-CHED
clone
O
shares
O
72
O
%
O
homology
O
with
O
the
O
region
O
of
O
mouse
B-DISO
hepatitis
I-DISO
coronavirus
B-SPEC
(
O
MHV
B-SPEC
)
O
gene
O
1b
O
that
O
contains
O
the
O
packaging
O
signal
O
.
O
The
O
data
O
demonstrate
O
that
O
the
O
BCV
B-SPEC
genome
O
contains
O
a
O
sequence
O
that
O
is
O
conserved
O
at
O
both
O
the
O
sequence
O
and
O
functional
O
levels
O
,
O
thus
O
broadening
O
our
O
insight
O
into
O
coronavirus
B-SPEC
packaging
O
.
O
TITLE
O
:
O
Comparison
O
of
O
systemic
O
cytokine
O
levels
O
in
O
patients
O
with
O
acute
B-DISO
respiratory
I-DISO
distress
I-DISO
syndrome
I-DISO
,
O
severe
O
pneumonia
O
,
O
and
O
controls
O
.
O
ABSTRACT
O
:
O
End of preview.

Named Entity Recognition for COVID-19 Bio Entities The dataset was taken from https://github.com/davidcampos/covid19-corpus

Dataset The dataset was then split into several datasets each one representing one entity. Namely, Disorder, Species, Chemical or Drug, Gene and Protein, Enzyme, Anatomy, Biological Process, Molecular Function, Cellular Component, Pathway and microRNA. Moreover, another dataset is also created with all those aforementioned that are non-overlapping in nature.

Dataset Formats The datasets are available in two formats IOB and Spacy's JSONL format.

IOB : https://github.com/tsantosh7/COVID-19-Named-Entity-Recognition/tree/master/Datasets/BIO

SpaCy JSONL: https://github.com/tsantosh7/COVID-19-Named-Entity-Recognition/tree/master/Datasets/SpaCy

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