Dataset Preview
The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1520, in _prepare_split_single
for key, record 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/webdataset/webdataset.py", line 130, in _generate_examples
for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 34, in _get_pipeline_from_tar
for filename, f in tar_iterator:
^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
for x in self.generator(*self.args):
~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1405, in _iter_from_urlpath
with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 982, in xopen
file_obj = fs.open(paths[0], mode)
File "<string>", line 3, in open
File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
return self._mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
return self._execute_mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
result = effect(*args, **kwargs)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
~~~^^^^^^^^
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
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 1382, 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 1560, 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.
txt string | __key__ string | __url__ string |
|---|---|---|
"test/PMC2268688_table_0.html\ntest/PMC5808191_table_2.html\ntest/PMC5809909_table_0.html\ntest/PMC2(...TRUNCATED) | test_filelist | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
"train/PMC5070146_table_0.html\ntrain/PMC4352559_table_0.html\ntrain/PMC2816221_table_3.html\ntrain/(...TRUNCATED) | train_filelist | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
"val/PMC4625814_table_1.html\nval/PMC3636047_table_2.html\nval/PMC3587592_table_1.html\nval/PMC61207(...TRUNCATED) | val_filelist | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC4797223_table_0 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC6171232_table_4 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC3581528_table_1 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC5747941_table_1 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC4872139_table_5 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC4962389_table_1 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
null | ./PMC3432589_table_0 | "hf://datasets/monoamine11231/pubtables-1m-html@6934abfc562424e298ccb44fe67d092868341cda/PubTables-1(...TRUNCATED) |
End of preview.
PubTables-1M-HTML
This is a version of the bsmock/pubtables-1m dataset, where the XML annotations and JSON tokens have been merged and converted together into HTML table representations using the monoamine11231/pubtables-1m-to-html script.
Structure
The HTML table representations are stored with the original name prefix as in the original dataset. The HTML tables include the header (if existant) and the body part, as directed by the table annotation files. Furthermore, the HTML table representations include bbox (xmin, ymin, xmax, ymax) attributes for <td>, <th>, and <tr> tags as it can be seen below:
<table>
<thead>
<tr bbox="[36, 36, 247, 52]">
<th bbox="[36, 36, 130, 52]">Protein</th>
<th bbox="[130, 36, 247, 52]">Percentage</th>
</tr>
</thead>
<tbody>
<tr bbox="[36, 52, 247, 72]">
<td bbox="[36, 52, 130, 72]">PCNA</td>
<td bbox="[130, 52, 247, 72]">15.93 ± 4.38</td>
</tr>
<tr bbox="[36, 72, 247, 92]">
<td bbox="[36, 72, 130, 92]">hMLH1</td>
<td bbox="[130, 72, 247, 92]">0.25 ± 1.11</td>
</tr>
<tr bbox="[36, 92, 247, 111]">
<td bbox="[36, 92, 130, 111]">hPMS1</td>
<td bbox="[130, 92, 247, 111]">0.6 ± 0.99</td>
</tr>
<tr bbox="[36, 111, 247, 131]">
<td bbox="[36, 111, 130, 131]">hPMS2</td>
<td bbox="[130, 111, 247, 131]">0 ± 0</td>
</tr>
<tr bbox="[36, 131, 247, 151]">
<td bbox="[36, 131, 130, 151]">hMSH2</td>
<td bbox="[130, 131, 247, 151]">72.7 ± 20.33</td>
</tr>
<tr bbox="[36, 151, 247, 166]">
<td bbox="[36, 151, 130, 166]">TP53</td>
<td bbox="[130, 151, 247, 166]">0 ± 0</td>
</tr>
</tbody>
</table>
The dataset can be found divided into multiple archives under 'Files and versions' and which can be unpacked by preserving the correct structure using the extract_structure_dataset.sh script.
Limitations
The HTML table representations do not contain any styling information about both the table cells and the table cell text; i.e there is no information included about the table cell border or if the table cell is bold or italic. In addition, there are no superscripts and subscripts in the table cell texts which is scheduled to be fixed in the near future with the usage of external OCR.
- Downloads last month
- 9