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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type string to null
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 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 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 1962, 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 string 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 1524, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1099, in stream_convert_to_parquet
builder._prepare_split(
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 2038, 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.
doi string | keywords sequence | license string | article dict |
|---|---|---|---|
10.1186/1472-6920-5-10 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "A qualitative study of the perceptions and experiences of Pre-Registration House Officers on teamwork and support",
"authors": "Lempp, Heidi, 1, 2, heidi.k.lempp@kcl.ac.uk, Cochrane, Mac, 1, macandjill@cornergreen.fsnet.co.uk, Rees, John, 1, john.rees@kcl.ac.uk",
"abstract": "Background Following the ... |
10.1186/1475-925X-4-20 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Review of \"Contemporary IMRT: Developing Physics and Clinical Implementation\"\nby Steve Webb",
"authors": "Panagiotopoulos, Vasos-Peter John, II, 1, vp57@columbia.edu",
"abstract": "",
"body_text": "IMRT is Intensity Modulated Radiation Therapy: Irradiating from several directions repeatedly targe... |
10.1186/1475-2875-4-17 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Data mining of the transcriptome of ",
"authors": "Bozdech, Zbynek, 1, ZBozdech@ntu.edu.sg, Ginsburg, Hagai, 2, hagai@vms.huji.ac.il",
"abstract": "The general paradigm that emerges from the analysis of the transcriptome of the malaria parasite Plasmodium falciparum + + + + P. falciparum +",
"body_t... |
10.1186/1471-2334-5-60 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": null,
"authors": "Ma, Edmond SK, 1, eskma@hksh.com, Wong, Chris LP, 1, lpwong@hksh.com, Lai, Kristi TW, 1, kristi_lai@yahoo.com.hk, Chan, Edmond CH, 2, edmondchch@hotmail.com, Yam, WC, 3, wcyam@hkucc.hku.hk, Chan, Angus CW, 4, acwchan@hksh.com",
"abstract": "Background Kocuria Micrococcus K. rosea K. k... |
10.1186/1471-2172-6-15 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Cloning and functional characterization of the rabbit C-C chemokine receptor 2",
"authors": "Lu, Deshun, 1, Lu_Deshun@lilly.com, Yuan, Xiu-juan, 1, yuanxi@lilly.com, Evans, Robert J, Jr, 1, evansro@lilly.com, Pappas, Amy T, 1, pappasam@lilly.com, Wang, He, 1, hwang@lilly.com, Su, Eric W, 1, ewsu@lilly.c... |
10.1186/1743-422X-2-77 | [
"acute retinal necrosis",
"acyclovir",
"contusion",
"corticosteroids",
"varicella zoster virus"
] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Varicella zoster virus acute retinal necrosis following eye contusion: case report",
"authors": "Svozílková, Petra, 1, psvoz@lf1.cuni.cz, Říhová, Eva, 1, evarihova@hotmail.com, Diblík, Pavel, 1, pavel.diblik@email.cz, Kuthan, Pavel, 1, pavel_kuth@yahoo.com, Kovařík, Zdeněk, 1, b.kovarikova@iol.cz, Kalvo... |
10.1186/1472-6963-5-61 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "The use of end-quintile comparisons to identify under-servicing of the poor and over-servicing of the rich: A longitudinal study describing the effect of socioeconomic status on healthcare",
"authors": "Brameld, Kate J, 1, kate@sph.uwa.edu.au, Holman, C D'Arcy J, 1, darcy@sph.uwa.edu.au",
"abstract": ... |
10.1371/journal.ppat.0010016 | [] | http://creativecommons.org/licenses/by/4.0/ | {
"title": "\n",
"authors": "Wong, Ka-Wing, 1, Isberg, Ralph R, 1, 2, *",
"abstract": "Yersinia pseudotuberculosis",
"body_text": "Introduction After ingestion by a host, Yersinia pseudotuberculosis 1 Y. enterocolitica, 2 3 1 1 4 Yersinia 5 6 7 8 Invasin-mediated uptake by cultured cells involves internalizatio... |
10.1186/ar1776 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Differential expression of chemokine receptors on peripheral blood B cells from patients with rheumatoid arthritis and systemic lupus erythematosus",
"authors": "Henneken, Maren, 1, marenh@landspitali.is, Dörner, Thomas, 2, thomas.doerner@charite.de, Burmester, Gerd-Rüdiger, 2, gerd.burmester@charite.de... |
10.1186/1743-8977-2-8 | [] | http://creativecommons.org/licenses/by/2.0 | {"title":"Principles for characterizing the potential human health effects from exposure to nanomate(...TRUNCATED) |
End of preview.
Scientific Openly-Licensed Publications
This repository contains companion material for the following publication:
Tim Tarsi, Heike Adel, Jan Hendrik Metzen, Dan Zhang, Matteo Finco, Annemarie Friedrich. SciOL and MuLMS-Img: Introducing A Large-Scale Multimodal Scientific Dataset and Models for Image-Text Tasks in the Scientific Domain. WACV 2024.
Please cite this paper if using the dataset, and direct any questions regarding the dataset to Tim Tarsi
Summary
Scientific Openly-Licensed Publications (SciOL) is the largest openly-licensed pre-training corpus for multimodal models in the scientific domain, covering multiple sciences including materials science, physics, and computer science. It consists of over 2.7M scientific scientific publications converted into semi-structured data. SciOL contains over 14 Billion tokens of extracted and structured text.
Note: This repository only contains the textual data of SciOL. For the figures and captions see:
SciOL-CI
Data Format
We provide the annotations of our dataset in the JSON format. Files are grouped and compressed as zip files. We provide a basic index to find annotations by DOI, PMID or DOAJ id and keywords.
Annotation Schema
Annotations are structured as in the following schema:
{
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"doi": {
"type": "string"
},
"keywords": {
"type": "array",
"items": {
"type": "string"
}
},
"license": {
"type": "string"
},
"article": {
"type": "object",
"properties": {
"title": {
"type": "string"
},
"authors": {
"type": "array",
"items": {
"type": "string"
}
},
"abstract": {
"type": "string"
},
"body_text": {
"type": "string"
},
"bibliography": {
"type": "string"
}
}
}
}
}
Citation
If you use our dataset in your scientific, please cite our paper:
@InProceedings{Tarsi_2024_WACV,
author = {Tarsi, Tim and Adel, Heike and Metzen, Jan Hendrik and Zhang, Dan and Finco, Matteo and Friedrich, Annemarie},
title = {SciOL and MuLMS-Img: Introducing a Large-Scale Multimodal Scientific Dataset and Models for Image-Text Tasks in the Scientific Domain},
booktitle = {Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV)},
month = {January},
year = {2024},
pages = {4560-4571}
}
License
The SciOL corpus is released under the CC BY 4.0 license.
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