task_categories:summarization size_categories:100K<n<1M language:en chemistry biology medical arxiv:2305.07615 region:us
---
task_categories:
- summarization
language:
- en
tags:
- chemistry
- biology
- medical
pretty_name: Generating Abstracts of Academic Chemistry Papers
size_categories:
- 100K<n<1M
---
# Dataset Card for ChemSum

## ChemSum Description

<!---- **Homepage:** 
- **Leaderboard:** 
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- **Paper:** [What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization ](https://arxiv.org/abs/2305.07615)
- **Journal:** ACL 2023
- **Point of Contact:** griffin.adams@columbia.edu
- **Repository:** https://github.com/griff4692/calibrating-summaries

### ChemSum Summary

We introduce a dataset with a pure chemistry focus by compiling a list of chemistry academic journals with Open-Access articles. For each journal, we downloaded full-text article PDFs from the Open-Access portion of the journal using available APIs, or scraping this content using [Selenium Chrome WebDriver](https://www.selenium.dev/documentation/webdriver/). 
Each PDF was processed with Grobid via a locally installed [client](https://pypi.org/project/grobid-client-python/) to extract free-text paragraphs with sections. 

The table below shows the journals from which Open Access articles were sourced, as well as the number of papers processed.

For all journals, we filtered for papers with the provided topic of Chemistry when papers from other disciplines were also available (e.g. PubMed).


| Source      | # of Articles |
| ----------- | ----------- |
| Beilstein      | 1,829    |
| Chem Cell   | 546        |
| ChemRxiv   | 12,231        |
| Chemistry Open   | 398        |
| Nature Communications Chemistry   | 572        |
| PubMed Author Manuscript   | 57,680        |
| PubMed Open Access  | 29,540        |
| Royal Society of Chemistry (RSC)   | 9,334        |
| Scientific Reports - Nature  |    6,826     |

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### Supported Tasks and Leaderboards

[More Information Needed]
--->

### Languages

English

## Dataset Structure

<!--- ### Data Instances --->

### Data Fields


| Column      | Description |
| ----------- | ----------- |
| `uuid`      | Unique Identifier for the Example  |
| `title`      | Title of the Article   |
| `article_source`      | Open Source Journal (see above for list)   |
| `abstract`      | Abstract (summary reference)   |
| `sections`      | Full-text sections from the main body of paper (<!> indicates section boundaries)|
| `headers`      | Corresponding section headers for `sections` field (<!> delimited)  |
| `source_toks`      | Aggregate number of tokens across `sections` |
| `target_toks`      | Number of tokens in the `abstract` |
| `compression`      | Ratio of `source_toks` to `target_toks` |

Please refer to `load_chemistry()` in https://github.com/griff4692/calibrating-summaries/blob/master/preprocess/preprocess.py for pre-processing as a summarization dataset. The inputs are `sections` and `headers` and the targets is the `abstract`.


### Data Splits

| Split      | Count |
| ----------- | ----------- |
| `train`      | 115,956 |
| `validation`      | 1,000   |
| `test`      | 2,000   |


### Citation Information

```
@article{adams2023desired,
  title={What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization},
  author={Adams, Griffin and Nguyen, Bichlien H and Smith, Jake and Xia, Yingce and Xie, Shufang and Ostropolets, Anna and Deb, Budhaditya and Chen, Yuan-Jyue and Naumann, Tristan and Elhadad, No{\'e}mie},
  journal={arXiv preprint arXiv:2305.07615},
  year={2023}
}
```

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## Dataset Creation

### Curation Rationale

[More Information Needed]

### Source Data

#### Initial Data Collection and Normalization

[More Information Needed]

#### Who are the source language producers?

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### Annotations

#### Annotation process

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#### Who are the annotators?

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### Personal and Sensitive Information

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## Considerations for Using the Data

### Social Impact of Dataset

[More Information Needed]

### Discussion of Biases

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### Other Known Limitations

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## Additional Information

### Dataset Curators

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### Licensing Information

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### Contributions

[More Information Needed]
--->
