README.md

---
license: cc-by-4.0
task_categories:
- summarization
tags:
- medical
pretty_name: Sci Lay - Biomedic Articles Lay Summarization Dataset
size_categories:
- 10K<n<100K
- 1K<n<10K
source_datasets:
- original
dataset_info:
- config_name: all
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
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  - name: topics
    sequence: string
  - name: keywords
    sequence: string
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  - name: validation
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  - name: test
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- config_name: NC
  features:
  - name: doi
    dtype: string
  - name: pmcid
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  - name: title
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  - name: plain_text
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  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
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  - name: topics
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  - name: keywords
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  - name: validation
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  - name: test
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- config_name: A
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
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  - name: keywords
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  - name: validation
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  - name: test
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- config_name: PLGEN
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
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  - name: topics
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  - name: keywords
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  - name: validation
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  - name: test
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- config_name: PLPAT
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
    sequence: string
  - name: keywords
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  - name: train
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  - name: validation
    num_examples: 365
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  - name: test
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- config_name: PLCB
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
    sequence: string
  - name: keywords
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  splits:
  - name: train
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  - name: validation
    num_examples: 324
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  - name: test
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- config_name: PLNTD
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
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  - name: keywords
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  splits:
  - name: train
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  - name: validation
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  - name: test
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- config_name: B
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
    sequence: string
  - name: keywords
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  splits:
  - name: train
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  - name: validation
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  - name: test
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- config_name: I
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
    sequence: string
  - name: keywords
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  splits:
  - name: train
    num_examples: 1181
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  - name: validation
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  - name: test
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- config_name: PLB
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
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  - name: plain_text
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    dtype: string
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    dtype: string
  - name: journal
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  - name: topics
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  splits:
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  - name: validation
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- config_name: CB
  features:
  - name: doi
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  - name: pmcid
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  - name: title
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  - name: plain_text
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  - name: technical_text
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  - name: journal
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  - name: topics
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  splits:
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  - name: validation
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  - name: test
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- config_name: SD
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
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  - name: topics
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  - name: keywords
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  splits:
  - name: train
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  - name: validation
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  - name: test
    num_examples: 91
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- config_name: MBIO
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
    sequence: string
  - name: keywords
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  splits:
  - name: train
    num_examples: 607
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  - name: validation
    num_examples: 76
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  - name: test
    num_examples: 76
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- config_name: C
  features:
  - name: doi
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  - name: pmcid
    dtype: string
  - name: title
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  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
    dtype: string
  - name: topics
    sequence: string
  - name: keywords
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  splits:
  - name: train
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  - name: validation
    num_examples: 848
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  - name: test
    num_examples: 848
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- config_name: OTHER
  features:
  - name: doi
    dtype: string
  - name: pmcid
    dtype: string
  - name: title
    dtype: string
  - name: plain_text
    dtype: string
  - name: technical_text
    dtype: string
  - name: full_text
    dtype: string
  - name: journal
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  - name: topics
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  - name: keywords
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  splits:
  - name: train
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  - name: validation
    num_examples: 251
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  - name: test
    num_examples: 251
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config_names:
- all
- NC
- A
- PLGEN
- PLPAT
- PLCB
- PLNTD
- B
- I
- PLB
- CB
- SD
- MBIO
- C
- OTHER
---

# Dataset Card for Sci Lay

## Table of Contents
- [Dataset Description](#dataset-description)
  - [Dataset Summary](#dataset-summary)
  - [Supported Tasks and Leaderboards](#supported-tasks-and-leaderboards)
  - [Languages](#languages)
- [Dataset Structure](#dataset-structure)
  - [Data Instances](#data-instances)
  - [Data Fields](#data-fields)
  - [Data Splits](#data-splits)
- [Dataset Creation](#dataset-creation)
  - [Curation Rationale](#curation-rationale)
  - [Source Data](#source-data)
  - [Annotations](#annotations)
  - [Personal and Sensitive Information](#personal-and-sensitive-information)
- [Considerations for Using the Data](#considerations-for-using-the-data)
  - [Social Impact of Dataset](#social-impact-of-dataset)
  - [Discussion of Biases](#discussion-of-biases)
  - [Other Known Limitations](#other-known-limitations)
- [Additional Information](#additional-information)
  - [Dataset Curators](#dataset-curators)
  - [Licensing Information](#licensing-information)
  - [Citation Information](#citation-information)
  - [Contributions](#contributions)

## Dataset Description

- **Homepage:** [Sci Lay](https://github.com/paniniDot/summarization-model)
- **Repository:**
- **Paper:** 
- **Leaderboard:**
- **Point of Contact:** [Mattia Panni](mailto:mattia.panni@studio.unibo.it)

### Dataset Summary

SCILAY comprises 43,790 instances, each representing a scientific article in the biomedical domain. 
Each instance in the dataset includes the following components:
    - plain_text: Containing a plain language summary of the scientific article. This section is written in a simple and accessible language, and is intended to be understandable by a wide audience.
    - technical_text: This section contains the abstract of the scientific article. It provides a detailed and technical description of the research conducted in the article.
    - full_text: This section contains the complete article of the scientific research.
In addition to the textual content, each instance is associated with the following metadata:
    - Keywords: Keywords that capture the main topics and themes addressed in the article.
    - Journal: The journal in which the article is published, providing context about the source of the research.
    - DOI (Digital Object Identifier): A unique identifier for the article, facilitating easy referencing.
The main objective of the SCILAY dataset is to support the development and evaluation of text summarization models that can effectively simplify complex scientific language while retaining the essential information. 
Each article is published by a scientific journal. There are fifteen such journal classifications:
  - NC: Nature Communications
  - A: Animals : an Open Access Journal from MDPI
  - PLGEN: PLoS Genetics
  - PLPAT: PLoS Pathogens
  - PLCB: PLoS Computational Biology
  - PLNTD: PLoS Neglected Tropical Diseases
  - B: Biology
  - I: Insects
  - PLB: PLoS Biology
  - CB: Communications Biology
  - SD: Scientific Data
  - MBIO: mBio
  - C: Cancers
  - OTHER: which includes additional journals that taken individually would not have contributed sufficient instances

Current defaults are 1.0.0 version (cased raw strings) and 'all' journals:
```python
from datasets import load_dataset

ds = load_dataset("paniniDot/sci_lay")  # default is 'all' journals
ds = load_dataset("paniniDot/sci_lay", "all")  # the same as above
ds = load_dataset("paniniDot/sci_lay", "NC")  # only 'NC' journal (Nature Communications)
ds = load_dataset("paniniDot/sci_lay", journals=["NC", "A"])
```


### Supported Tasks and Leaderboards

[More Information Needed]

### Languages

English

## Dataset Structure

### Data Instances

Each instance contains a set of `doi`, `pmcid`, `plain_text`, `technical_text`, `journal`, `topics`, `keywords`. Each of which was extracted by scraping articles in XML and HTML format.
```
{
  'doi': '10.3390/ani12040445',
  'pmcid': 'PMC8868321',
  'plain_text': 'PPP3CA is one of the candidate genes for goat reproduction, but no studies have been carried out yet. Therefore, the purpose of this study was to determine the associations between copy number variations in the goat PPP3CA gene and litter size and semen quality in goats, including Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima (GZHM) goats (n = 64). Based on the association analysis, the results showed that only CNV1 (copy number variation 1) and CNV2 (copy number variation 2) were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10−11; p = 5.0895 × 10−9), and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). These findings prove that the PPP3CA gene plays an important role in reproduction traits in goats.',
  'technical_text': 'Copy number variations (CNVs) have many forms of variation structure, and they play an important role in the research of variety diversity, biological evolution and disease correlation. Since CNVs have a greater impact on gene regulation and expression, more studies are being finalized on CNVs in important livestock and poultry species. The protein phosphatase 3 catalytic subunit alpha (PPP3CA) is a key candidate gene involved in the goat fecundity trait, and has important effects on precocious puberty, estrogen signal transduction pathways and oocyte meiosis. Additionally, PPP3CA also has a dephosphorylation effect in the process of spermatogonial stem cell meiosis and spermatogenesis. So far, there is no research on the relationship between the copy number variations of the PPP3CA gene and reproduction traits. Therefore, the purpose of this study was to determine the association between copy number variations in the goat PPP3CA gene and litter size and semen quality in Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima goats (n = 64). Based on the association analysis, the results showed that only CNV1 and CNV2 within the PPP3CA gene were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10−11; p = 5.0895 × 10−9, respectively) and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). In addition, individuals with Loss genotypes demonstrated better phenotypic performance compared to those with other types. Therefore, CNV1 and CNV2 of the PPP3CA gene are potentially useful for breeding, as they are linked to important goat reproduction traits.',
  'full_text': '...'
  'journal': 'Animals : an Open Access Journal from MDPI',
  'topics': [ 'Article' ],
  'keywords': [ 'goat', 'PPP3CA', 'copy number variation (CNV)', 'litter size', 'semen quality' ]
}
```

### Data Fields

- `doi`: (Digital Object Identifier). It is a unique alphanumeric string assigned to a digital document, such as a research paper, article, or dataset. Not all istances have it.
- `pmcid`: A unique identifier in the [PubMed Central library](https://www.ncbi.nlm.nih.gov/pmc/) database. Not all istances have it.
- `plain_text`: The summary of the article in plain english.
- `technical_text`: The abstract of the article.
- `full_text`: The complete article.
- `journal`: The journal which published the article.
- `topics`: An object containing the types in which the article is classified (i.e. Research Article, Review, ecc.). Not all istances have it.
- `keywords`: An object containing the keywords of the article. Not all istances have it.

### Data Splits

|       | train | validation | test |
|-------|-------|------------|------|
| all   | 35026 | 4380       | 4384 |
| NC    | 5549  | 694        | 694  |
| A     | 3909  | 489        | 489  |
| PLGEN | 3087  | 386        | 386  |
| PLPAT | 2920  | 365        | 365  |
| PLCB  | 2589  | 324        | 324  |
| PLNTD | 2289  | 286        | 287  |
| B     | 1617  | 202        | 203  |
| I     | 1181  | 148        | 148  |
| PLB   | 896   | 112        | 113  |
| CB    | 867   | 108        | 109  |
| SD    | 725   | 91         | 91   |
| MBIO  | 607   | 76         | 76   |
| C     | 6782  | 848        | 848  |
| OTHER | 2008  | 251        | 251  |

## Dataset Creation

### Curation Rationale

[More Information Needed]

### Source Data

#### Initial Data Collection and Normalization

[More Information Needed]

#### Who are the source language producers?

[More Information Needed]

### Annotations

#### Annotation process

[More Information Needed]

#### Who are the annotators?

[More Information Needed]

### Personal and Sensitive Information

[More Information Needed]

## Considerations for Using the Data

### Social Impact of Dataset

[More Information Needed]

### Discussion of Biases

[More Information Needed]

### Other Known Limitations

[More Information Needed]

## Additional Information

### Dataset Curators

[More Information Needed]

### Licensing Information

[More Information Needed]

### Citation Information

[More Information Needed]