Dataset Card for Sci Lay

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:

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 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]