--- dataset_info: - config_name: A features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 128936951 num_examples: 3909 - name: validation num_bytes: 15912431 num_examples: 489 - name: test num_bytes: 16235251 num_examples: 489 download_size: 83830061 dataset_size: 161084633 - config_name: B features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 57956055 num_examples: 1617 - name: validation num_bytes: 6860452 num_examples: 202 - name: test num_bytes: 7422716 num_examples: 203 download_size: 37654668 dataset_size: 72239223 - config_name: C features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 242721690 num_examples: 6782 - name: validation num_bytes: 30735056 num_examples: 848 - name: test num_bytes: 31018214 num_examples: 848 download_size: 158704561 dataset_size: 304474960 - config_name: CB features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 43533134 num_examples: 867 - name: validation num_bytes: 5664682 num_examples: 108 - name: test num_bytes: 5455500 num_examples: 109 download_size: 27189215 dataset_size: 54653316 - config_name: I features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 37682107 num_examples: 1181 - name: validation num_bytes: 4967810 num_examples: 148 - name: test num_bytes: 4945533 num_examples: 148 download_size: 24754627 dataset_size: 47595450 - config_name: MBIO features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 30528726 num_examples: 607 - name: validation num_bytes: 3905117 num_examples: 76 - name: test num_bytes: 3830514 num_examples: 76 download_size: 18844836 dataset_size: 38264357 - config_name: NC features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 286453072 num_examples: 5549 - name: validation num_bytes: 35652636 num_examples: 694 - name: test num_bytes: 35869803 num_examples: 694 download_size: 174664205 dataset_size: 357975511 - config_name: OTHER features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 89884204 num_examples: 2008 - name: validation num_bytes: 11198113 num_examples: 251 - name: test num_bytes: 11665218 num_examples: 251 download_size: 56488155 dataset_size: 112747535 - config_name: PLB features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 54106804 num_examples: 896 - name: validation num_bytes: 6575630 num_examples: 112 - name: test num_bytes: 6563666 num_examples: 113 download_size: 33228217 dataset_size: 67246100 - config_name: PLCB features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 149165851 num_examples: 2589 - name: validation num_bytes: 18844485 num_examples: 324 - name: test num_bytes: 18926571 num_examples: 324 download_size: 90880208 dataset_size: 186936907 - config_name: PLGEN features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 176933946 num_examples: 3087 - name: validation num_bytes: 21857559 num_examples: 386 - name: test num_bytes: 21226953 num_examples: 386 download_size: 108531011 dataset_size: 220018458 - config_name: PLNTD features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 90159685 num_examples: 2289 - name: validation num_bytes: 11227802 num_examples: 286 - name: test num_bytes: 11587156 num_examples: 287 download_size: 57806998 dataset_size: 112974643 - config_name: PLPAT features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 167781149 num_examples: 2920 - name: validation num_bytes: 20760947 num_examples: 365 - name: test num_bytes: 21113922 num_examples: 365 download_size: 102858284 dataset_size: 209656018 - config_name: SD features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 23671697 num_examples: 725 - name: validation num_bytes: 3033467 num_examples: 91 - name: test num_bytes: 2972947 num_examples: 91 download_size: 15082066 dataset_size: 29678111 - config_name: all features: - name: doi dtype: string - name: pmcid 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 sequence: string splits: - name: train num_bytes: 1579515071 num_examples: 35026 - name: validation num_bytes: 197196187 num_examples: 4380 - name: test num_bytes: 198833964 num_examples: 4384 download_size: 990169794 dataset_size: 1975545222 configs: - config_name: A data_files: - split: train path: A/train-* - split: validation path: A/validation-* - split: test path: A/test-* - config_name: B data_files: - split: train path: B/train-* - split: validation path: B/validation-* - split: test path: B/test-* - config_name: C data_files: - split: train path: C/train-* - split: validation path: C/validation-* - split: test path: C/test-* - config_name: CB data_files: - split: train path: CB/train-* - split: validation path: CB/validation-* - split: test path: CB/test-* - config_name: I data_files: - split: train path: I/train-* - split: validation path: I/validation-* - split: test path: I/test-* - config_name: MBIO data_files: - split: train path: MBIO/train-* - split: validation path: MBIO/validation-* - split: test path: MBIO/test-* - config_name: NC data_files: - split: train path: NC/train-* - split: validation path: NC/validation-* - split: test path: NC/test-* - config_name: OTHER data_files: - split: train path: OTHER/train-* - split: validation path: OTHER/validation-* - split: test path: OTHER/test-* - config_name: PLB data_files: - split: train path: PLB/train-* - split: validation path: PLB/validation-* - split: test path: PLB/test-* - config_name: PLCB data_files: - split: train path: PLCB/train-* - split: validation path: PLCB/validation-* - split: test path: PLCB/test-* - config_name: PLGEN data_files: - split: train path: PLGEN/train-* - split: validation path: PLGEN/validation-* - split: test path: PLGEN/test-* - config_name: PLNTD data_files: - split: train path: PLNTD/train-* - split: validation path: PLNTD/validation-* - split: test path: PLNTD/test-* - config_name: PLPAT data_files: - split: train path: PLPAT/train-* - split: validation path: PLPAT/validation-* - split: test path: PLPAT/test-* - config_name: SD data_files: - split: train path: SD/train-* - split: validation path: SD/validation-* - split: test path: SD/test-* - config_name: all data_files: - split: train path: all/train-* - split: validation path: all/validation-* - split: test path: all/test-* --- # Dataset Card for SciLay ## Table of Contents - [Dataset Description](#dataset-description) - [Dataset Summary](#dataset-summary) - [Languages](#languages) - [Dataset Structure](#dataset-structure) - [Data Instances](#data-instances) - [Data Fields](#data-fields) - [Data Splits](#data-splits) ## Dataset Description - **Homepage:** [Sci Lay](https://github.com/disi-unibo-nlp/sci-lay) - **Point of Contact:** [Paolo Italiani](mailto:paolo.italiani@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 15 journal sources: - 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("disi-unibo-nlp/SciLay") # default is 'all' journals ds = load_dataset("disi-unibo-nlp/SciLay", "all") # the same as above ds = load_dataset("disi-unibo-nlp/SciLay", "NC") # only 'NC' journal (Nature Communications) ds = load_dataset("disi-unibo-nlp/SciLay", journals=["NC", "A"]) ``` ### 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 |