Datasets:
Tasks:
Text Classification
Languages:
English
Multilinguality:
monolingual
Size Categories:
100K<n<1M
Source Datasets:
original
ArXiv:
DOI:
License:
| pretty_name: CogText PubMed Abstracts | |
| license: | |
| - cc-by-4.0 | |
| language: | |
| - en | |
| multilinguality: | |
| - monolingual | |
| task_categories: | |
| - text-classification | |
| task_ids: | |
| - topic-classification | |
| - semantic-similarity-classification | |
| size_categories: | |
| - 100K<n<1M | |
| paperswithcode_id: linking-theories-and-methods-in-cognitive | |
| inference: false | |
| model-index: | |
| - name: cogtext-pubmed | |
| results: [] | |
| source_datasets: | |
| - original | |
| language_creators: | |
| - found | |
| - expert-generated | |
| configs: | |
| - config_name: abstracts (2023) | |
| data_files: "pubmed/abstracts2023.csv.gz" | |
| - config_name: abstracts (2021) | |
| data_files: "pubmed/abstracts2021.csv.gz" | |
| tags: | |
| - Cognitive Control | |
| - PubMed | |
| # Dataset Card for CogText PubMed Abstracts | |
| ## Table of Contents | |
| - [Dataset Description](#dataset-description) | |
| - [Dataset Summary](#dataset-summary) | |
| - [Supported Tasks](#supported-tasks-and-leaderboards) | |
| - [Languages](#languages) | |
| - [Dataset Structure](#dataset-structure) | |
| - [Data Instances](#data-instances) | |
| - [Data Fields](#data-instances) | |
| - [Data Splits](#data-instances) | |
| - [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) | |
| ## Dataset Description | |
| The **CogText** dataset is a curated collection of abstracts about cognitive tasks and constructs from PubMed. | |
| This dataset contains the original abstracts and their corresponding embeddings. | |
| Please visit [CogText on GitHub](https://github.com/morteza/cogtext) for the details and codes. | |
| - **Homepage:** https://github.com/morteza/cogtext | |
| - **Repository:** https://github.com/morteza/cogtext | |
| - **Point of Contact:** [Morteza Ansarinia](mailto:ansarinia@me.com) | |
| - **Paper:** https://arxiv.org/abs/2203.11016 | |
| ### Dataset Summary | |
| The 2021 dataset, collected in December 2021, contains 385,705 distinct scientific articles, featuring their title, abstract, relevant metadata, and embeddings. | |
| The articles were specifically selected for their relevance to cognitive control constructs and associated tasks. | |
| ### Supported Tasks and Leaderboards | |
| Topic Modeling, Text Embedding | |
| ### Languages | |
| English | |
| ## Dataset Structure | |
| ### Data Instances | |
| 522,972 scientific articles, of which 385,705 are unique. | |
| ### Data Fields | |
| The CSV files contain the following fields: | |
| | Field | Description | | |
| | ----- | ----------- | | |
| | `index` | (int) Index of the article in the current dataset | | |
| | `pmid` | (int) PubMed ID | | |
| | `doi` | (str) Digital Object Identifier | | |
| | `year` | (int) Year of publication (yyyy format)| | |
| | `journal_title` | (str) Title of the journal | | |
| | `journal_iso_abbreviation` | (str) ISO abbreviation of the journal | | |
| | `title` | (str) Title of the article | | |
| | `abstract` | (str) Abstract of the article | | |
| | `category` | (enum) Category of the article, either "CognitiveTask" or "CognitiveConstruct" | | |
| | `label` | (enum) Label of the article, which refers to the class labels in the `ontologies/efo.owl` ontology | | |
| | `original_index` | (int) Index of the article in the full dataset (see `pubmed/abstracts.csv.gz`) | | |
| ### Data Splits | |
| | Dataset | Description | | |
| | ------- | ----------- | | |
| | `pubmed/abstracts.csv.gz` | Full dataset | | |
| | `pubmed/abstracts20pct.csv.gz` | 20% of the dataset (stratified random sample by `label`) | | |
| | `gpt3/abstracts_gp3ada.nc` | GPT-3 embeddings of the entire dataset in XArray/CDF4 format, indexed by `pmid` | | |
| ## Dataset Creation | |
| ### Curation Rationale | |
| [Needs More Information] | |
| ### Source Data | |
| #### Initial Data Collection and Normalization | |
| [Needs More Information] | |
| ### Annotations | |
| #### Annotation process | |
| [Needs More Information] | |
| ### Personal and Sensitive Information | |
| [Needs More Information] | |
| ## Considerations for Using the Data | |
| ### Social Impact of Dataset | |
| [Needs More Information] | |
| ### Discussion of Biases | |
| [Needs More Information] | |
| ### Other Known Limitations | |
| [Needs More Information] | |
| ## Additional Information | |
| ### Dataset Curators | |
| [Needs More Information] | |
| ### Licensing Information | |
| [Needs More Information] | |
| ### Acknowledgments | |
| This research was supported by the Luxembourg National Research Fund (ATTRACT/2016/ID/11242114/DIGILEARN and INTER Mobility/2017-2/ID/11765868/ULALA). | |
| ### Citation Information | |
| To cite the paper use the following entry: | |
| ``` | |
| @misc{cogtext2022, | |
| author = {Morteza Ansarinia and | |
| Paul Schrater and | |
| Pedro Cardoso-Leite}, | |
| title = {Linking Theories and Methods in Cognitive Sciences via Joint Embedding of the Scientific Literature: The Example of Cognitive Control}, | |
| year = {2022}, | |
| url = {https://arxiv.org/abs/2203.11016} | |
| } | |
| ``` |