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Related Experiment Video

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A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

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Published on: September 20, 2018

OpCitance: Citation contexts identified from the PubMed Central open access articles.

Tzu-Kun Hsiao¹, Vetle I Torvik²

¹School of Information Sciences, University of Illinois at Urbana-Champaign, 501 E. Daniel Street, Champaign, IL, 61820, USA. tkhsiao2@illinois.edu.

Scientific Data

|April 28, 2023

Summary

OpCitance annotates 137 million inline citations from open-access articles, improving citation context studies. This dataset offers a high identification rate and accurate PubMed ID mapping for text-mining research.

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Area of Science:

Bibliometrics
Computational Biology
Bioinformatics

Background:

Extracting citation contexts from scientific literature is challenging due to diverse referencing styles.
Previous methods had limitations in accurately linking inline citations to references.

Purpose of the Study:

To present OpCitance, a comprehensive dataset of annotated citation contexts from PubMed Central open-access articles.
To improve the accuracy of citation mapping and facilitate citation context analysis.

Main Methods:

Parsed 2 million PubMed Central open-access (PMCOA) articles to identify 137 million inline citations and their contexts.
Developed and utilized an in-house citation matcher, Patci, to correct and supplement PubMed IDs (PMIDs).
Compared citation data with NCBI E-Utilities and addressed discrepancies.

Main Results:

Achieved a high inline citation identification rate, with only 0.5% of contexts remaining unidentified.
Corrected and supplemented 6.84% of referenced PMIDs using the Patci matcher.
OpCitance demonstrates superior accuracy in reference mapping to PMIDs compared to other corpora.

Conclusions:

OpCitance provides a valuable resource for citation context studies and text-mining research.
The dataset's high accuracy and coverage enhance the utility of open-access scientific literature for computational analysis.