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PubExN: An Automated PubMed Bulk Article Extractor with Affiliation Normalization Package.

Ashutosh Kumar1, Aakanksha Sharaff1

  • 1Department of Computer Science and Engineering, National Institute of Technology Raipur, G. E. Road, Raipur, 492001 Chhattisgarh India.

SN Computer Science
|May 2, 2023
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Summary

PubExN is a Python package that automates bulk biomedical article extraction from PubMed, saving time and effort in data mining. This tool aids in named entity recognition, relation extraction, and knowledgebase creation for biomedical research.

Keywords:
Affiliation normalizationArticles extractionBiomedical text miningBulk extractionNCBI PubMedPython package

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Area of Science:

  • Biomedical Informatics
  • Natural Language Processing
  • Data Science

Background:

  • Biomedical article extraction is crucial for applications like gene and drug discovery.
  • Manual extraction is time-consuming and prone to errors, missing vital information.
  • Existing methods lack efficient bulk processing capabilities for biomedical literature.

Purpose of the Study:

  • To introduce PubExN, a Python package for automated bulk extraction of biomedical articles from PubMed.
  • To provide a flexible and efficient solution for retrieving citation information and abstracts.
  • To support various biomedical text mining and NLP tasks.

Main Methods:

  • Developed a Python package, PubExN, for automated data extraction.
  • Implemented a batch processing approach for efficient bulk extraction.
  • Focused on retrieving comprehensive citation details and abstracts from the PubMed database.

Main Results:

  • PubExN automates the extraction of citation information and abstracts from PubMed.
  • The package facilitates bulk data retrieval using a batch approach.
  • Successfully demonstrated the utility for biomedical named entity recognition and relation extraction.

Conclusions:

  • PubExN significantly reduces time and effort in biomedical data extraction.
  • The package enhances efficiency for tasks like literature discovery and knowledgebase creation.
  • PubExN is a valuable tool for biomedical NLP research and drug discovery initiatives.