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Citizen Science for Mining the Biomedical Literature.

Ginger Tsueng1, Steven M Nanis1, Jennifer Fouquier1

  • 1Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Citizen Science : Theory and Practice
|November 13, 2018
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Summary

Citizen scientists accurately perform named entity recognition (NER) on biomedical literature via Mark2Cure. This approach scales information extraction beyond paid microtask platforms for biomedical knowledge discovery.

Keywords:
biocurationbiomedical literaturecitizen scienceinformation extractionmicrotasknatural language processing

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Area of Science:

  • Biomedical Informatics
  • Computational Biology
  • Natural Language Processing

Background:

  • Biomedical literature is vast and unstructured, making information extraction challenging.
  • Manual curation and computational methods are traditional approaches to information extraction.
  • Previous work showed paid microtask platforms can crowdsource named entity recognition (NER).

Purpose of the Study:

  • To demonstrate that volunteer citizen scientists can perform NER tasks with high accuracy.
  • To explore the scalability of citizen science for biomedical information extraction.
  • To provide a framework for transitioning crowdsourcing workflows to citizen science platforms.

Main Methods:

  • Developed and utilized the web-based application Mark2Cure.
  • Recruited and engaged volunteer citizen scientists for NER tasks.
  • Applied Zooniverse Matrices of Citizen Science Success metrics for evaluation.

Main Results:

  • Citizen scientists achieved high accuracy in performing NER tasks.
  • The Mark2Cure platform demonstrated the feasibility of citizen science for NLP.
  • The study provides a basis for comparison for future citizen science projects.

Conclusions:

  • Citizen science is a viable and accurate method for biomedical named entity recognition.
  • Citizen science offers a scalable solution for extracting knowledge from large biomedical corpora.
  • The Mark2Cure project successfully transitioned a crowdsourcing workflow to citizen science.