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Can we replace curation with information extraction software?

Peter D Karp1

  • 1Bioinformatics Research Group, SRI, International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA. Tel:650-859-4358; Fax: 650-859-3735;

Database : the Journal of Biological Databases and Curation
|December 28, 2016
PubMed
Summary
This summary is machine-generated.

Automated information extraction (IE) programs have high error rates and limited scope, failing to replace professional curation for scientific databases. Semi-automated tools show promise but require cost-benefit analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Literature Analysis

Background:

  • Professional curation is vital for creating comprehensive scientific databases like EcoCyc.
  • Automated and semi-automated information extraction (IE) tools are being developed to aid this process.
  • The feasibility of replacing professional curators with IE programs is under investigation.

Purpose of the Study:

  • To evaluate the current capabilities of automated and semi-automated information extraction (IE) programs.
  • To determine if IE programs can serve as practical alternatives to professional curation.
  • To assess the potential of IE tools in enhancing curator productivity and reducing costs.

Main Methods:

  • Review of current information extraction (IE) programs and their error rates.
  • Comparison of the scope and depth of information extracted by IE programs versus professional curators.
  • Analysis of the ability of IE programs to handle conflicting information in scientific literature.
  • Evaluation of semi-automated tools designed to improve curator efficiency.

Main Results:

  • Current IE programs exhibit error rates too high for professional curation replacement.
  • IE programs extract narrow data slivers (e.g., protein interactions), lacking the breadth of professional curation.
  • IE programs cannot arbitrate conflicting scientific statements, a key curator function.
  • Semi-automated tools show potential for enhancing curator productivity, but cost-benefit analyses are absent.

Conclusions:

  • Automated IE programs are not yet viable replacements for professional curation due to high error rates and limited scope.
  • Funding agencies should continue supporting professional curation efforts.
  • Semi-automated IE tools warrant further investigation, including rigorous cost-benefit analyses, to assess their true impact on curation costs and efficiency.