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A machine reading system for assembling synthetic paleontological databases.

Shanan E Peters1, Ce Zhang2, Miron Livny2

  • 1Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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|December 2, 2014
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Summary
This summary is machine-generated.

A new machine reading system, PaleoDeepDive, automates paleontological data extraction from publications. This system creates a probabilistic database that improves over time, enabling new macroevolutionary research.

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Area of Science:

  • Paleontology
  • Computational Biology
  • Macroevolutionary Theory

Background:

  • Macroevolutionary theory and understanding biotic responses to global environmental change rely on paleontological data.
  • Current literature-based databases are often incomplete and challenging to update with new data types.

Purpose of the Study:

  • To develop and validate a machine reading system, PaleoDeepDive, for automated data extraction from scientific publications.
  • To assess PaleoDeepDive's performance in data extraction and inference tasks compared to human capabilities.

Main Methods:

  • Development of a machine reading system (PaleoDeepDive) to automatically extract data from text, tables, and figures.
  • Validation of the system's quality and performance on complex data extraction and inference tasks.
  • Integration of sophisticated data types, including morphological data from illustrations and text.

Main Results:

  • PaleoDeepDive performs comparably to humans in data extraction and inference.
  • The system generates synthetic results on taxonomic diversity, origination, and extinction rates.
  • PaleoDeepDive creates a probabilistic database that enhances systematically with new information.

Conclusions:

  • Machine reading offers a powerful approach for scientific data integration and synthesis in paleontology.
  • PaleoDeepDive facilitates the investigation of previously intractable macroevolutionary questions.
  • This approach may foster novel research directions in macroevolution and environmental change studies.