Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

Journal: Bioinformatics (Oxford, England)
Published Date: Mar 4, 2024

Abstract

MOTIVATION: Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas.

Authors

  • J Harry Caufield
    Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
  • Harshad Hegde
  • Vincent Emonet
    Laboratory of Informatics, Robotics and Microelectronics of Montpellier (LIRMM), University of Montpellier & CNRS, Montpellier 34090, France.
  • Nomi L Harris
    Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Marcin P Joachimiak
    Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Nicolas Matentzoglu
    School of Computer Science, University of Manchester, Oxford Road, Manchester, UK. nicolas.matentzoglu@manchester.ac.uk.
  • HyeongSik Kim
    Robert Bosch LLC, Sunnyvale, CA 94085, USA.
  • Sierra Moxon
    Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
  • Justin T Reese
    Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
  • Melissa A Haendel
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Peter N Robinson
    The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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