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Using the PubMed Abstract Sifter for �Computational Modeling of Complex Biological Processes�

NANCY C. BAKER PHD

LEIDOS, CONTRACTOR TO THE USEPA

PRESENTATION TO IMAG – MSM WORKING GROUP

AUGUST 11, 2022

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Does not necessarily represent US EPA policy.

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Acknowledgments

  • Tom Knudsen and the Virtual Tissues Modeling project
  • CCTE management and scientists

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The problem – lots of publications

Aerosol transport modeling:

2K PubMed citations

Chondrogenesis:

9K PubMed citations

Epiblast:

33K PubMed citations

Chagas disease:

20K PubMed citations

Where to start?

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Recent example: Computational systems model for retinoic signaling during neurulation

Literature review

    • Physiological information
    • Cellular compartments
    • Biochemical gradients
    • Critical cell fate and behavior
    • Reduced to the essence

Systems biology map

    • Useful for AOP elucidation
    • Starting point for in silico simulation

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Job Berkhout, RIVM (work in progress, compucell3d.org prototype)

Heusinkveld et al. (2021) Reprod Toxicol

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Today – information retrieval to support rapid model construction

  1. Show how with the Abstract Sifter you can take a biological corpus and explore the gene and protein players. (In an unbiased way)
  2. Show how you can take a complex list of gene or protein players and find their relationships to each other, both in your biological context and outside it.
  3. Show how you can take a set of genes or proteins of interest to your group and measure their occurrence in your biological corpus.
  4. Show how you can find chemicals that perturb players in your network and investigate their downstream adverse effects.

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But first …

  • The PubMed Abstract Sifter is a free tool downloadable from the Comptox Chemicals Dashboard (CCD):
  • https://comptox.epa.gov/dashboard/downloads

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