Visualizing Interaction Networks and Evidence in Biomedical Corpora

Enrique Noriega-Atala, Md Rahat-Uz-Zaman, Ruchika Bhat, Mladen Jergovic, Stephen G Kobourov, Janko Nikolich-Zugich

Research output: Chapter in Book/Report/Conference proceedingConference contribution


The abundance of scientific articles published and indexed in publicly accessible repositories has spurred the research and development of automated information extraction systems. The output of such systems can be used to assemble large networks capturing the understanding of mechanistic pathways and their interactions as represented in the underlying body of research.We describe a system designed to help researchers search, visualize and interact with biological networks derived via information extraction tools. As input, the system takes a dataset of biological and biochemical interactions automatically generated by an information extraction system and provides an interface designed to search, visualize and interact with the data. The usage paradigm consists of identifying a starting point for a search, then using the data's network structure by incrementally exploring the immediate neighborhood of the elements displayed by the system.Our system differs from prior work as it leverages both the network structure in the data and the natural language text backing those connections: every connection displayed is traceable back to the documents and phrases in the corpus that support that specific piece of information. We also present two case studies with immunobiology researchers using the system to find previously unknown relationships between biological entities. While the evidence suggesting these relationships already existed, it was scattered across the literature, and existing specialized web databases and domain-search engines could not find it. The system is open-source, with the code publicly available on GitHub.

Original languageEnglish (US)
Title of host publicationProceedings - 2023 IEEE 16th Pacific Visualization Symposium, PacificVis 2023
PublisherIEEE Computer Society
Number of pages10
ISBN (Electronic)9798350321241
StatePublished - 2023
Event16th IEEE Pacific Visualization Symposium, PacificVis 2023 - Seoul, Korea, Republic of
Duration: Apr 18 2023Apr 21 2023

Publication series

NameIEEE Pacific Visualization Symposium
ISSN (Print)2165-8765
ISSN (Electronic)2165-8773


Conference16th IEEE Pacific Visualization Symposium, PacificVis 2023
Country/TerritoryKorea, Republic of


  • Computing methodologies-Visualization-Information extraction
  • Information systems-Search interfaces

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Computer Vision and Pattern Recognition
  • Hardware and Architecture
  • Software


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