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Analyzing user interactions with biomedical ontologies: A visual perspective.

Maulik R Kamdar1, Simon Walk1, Tania Tudorache1

  • 1Stanford Center for Biomedical Informatics Research, Stanford University, USA.

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|April 17, 2018
PubMed
Summary
This summary is machine-generated.

Understanding how biomedical researchers use large biomedical ontologies is key. User exploration, querying, and reuse behaviors rarely align, indicating diverse usage patterns within the BioPortal repository.

Keywords:
data visualizationknowledge explorationlog analysisontology explorationontology reuseuser behavior

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Area of Science:

  • Biomedical Informatics
  • Knowledge Representation
  • Data Science

Background:

  • Biomedical ontologies are essential but large, posing development and maintenance challenges.
  • Understanding user interaction with these ontologies is crucial for supporting researchers and developers.

Purpose of the Study:

  • To empirically analyze user activities within the BioPortal ontology repository.
  • To investigate how biomedical researchers explore, query, and reuse ontologies and their classes.
  • To compare user browsing/querying behaviors with real-world ontology usage in annotation tasks.

Main Methods:

  • Analysis of BioPortal interaction logs over several years across different access modes.
  • Utilized and extended the PolygOnto visualization method for analyzing interaction, reuse, and usage data.
  • Examined three real-world scenarios for ontology annotation tasks.

Main Results:

  • User exploration, querying, reuse, and actual usage behaviors rarely align.
  • Different users exhibit distinct patterns in how they interact with and utilize ontology components.
  • Identified commonalities and differences in user behaviors within the BioPortal repository.

Conclusions:

  • User interaction with large biomedical ontologies is diverse and fragmented.
  • Tailored support and visualization tools may be needed for different user groups and their specific tasks.
  • Further research can refine understanding of ontology usage to improve ontology engineering and application development.