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Related Experiment Video

Updated: Jun 1, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Toward an interactive article: integrating journals and biological databases.

Arun Rangarajan1, Tim Schedl, Karen Yook

  • 1Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

BMC Bioinformatics
|May 21, 2011
PubMed
Summary
This summary is machine-generated.

We developed a semi-automated pipeline to link biological journal articles to databases like WormBase, improving data discovery. Manual quality control ensures accuracy, benefiting researchers and publications.

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Related Experiment Videos

Last Updated: Jun 1, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Area of Science:

  • Biological sciences
  • Bioinformatics
  • Scientific communication

Background:

  • Integrating journal articles and databases is crucial for accelerating biological discovery.
  • Automated tools for entity recognition and database linking are increasing but struggle with ambiguity.
  • Manual oversight is necessary to resolve ambiguities and ensure accurate linking.

Purpose of the Study:

  • To develop a semi-automated pipeline for linking journal articles to model organism databases.
  • To improve the accuracy and efficiency of connecting biological literature with curated data.
  • To create data-rich, interactive articles for enhanced scientific understanding.

Main Methods:

  • Established a pipeline linking GENETICS journal articles to the WormBase database.
  • Utilized a lexicon of database entities for initial markup.
  • Implemented a manual quality control (QC) step involving database curators and author feedback.
  • Extended the pipeline to other databases like Saccharomyces Genome Database (SGD) and FlyBase.

Main Results:

  • Successfully linked GENETICS articles to WormBase, covering over nine object classes (genes, proteins, alleles, phenotypes, etc.).
  • Identified and resolved new entities and ambiguities through manual QC.
  • Achieved accurate linking of ambiguous entities via manual resolution.
  • Demonstrated pipeline applicability to multiple databases and multi-database linking.

Conclusions:

  • The semi-automated pipeline creates interactive, data-rich articles with high accuracy.
  • Manual QC is a key differentiator, enhancing the reliability of hyperlinked content.
  • The system benefits authors, journals, readers, and databases by improving data accessibility and integration.