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Updated: May 7, 2026

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

Groups: knowledge spreadsheets for symbolic biocomputing.

Michael Travers¹, Suzanne M Paley, Jeff Shrager

¹Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.

Database : the Journal of Biological Databases and Curation

|September 17, 2013

Summary

This summary is machine-generated.

Knowledge Spreadsheets (KSs) enable interactive data analysis using symbolic knowledge. The Groups feature in Pathway Tools allows biologists to manipulate biological data, reducing the need for programming assistance.

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

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Published on: February 8, 2017

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

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

Published on: February 8, 2017

Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Traditional spreadsheets focus on numeric data.
Knowledge Spreadsheets (KSs) offer a visual approach for data analysis.
KSs utilize symbolic knowledge representation and domain semantics.

Purpose of the Study:

Introduce 'Groups,' an implementation of KSs within the Pathway Tools system.
Demonstrate the utility of Groups for biological data manipulation.
Empower biologists to perform data analysis independently.

Main Methods:

Development of the 'Groups' feature in Pathway Tools.
Definition and transformation of object groups (genes, metabolites).
Application of set operations, enrichment analysis, and visualization on groups.

Main Results:

Extensive utilization of Groups by users on the BioCyc.org website.
Informal user surveys indicate successful self-service data manipulation.
Groups facilitate complex data operations without requiring programming expertise.

Conclusions:

Groups within Pathway Tools effectively serve as a Knowledge Spreadsheet.
The tool empowers biologists with enhanced data analysis capabilities.
Groups streamline biological data exploration and manipulation for researchers.