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

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STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.

Tobias Wittkop¹, Emily TerAvest, Uday S Evani

¹Buck Institute for Research on Aging, Novato, CA, USA.

BMC Bioinformatics

|February 16, 2013

Summary

Researchers can now generate more hypotheses from gene lists using the Statistical Tracking of Ontological Phrases (STOP) tool. STOP integrates automated annotations from biomedical ontologies, expanding beyond traditional Gene Ontology (GO) enrichment analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Gene Ontology (GO) enrichment analysis is a common method for hypothesis generation from high-throughput data.
Existing methods may not cover all hypotheses researchers wish to test.
There is a need for tools that expand hypothesis generation beyond GO.

Purpose of the Study:

To develop and evaluate a tool for hypothesis generation from gene or protein lists.
To utilize ontological concepts from manually curated text describing genes and proteins.
To expand the scope of testable hypotheses in gene set enrichment analyses.

Main Methods:

Developed the Statistical Tracking of Ontological Phrases (STOP) method.
Integrated automated annotations of genes to terms from over 200 biomedical ontologies.
Used a dataset combining manually curated GO terms and automatically recognized concepts from curated text.

Main Results:

The STOP method expands the range of testable hypotheses in gene set enrichment analyses.
Automated annotations from biomedical ontologies provide valuable enriched concepts.
These additional concepts are beneficial when used alongside traditional GO enrichment analyses.

Conclusions:

Utilizing multiple ontologies, including automatically recognized concepts from curated text, expands the scope of discoverable hypotheses.
The STOP tool offers a novel approach to hypothesis generation in bioinformatics.
The STOP web application is publicly available for researchers.