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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Applying evolutionary terminology auditing to the Gene Ontology
1New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Suite B2-160, Suite B2-160, Buffalo, NY 14203, USA. ceusters@buffalo.edu
Journal of Biomedical Informatics
|January 24, 2009
Summary
Evolutionary Terminology Auditing (ETA) assesses terminology quality by comparing versions to reality. This method identifies unjustified term absences or presences, aiding in quality forecasting for evolving vocabularies like the Gene Ontology.
Area of Science:
- Bioinformatics
- Ontology Engineering
- Computational Biology
Background:
- Controlled vocabularies and ontologies are crucial for data annotation in biology.
- Assessing and ensuring the quality of these terminologies over time is essential for scientific reproducibility.
- Existing methods for terminology quality assessment may not fully capture evolutionary dynamics.
Purpose of the Study:
- To introduce and apply Evolutionary Terminology Auditing (ETA) as a novel method for assessing terminology quality.
- To benchmark terminology evolution against reality, identifying unjustified absences and presences.
- To evaluate the utility of ETA for quantifying and forecasting the quality evolution of the Gene Ontology (GO).
Main Methods:
- ETA was developed to audit terminologies by comparing successive versions against a reality benchmark.
- The method requires authors to track and motivate changes between terminology versions.
- The ETA method was applied to the Gene Ontology (GO), a widely used biological vocabulary.
Main Results:
- The application of ETA to GO demonstrated its utility even with partially met requirements.
- The audit identified unjustified absences and presences in GO terminology evolution.
- Results provide a basis for quantifying and forecasting the quality of evolving terminologies.
Conclusions:
- Evolutionary Terminology Auditing (ETA) offers a novel approach to evaluate and monitor the quality of scientific terminologies.
- The method is applicable to complex biological ontologies like the Gene Ontology.
- ETA provides valuable insights into terminology evolution, aiding in quality management and future development.
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