A Similarity Metric for Biological Processes
Author Information
Author(s): Chagoyen Monica, Carmona-Saez Pedro, Gil Concha, Carazo Jose M, Pascual-Montano Alberto
Primary Institution: Centro Nacional de Biotecnologia – CSIC, Madrid, Spain
Hypothesis
Can scientific literature be used to establish relationships among biological processes?
Conclusion
The scientific literature is a valuable source of information for computing similarities among biological processes.
Supporting Evidence
- The method was applied to the biological processes annotated for the Saccharomyces cerevisiae genome.
- The literature-based metric conserves most direct ontological relationships.
- The study revealed biologically sound similarities not obtained using ontology-based metrics.
Takeaway
This study shows that reading scientific papers can help us understand how different biological processes are related to each other.
Methodology
The study used a document-based similarity method to compute pair-wise similarities of biological processes described in the Gene Ontology.
Potential Biases
Differences in the amount of documents associated with each process might bias the similarity measure.
Limitations
The approach is limited by the availability of a minimum number of relevant references per biological process.
Digital Object Identifier (DOI)
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