Metrics for GO based protein semantic similarity: a systematic evaluation

Background: Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However, it is still unclear which is the best approach to semantic similarity in this context, since there is no conclusive evaluation of the various measures. Another issue, is whether electronic annotations should or not be used in semantic similarity calculations. Results: We conducted a systematic evaluation of GO-based semantic similarity measures using the relationship with sequence similarity as a means to quantify their performance, and assessed the influence of electronic annotations by testing the measures in the presence and absence of these annotations. We verified that the relationship between semantic and sequence similarity is not linear, but can be well approximated by a rescaled Normal cumulative distribution function. Given that the majority of the semantic similarity measures capture an identical ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Catia Pesquita, Daniel Faria, Hugo P. Bastos, António E. N. Ferreira, André O. Falcão, Francisco M. Couto
• Keywords: BMCBI 2008, Semantic Similarity, Semantic Similarity Measures, Sequence Similarity