Semantic Similarity in Biomedical Ontologies (Pesquita et al., 2009) Benchmark Task

A Semantic Similarity in Biomedical Ontologies (Pesquita et al., 2009) Benchmark Task is a Gene Semantic Similarity Benchmark Task that evaluates the performance of GO-based semantic similarity measures.

• Context:
  • It was performed by Pesquita et al. (2009).
  • It evaluates the performance of node-based versus edge-based as well as pairwise versus groupwise.
• Example(s):
  • Benchmark's best SSM systems:

Application	Best Measure	Reference
Functiona p/v	BMA(Resnik)/simGIC	Pesquita et al. (2008)
Protein-protein interaction p/v	Max(Resnik)	Guo et al. (2006), Xu et al., (2008)
Cellular location prediction	SUM(EM)	Lei & Dai (2006)

• Counter-Example(s):
  • SemEval Benchmark Task.
• See: Semantic Similarity Measure, Semantic Similarity Benchmark Task, NLP Benchmark Task, Go Ontology, Biomedical Research Field, Gene Sequence Similarity Measure.

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References

2009

• (Pesquita et al., 2009 ) ⇒ Catia Pesquita, Daniel Faria, Andre O. Falcao, Phillip Lord, and Francisco M. Couto (2009). "Semantic Similarity in Biomedical Ontologies". In: PLoS Computational Biology 5(7): e1000443.
  • QUOTE: However, based on the few comparative studies that exist, we can identify the most successful measures so far in the three main applications of GO-based semantic similarity: function prediction validation, protein–protein interaction prediction/validation, and cellular location prediction (see Table 6).

Table 6: Best measures for the main applications of GO-based semantic similarity measures. ^aIdentified by sequence similarity. p/v, prediction/validation.

Application	Best Measure	Reference
Functiona p/v	BMA(Resnik)/simGIC	Pesquita et al. (2008)
Protein-protein interaction p/v	Max(Resnik)	Guo et al. (2006), Xu et al., (2008)
Cellular location prediction	SUM(EM)	Lei & Dai (2006)

2008a

• (Pesquita et al., 2008) &rArr Catia Pesquita, Daniel Faria, Hugo Bastos, Antonio EN Ferreira, Andre O Falcao, and Francisco M Couto (2008). "Metrics for GO based protein semantic similarity: a systematic evaluation". In: BMC Bioinformatics volume 9, Article number: S4.

2008b

• (Xu et al., 2008) ⇒ Tao Xu, LinFang Du, and Yan Zhou (2008)."Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data". In: BMC Bioinformatics. 2008;9.

2006a

• (Guo et al., 2006) ⇒ Xiang Guo, Rongxiang Liu, Craig D. Shriver, Hai Hu, and Michael N. Liebman (2006). "Assessing Semantic Similarity Measures For The Characterization Of Human Regulatory Pathways". In: Bioinformatics, Volume 22, Issue 8.

2006b

• (Lei & Dai, 2006) ⇒ Zhengdeng Lei, and Yang Dai (2006)."Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction". In: BMC Bioinformatics. 2006;7.

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