ArticleAdvances in bioinformatics2012
A topology-based metric for measuring term similarity in the gene ontology.
Article in Advances in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- simona: a comprehensive R package for semantic similarity analysis on bio-ontologies.BMC genomics · 2024Article
- HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball.Bioinformatics (Oxford, England) · 2021Article
- GSAn: an alternative to enrichment analysis for annotating gene sets.NAR genomics and bioinformatics · 2020Article
- Rv1717 Is a Cell Wall - Associated β-Galactosidase ofFrontiers in microbiology · 2020Article
- Article
- Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.Scientific reports · 2018Article
- A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets.PloS one · 2018Article
- A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1.BMC plant biology · 2017Article
- The effects of shared information on semantic calculations in the gene ontology.Computational and structural biotechnology journal · 2017Article
- A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics.Genome medicine · 2016Article
- OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization.Bioinformatics (Oxford, England) · 2015Article
- Article
- Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity.BMC genomics · 2014Article
- Using biological networks to improve our understanding of infectious diseases.Computational and structural biotechnology journal · 2014Review
- Semantic particularity measure for functional characterization of gene sets using gene ontology.PloS one · 2014Article
- Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?PloS one · 2014Article
- The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines.Frontiers in genetics · 2014Article
- DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.BMC bioinformatics · 2013Article
- Information content-based gene ontology semantic similarity approaches: toward a unified framework theory.BioMed research international · 2013Article
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2 authors.
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Abstract
The wide coverage and biological relevance of the Gene Ontology (GO), confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.