ArticleJournal of biomedical semantics2011
Disjunctive shared information between ontology concepts: application to Gene Ontology.
Article in Journal of biomedical semantics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human-Coronavirus Family Interactome.Vaccines · 2023Article
- HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball.Bioinformatics (Oxford, England) · 2021Article
- Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures.BioMed research international · 2019Article
- STS-NLSP: A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity.Frontiers in bioengineering and biotechnology · 2019Article
- Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions.Briefings in functional genomics · 2018Review
- GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.Scientific reports · 2018Article
- Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes.Scientific reports · 2018Article
- Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology.PloS one · 2018Article
- The effects of shared information on semantic calculations in the gene ontology.Computational and structural biotechnology journal · 2017Article
- TopoICSim: a new semantic similarity measure based on gene ontology.BMC bioinformatics · 2016Article
- Determining similarity of scientific entities in annotation datasets.Database : the journal of biological databases and curation · 2015Article
- Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity.BMC genomics · 2014Article
- M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations.Proteome science · 2013Article
- COEUS: "semantic web in a box" for biomedical applications.Journal of biomedical semantics · 2012Article
- A novel method to quantify gene set functional association based on gene ontology.Journal of the Royal Society, Interface · 2012Article
- Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.BMC bioinformatics · 2012Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities described therein. A common approach, known as semantic similarity, compares ontology concepts through the information content they share in the ontology. However, different disjunctive ancestors in the ontology are frequently neglected, or not properly explored, by semantic similarity measures.
resultsThis paper proposes a novel method, dubbed DiShIn, that effectively exploits the multiple inheritance relationships present in many biomedical ontologies. DiShIn calculates the shared information content of two ontology concepts, based on the information content of the disjunctive common ancestors of the concepts being compared. DiShIn identifies these disjunctive ancestors through the number of distinct paths from the concepts to their common ancestors.
conclusionsDiShIn was applied to Gene Ontology and its performance was evaluated against state-of-the-art measures using CESSM, a publicly available evaluation platform of protein similarity measures. By modifying the way traditional semantic similarity measures calculate the shared information content, DiShIn was able to obtain a statistically significant higher correlation between semantic and sequence similarity. Moreover, the incorporation of DiShIn in existing applications that exploit multiple inheritance would reduce their execution time.
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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.