ReviewTheScientificWorldJournal2013
From ontology to semantic similarity: calculation of ontology-based semantic similarity.
Review in TheScientificWorldJournal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Pathway Analysis Interpretation in the Multi-Omic Era.Biotech (Basel (Switzerland)) · 2025Review
- Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond.BMC bioinformatics · 2024Article
- DAPNet: multi-view graph contrastive network incorporating disease clinical and molecular associations for disease progression prediction.BMC medical informatics and decision making · 2024Article
- Unveiling inter-embryo variability in spindle length over time: Towards quantitative phenotype analysis.PLoS computational biology · 2024Article
- Evaluating semantic similarity methods for comparison of text-derived phenotype profiles.BMC medical informatics and decision making · 2022Article
- Establishing a Common Nutritional Vocabulary - From Food Production to Diet.Frontiers in nutrition · 2022Article
- MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases.Nucleic acids research · 2021Article
- Towards similarity-based differential diagnostics for common diseases.Computers in biology and medicine · 2021Article
- Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity.Frontiers in digital health · 2021Article
- Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities.BMC bioinformatics · 2020Article
- A Decision Method for Construction Safety Risk Management Based on Ontology and Improved CBR: Example of a Subway Project.International journal of environmental research and public health · 2020Article
- Ontology-driven integrative analysis of omics data through Onassis.Scientific reports · 2020Article
- A case-based reasoning framework for early detection and diagnosis of novel coronavirus.Informatics in medicine unlocked · 2020Article
- APID database: redefining protein-protein interaction experimental evidences and binary interactomes.Database : the journal of biological databases and curation · 2019Article
- Development and Validation of a Functional Behavioural Assessment Ontology to Support Behavioural Health Interventions.JMIR medical informatics · 2018Article
- Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework.Scientific reports · 2017Article
- Functional coherence metrics in protein families.Journal of biomedical semantics · 2016Article
- Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective.Frontiers in physiology · 2015Article
- An ontology approach to comparative phenomics in plants.Plant methods · 2015Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in high-throughput experimental techniques in the past decade have enabled the explosive increase of omics data, while effective organization, interpretation, and exchange of these data require standard and controlled vocabularies in the domain of biological and biomedical studies. Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. Nevertheless, with a variety of methods available, how to choose a suitable method for a specific application becomes a problem. With this understanding, we review a majority of existing methods that rely on ontologies to calculate semantic similarity between terms. We classify existing methods into five categories: methods based on semantic distance, methods based on information content, methods based on properties of terms, methods based on ontology hierarchy, and hybrid methods. We summarize characteristics of each category, with emphasis on basic notions, advantages and disadvantages of these methods. Further, we extend our review to software tools implementing these methods and applications using these methods.
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Registered trials
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.