ArticleBioinformatics (Oxford, England)2016
A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- simona: a comprehensive R package for semantic similarity analysis on bio-ontologies.BMC genomics · 2024Article
- Protein homeostasis imprinting across evolution.NAR genomics and bioinformatics · 2024Article
- HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey.BMC bioinformatics · 2022Article
- Semantic similarity and machine learning with ontologies.Briefings in bioinformatics · 2021Review
- Article
- A Literature Review of Gene Function Prediction by Modeling Gene Ontology.Frontiers in genetics · 2020Review
- Screening of genes involved in epithelial-mesenchymal transition and differential expression of complement-related genes induced by PAX2 in renal tubules.Nephrology (Carlton, Vic.) · 2019Article
- 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
- 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
- Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework.Scientific reports · 2017Article
- Margin based ontology sparse vector learning algorithm and applied in biology science.Saudi journal of biological sciences · 2017Article
- Corpus domain effects on distributional semantic modeling of medical terms.Bioinformatics (Oxford, England) · 2016Article
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4 authors.
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Abstract
summaryGene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. AVAILABILITY AND IMPLEMENTATION: A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). CONTACT: gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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