ArticleGenome research2014
Variation Ontology for annotation of variation effects and mechanisms.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed.
- Proteome-Wide Analysis of Human Deletions.Proteins · 2026Article
- PON-Del predictor for sequence retaining protein deletions.PLoS computational biology · 2026Article
- Nonsynonymous Synonymous Variants Demand for a Paradigm Shift in Genetics.Current genomics · 2023Review
- Systematic errors in annotations of truncations, loss-of-function and synonymous variants.Frontiers in genetics · 2023Article
- BTKbase, Bruton Tyrosine Kinase Variant Database in X-Linked Agammaglobulinemia: Looking Back and Ahead.Human mutation · 2023Article
- Individual Genetic Heterogeneity.Genes · 2022Review
- When a Synonymous Variant Is Nonsynonymous.Genes · 2022Article
- Computational approaches for predicting variant impact: An overview from resources, principles to applications.Frontiers in genetics · 2022Review
- Systematics for types and effects of RNA variations.RNA biology · 2021Article
- Inferring the molecular and phenotypic impact of amino acid variants with MutPred2.Nature communications · 2020Article
- Variation benchmark datasets: update, criteria, quality and applications.Database : the journal of biological databases and curation · 2020Article
- Poikilosis - pervasive biological variation.F1000Research · 2020Article
- Systematics for types and effects of DNA variations.BMC genomics · 2018Review
- Harnessing formal concepts of biological mechanism to analyze human disease.PLoS computational biology · 2018Article
- Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.Bioinformatics (Oxford, England) · 2018Article
- NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database.Database : the journal of biological databases and curation · 2018Article
- PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned.Human mutation · 2017Article
- Human Variome Project Quality Assessment Criteria for Variation Databases.Human mutation · 2016Article
- ClinVar: public archive of interpretations of clinically relevant variants.Nucleic acids research · 2016Article
- Human genotype-phenotype databases: aims, challenges and opportunities.Nature reviews. Genetics · 2015Review
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism.
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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.