ArticleJournal of biomedical semantics2015
Improving the Sequence Ontology terminology for genomic variant annotation.
Article in Journal of biomedical semantics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer.Molecular oncology · 2025Article
- Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial.Human mutation · 2022Article
- Computational approaches for predicting variant impact: An overview from resources, principles to applications.Frontiers in genetics · 2022Review
- The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.Cell genomics · 2021Article
- A novel machine learning-based approach for the computational functional assessment of pharmacogenomic variants.Human genomics · 2021Article
- Cyberinfrastructure and resources to enable an integrative approach to studying forest trees.Evolutionary applications · 2020Article
- g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).Nucleic acids research · 2019Article
- Computational Molecular Phenotypic Analysis of PTPN22 (W620R), IL6R (D358A), and TYK2 (P1104A) Gene Mutations of Rheumatoid Arthritis.Frontiers in genetics · 2019Article
- A new bioinformatics tool to help assess the significance of BRCA1 variants.Human genomics · 2018Article
- Article
- Ensembl variation resources.Database : the journal of biological databases and curation · 2018Article
- Settling the score: variant prioritization and Mendelian disease.Nature reviews. Genetics · 2017Review
- MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers.Journal of medical Internet research · 2017Article
- Identification of a novelCold Spring Harbor molecular case studies · 2017Article
- The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching.Nucleic acids research · 2017Article
- Ensembl 2017.Nucleic acids research · 2017Article
- Tutorial on Protein Ontology Resources.Methods in molecular biology (Clifton, N.J.) · 2017Article
- The Ensembl Variant Effect Predictor.Genome biology · 2016Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundThe Genome Variant Format (GVF) uses the Sequence Ontology (SO) to enable detailed annotation of sequence variation. The annotation includes SO terms for the type of sequence alteration, the genomic features that are changed and the effect of the alteration. The SO maintains and updates the specification and provides the underlying ontologicial structure.
methodsA requirements analysis was undertaken to gather terms missing in the SO release at the time, but needed to adequately describe the effects of sequence alteration on a set of variant genomic annotations. We have extended and remodeled the SO to include and define all terms that describe the effect of variation upon reference genomic features in the Ensembl variation databases.
resultsThe new terminology was used to annotate the human reference genome with a set of variants from both COSMIC and dbSNP. A GVF file containing 170,853 sequence alterations was generated using the SO terminology to annotate the kinds of alteration, the effect of the alteration and the reference feature changed. There are four kinds of alteration and 24 kinds of effect seen in this dataset. (Ensembl Variation annotates 34 different SO consequence terms: http://www.ensembl.org/info/docs/variation/predicted_data.html).
conclusionsWe explain the updates to the Sequence Ontology to describe the effect of variation on existing reference features. We have provided a set of annotations using this terminology, and the well defined GVF specification. We have also provided a provisional exploration of this large annotation dataset.
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