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dc.contributor.authorCunningham, Fiona
dc.contributor.authorMoore, Barry
dc.contributor.authorRuiz-Schultz, Nicole
dc.contributor.authorRitchie, Graham R
dc.contributor.authorEilbeck, Karen
dc.date.accessioned2015-09-01T18:52:17Z
dc.date.available2015-09-01T18:52:17Z
dc.date.issued2015-07-31
dc.identifier.citationJournal of Biomedical Semantics. 2015 Jul 31;6(1):32
dc.identifier.urihttp://dx.doi.org/10.1186/s13326-015-0030-4
dc.identifier.urihttp://hdl.handle.net/10724/32096
dc.description.abstractAbstract Background The 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. Methods A 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. Results The 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 ). Conclusions We 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.
dc.titleImproving the Sequence Ontology terminology for genomic variant annotation
dc.typeJournal Article
dc.date.updated2015-07-31T03:53:42Z
dc.language.rfc3066en
dc.rights.holderCunningham et al.


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