VariOtator, A Software Tool for Variation Annotation with the Variation Ontology.
Schaafsma, Gerard LU
and Vihinen, Mauno
LU
(2016)
In Human Mutation
37(4).
p.344-349
- Abstract
- The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, i.e. all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels - function, structure and property -... (More)
- The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, i.e. all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels - function, structure and property - annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and Evidence Code (ECO) terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences. This article is protected by copyright. All rights reserved. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/8577556
- author
- Schaafsma, Gerard
LU
and Vihinen, Mauno
LU
- organization
- publishing date
- 2016-01-15
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Human Mutation
- volume
- 37
- issue
- 4
- pages
- 344 - 349
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- pmid:26773573
- scopus:84960487212
- wos:000372322400003
- pmid:26773573
- ISSN
- 1059-7794
- DOI
- 10.1002/humu.22954
- language
- English
- LU publication?
- yes
- id
- a538a53f-49dc-40fc-8a2a-802a53f56ffe (old id 8577556)
- alternative location
- http://www.ncbi.nlm.nih.gov/pubmed/26773573?dopt=Abstract
- date added to LUP
- 2016-04-04 08:00:10
- date last changed
- 2022-02-20 21:07:40
@article{a538a53f-49dc-40fc-8a2a-802a53f56ffe,
abstract = {{The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, i.e. all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels - function, structure and property - annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and Evidence Code (ECO) terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences. This article is protected by copyright. All rights reserved.}},
author = {{Schaafsma, Gerard and Vihinen, Mauno}},
issn = {{1059-7794}},
language = {{eng}},
month = {{01}},
number = {{4}},
pages = {{344--349}},
publisher = {{John Wiley & Sons Inc.}},
series = {{Human Mutation}},
title = {{VariOtator, A Software Tool for Variation Annotation with the Variation Ontology.}},
url = {{https://lup.lub.lu.se/search/files/12619644/5162517.pdf}},
doi = {{10.1002/humu.22954}},
volume = {{37}},
year = {{2016}},
}