Variation ontology: Annotator guide

Journal of Biomedical Semantics

Volumn 5, Issue 1, 2014, Pages

  Vihinen, Mauno ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Annotation instructions; Mutation; Ontology; Systematics; Variation effects; Variation ontology

Indexed keywords

EID: 84925504770     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-5-9     Document Type: Article

References (27)

1. Vihinen M. Variation Ontology for annotation of variation effects and mechanisms. Genome Res 24:356-364.
2. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. LOVD v. 2.0: the next generation in gene variant databases. Hum Mutat 2011, 32:557-563. 10.1002/humu.21438, 21520333.
3. The UniProt Consortium Update on activities at the universal protein resource (UniProt) in 2013. Nucleic Acids Res 2013, 41:D43-D47. 3531094, 23161681, The UniProt Consortium.
4. ClinVar [https://www.ncbi.nlm.nih.gov/clinvar/], ClinVar.
5. van Baal S, Zlotogora J, Lagoumintzis G, Gkantouna V, Tzimas I, Poulas K, Tsakalidis A, Romeo G, Patrinos GP. ETHNOS: a versatile electronic tool for the development and curation of national genetic databases. Hum Genomics 2010, 4:361-368. 10.1186/1479-7364-4-5-361, 3500166, 20650823.
6. Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res 2013, 41:D936-D941. 10.1093/nar/gks1213, 3531204, 23193291.
7. Georgitsi M, Viennas E, Antoniou DI, Gkantouna V, van Baal S, Petricoin EF, Poulas K, Tzimas G, Patrinos GP. FINDbase: a worldwide database for genetic variation allele frequencies updated. Nucleic Acids Res 2011, 39:D926-D932. 10.1093/nar/gkq1236, 3013745, 21113021.
8. Kumar MD, Bava KA, Gromiha MM, Parabakaran P, Kitajima K, Uedaira H, Sarai A. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res 2006, 34:D204-D206. 10.1093/nar/gkj103, 1347465, 16381846.
9. Nair PS, Vihinen M. VariBench: a benchmark database for variations. Hum Mutat 2013, 34:42-49. 10.1002/humu.22204, 22903802.
10. den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 2000, 15:7-12. 10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N, 10612815.
11. Howard HJ, Horaitis O, Cotton RGH, den Dunnen JT, Vihinen M, Dalgleish R, Robinson P, Brookes AJ, Axton M, Hoffman R, Tavtigian SV, Tuffery-Giraud S. The human variome project (2009) towards establishing standards. Hum Mutat 2010, 31:366-367. 10.1002/humu.21175, 20052753.
12. Kohonen-Corish M, Al-Aama J, Auerbach A, Axton M, Barach CI, Bernstein I, Béroud C, Burn J, Cunningham F, Cutting G, den Dunnen J, Greenblatt M, Kaput J, Katz M, Lindblom A, Macrae F, Maglott D, Möslein G, Povey S, Ramesar R, Richards S, Seminara D, Sobrido M-J, Tavtigian S, Taylor G, Vihinen M, Winship I, Cotton RGH. How to catch all those mutations - the report of the third human variome project meeting, UNESCO Paris, May 2010. Hum Mutat 2010, 31:1374-1381. 10.1002/humu.21379, 3119486, 20960468.
13. Celli J, Dalgleish R, Vihinen M, Taschner PEM, den Dunnen JT. Curating gene sequence variant databases (LSDBs). Hum Mutat 2012, 33:291-297. 10.1002/humu.21626, 21990126.
14. Vihinen M, den Dunnen JT, Dalgleish R, Cotton RGH. Guidelines for establishing locus specific databases. Hum Mutat 2012, 33:298-305. 10.1002/humu.21646, 22052659.
15. Webb AJ, Thorisson GA, Brookes AJ. GEN2PHEN consortium. An informatics project and online "knowledge centre" supporting modern genotype-to-phenotype research. Hum Mutat 2011, 32:543-550. 10.1002/humu.21469, 21438073.
16. Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum Mutat 2008, 29:6-13. 10.1002/humu.20654, 18000842.
17. The evidence ontology. [http://www.evidenceontology.org/].
18. VariOtator. [http://variationontology.org/VariOtator.php].
19. Heino M, Scott HS, Chen Q, Peterson P, Mäenpää U, Papasavvas MP, Mittaz L, Barras C, Rossier C, Chrousos GP, Stratakis CA, Nagamine K, Kudoh J, Shimizu N, Maclaren N, Antonarakis SE, Krohn K. Mutation analyses of North American APS-1 patients. Hum Mutat 1999, 13:69-74. 10.1002/(SICI)1098-1004(1999)13:1<69::AID-HUMU8>3.0.CO;2-6, 9888391.
20. AIREbase. [http://structure.bmc.lu.se/idbase/ADAbase].
21. Piirilä H, Väliaho J, Vihinen M. Immunodeficiency mutation databases (IDbases). Hum Mutat 2006, 27:1200-1208. 10.1002/humu.20405, 17004234.
22. Halonen M, Kangas H, Rüppel T, Ilmarinen T, Ollila J, Kolmer M, Vihinen M, Palvimo J, Saarela J, Ulmanen I, Eskelin P. APECED-causing mutations in AIRE reveal the functional domains of the protein. Hum Mutat 2004, 23:245-257. 10.1002/humu.20003, 14974083.
23. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon - level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 2007, 5:44. 10.1186/1741-7007-5-44, 2189715, 17925023.
24. Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Béroud C, Dobson G, Lehväslaiho H, Taschner PE, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR. Locus reference genomic sequences: an improved basis for describing human DNA variants. Genome Med 2010, 2:24. 10.1186/gm145, 2873802, 20398331.
25. Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. genenames.org: the HGNC resources in 2011. Nucleic Acids Res 2011, 39:D514-D519. 10.1093/nar/gkq892, 3013772, 20929869.
26. Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S. The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet 2008, 83:610-615. 10.1016/j.ajhg.2008.09.017, 2668030, 18950739.
27. Allanson JE, Biesecker LG, Carey JC, Hennekam RCM. Elements of morphology: introduction. Am J Med Genet 2009, 149A:2-5. 10.1002/ajmg.a.32601, 2774524, 19127575.