{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T22:53:49Z","timestamp":1777416829313,"version":"3.51.4"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,7,31]],"date-time":"2015-07-31T00:00:00Z","timestamp":1438300800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s13326-015-0030-4","type":"journal-article","created":{"date-parts":[[2015,7,30]],"date-time":"2015-07-30T10:23:21Z","timestamp":1438251801000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Improving the Sequence Ontology terminology for genomic variant annotation"],"prefix":"10.1186","volume":"6","author":[{"given":"Fiona","family":"Cunningham","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barry","family":"Moore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Ruiz-Schultz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graham RS","family":"Ritchie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen","family":"Eilbeck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,7,31]]},"reference":[{"key":"30_CR1","doi-asserted-by":"publisher","first-page":"R44","DOI":"10.1186\/gb-2005-6-5-r44","volume":"6","author":"K Eilbeck","year":"2005","unstructured":"Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6:R44.","journal-title":"Genome Biol"},{"key":"30_CR2","unstructured":"Generic Model Organism Database (GMOD). [http:\/\/gmod.org]."},{"key":"30_CR3","doi-asserted-by":"publisher","first-page":"2069","DOI":"10.1093\/bioinformatics\/btq330","volume":"26","author":"W McLaren","year":"2010","unstructured":"McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010;26:2069\u201370.","journal-title":"Bioinformatics"},{"key":"30_CR4","doi-asserted-by":"publisher","first-page":"1529","DOI":"10.1101\/gr.123158.111","volume":"21","author":"M Yandell","year":"2011","unstructured":"Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, et al. A probabilistic disease-gene finder for personal genomes. Genome Res. 2011;21:1529\u201342.","journal-title":"Genome Res"},{"key":"30_CR5","unstructured":"1000 Genomes Progect Structural Variant group specification. [http:\/\/www.1000genomes.org\/wiki\/Analysis\/Variant%20Call%20Format\/VCF%20(Variant%20Call%20Format)%20version%204.0\/encoding-structural-variants]."},{"key":"30_CR6","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1126\/science.1215040","volume":"335","author":"DG MacArthur","year":"2012","unstructured":"MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012;335:823\u20138.","journal-title":"Science"},{"key":"30_CR7","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.ajhg.2011.05.017","volume":"89","author":"AF Rope","year":"2011","unstructured":"Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, et al. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet. 2011;89:28\u201343.","journal-title":"Am J Hum Genet"},{"key":"30_CR8","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1038\/nrg3031","volume":"12","author":"MJ Bamshad","year":"2011","unstructured":"Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12:745\u201355.","journal-title":"Nat Rev Genet"},{"key":"30_CR9","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1038\/ng.499","volume":"42","author":"SB Ng","year":"2010","unstructured":"Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010;42:30\u20135.","journal-title":"Nat Genet"},{"key":"30_CR10","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","volume":"38","author":"PJ Cock","year":"2010","unstructured":"Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants. Nucleic Acids Res. 2010;38:1767\u201371.","journal-title":"Nucleic Acids Res"},{"key":"30_CR11","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25:2078\u20139.","journal-title":"Bioinformatics"},{"key":"30_CR12","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27:2156\u20138.","journal-title":"Bioinformatics"},{"key":"30_CR13","doi-asserted-by":"publisher","first-page":"R88","DOI":"10.1186\/gb-2010-11-8-r88","volume":"11","author":"MG Reese","year":"2010","unstructured":"Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, et al. A standard variation file format for human genome sequences. Genome Biol. 2010;11:R88.","journal-title":"Genome Biol"},{"key":"30_CR14","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1002\/humu.20038","volume":"23","author":"O Horaitis","year":"2004","unstructured":"Horaitis O, Cotton RG. The challenge of documenting mutation across the genome: the human genome variation society approach. Hum Mutat. 2004;23:447\u201352.","journal-title":"Hum Mutat"},{"key":"30_CR15","unstructured":"An International System for Human Cytogenetic Nomenclature. Basel: S. Karger AG; 2009."},{"key":"30_CR16","doi-asserted-by":"publisher","first-page":"D48","DOI":"10.1093\/nar\/gks1236","volume":"41","author":"P Flicek","year":"2013","unstructured":"Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48\u201355.","journal-title":"Nucleic Acids Res"},{"key":"30_CR17","doi-asserted-by":"publisher","first-page":"D936","DOI":"10.1093\/nar\/gks1213","volume":"41","author":"I Lappalainen","year":"2013","unstructured":"Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013;41:D936\u201341.","journal-title":"Nucleic Acids Res"},{"key":"30_CR18","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1101\/gr.361602","volume":"12","author":"JE Stajich","year":"2002","unstructured":"Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12:1611\u20138.","journal-title":"Genome Res"},{"key":"30_CR19","doi-asserted-by":"publisher","first-page":"2176","DOI":"10.1093\/bioinformatics\/bts358","volume":"28","author":"T Song","year":"2012","unstructured":"Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW. gSearch: a fast and flexible general search tool for whole-genome sequencing. Bioinformatics. 2012;28:2176\u20137.","journal-title":"Bioinformatics"},{"key":"30_CR20","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1186\/1471-2164-11-293","volume":"11","author":"Y Chen","year":"2010","unstructured":"Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, et al. Ensembl variation resources. BMC Genomics. 2010;11:293.","journal-title":"BMC Genomics"},{"key":"30_CR21","unstructured":"Ensembl predicted data. [http:\/\/www.ensembl.org\/info\/genome\/variation\/predicted_data.html]."},{"key":"30_CR22","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1101\/gr.157495.113","volume":"24","author":"M Vihinen","year":"2014","unstructured":"Vihinen M. Variation ontology for annotation of variation effects and mechanisms. Genome Res. 2014;24:356\u201364.","journal-title":"Genome Res"},{"key":"30_CR23","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/1471-2105-11-238","volume":"11","author":"D Rios","year":"2010","unstructured":"Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, et al. A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics. 2010;11:238.","journal-title":"BMC Bioinformatics"},{"key":"30_CR24","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1093\/nar\/29.1.308","volume":"29","author":"ST Sherry","year":"2001","unstructured":"Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308\u201311.","journal-title":"Nucleic Acids Res"},{"key":"30_CR25","first-page":"Unit 10 11","volume":"Chapter 10","author":"SA Forbes","year":"2008","unstructured":"Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008;Chapter 10:Unit 10 11.","journal-title":"Curr Protoc Hum Genet"},{"key":"30_CR26","doi-asserted-by":"publisher","first-page":"D64","DOI":"10.1093\/nar\/gks1048","volume":"41","author":"LR Meyer","year":"2013","unstructured":"Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, et al. The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res. 2013;41:D64\u20139.","journal-title":"Nucleic Acids Res"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-015-0030-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13326-015-0030-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-015-0030-4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-015-0030-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T17:49:19Z","timestamp":1630604959000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/s13326-015-0030-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,7,31]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["30"],"URL":"https:\/\/doi.org\/10.1186\/s13326-015-0030-4","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,7,31]]},"assertion":[{"value":"19 February 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 July 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"32"}}