{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T22:09:04Z","timestamp":1772489344201,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":765,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics.<\/jats:p>\n               <jats:p>Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http:\/\/bitbucket.org\/hgvs\/hgvs\/ . Python packages are available at PyPI ( https:\/\/pypi.python.org\/pypi\/hgvs ).<\/jats:p>\n               <jats:p>Contact: \u00a0reecehart@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu630","type":"journal-article","created":{"date-parts":[[2014,10,2]],"date-time":"2014-10-02T06:07:10Z","timestamp":1412230030000},"page":"268-270","source":"Crossref","is-referenced-by-count":37,"title":["A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature"],"prefix":"10.1093","volume":"31","author":[{"given":"Reece K.","family":"Hart","sequence":"first","affiliation":[{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"},{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rudolph","family":"Rico","sequence":"additional","affiliation":[{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily","family":"Hare","sequence":"additional","affiliation":[{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Garcia","sequence":"additional","affiliation":[{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jody","family":"Westbrook","sequence":"additional","affiliation":[{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent A.","family":"Fusaro","sequence":"additional","affiliation":[{"name":"1 Invitae Inc., San Francisco, CA 94107 and 2 23andMe Inc., Mountain View, CA 94043, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,9,30]]},"reference":[{"key":"2023020116155184300_btu630-B1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of \n              Drosophila melanogaster\n               strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2023020116155184300_btu630-B2","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1093\/bioinformatics\/btq658","article-title":"MU2A\u2014reconciling the genome and transcriptome to determine the effects of base substitutions","volume":"27","author":"Garla","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020116155184300_btu630-B3","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1038\/gim.2013.73","article-title":"ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing","volume":"15","author":"Green","year":"2013","journal-title":"Genet. 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