HGVbase:: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
HGVbase:: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
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DOI：
10.1093/nar/30.1.387
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发表时间：
2002-01-01
影响因子：
14.9
通讯作者：
Brookes, AJ
中科院分区：
文献类型：
--
作者：
Fredman, D;Siegfried, M;Brookes, AJ
HGVbase（人类基因组变异数据库；http://hgvbase.cgb.ki.se，以前称为HGBASE）是一项学术性工作，旨在提供一个高质量且无冗余的各类可用基因组变异数据的数据库，其中主要包含单核苷酸多态性（SNPs）。记录包括中性多态性以及与疾病相关的突变。在线搜索工具便于通过序列相似性和关键词查询来检索数据，并且目前正在实现通过基因组坐标进行搜索。可免费下载XML、Fasta、SRS、SQL和标记文本文件格式。每个条目都在其周边序列的背景下呈现，并且许多记录与邻近的人类基因及其中受影响的特征相关。只要有可用的群体等位基因频率信息都会包含在内。全面的半自动数据检查确保了内部一致性，并处理了源信息中的常见错误。为了跟上该领域近期的发展，我们开发了全自动注释工具。所有变异都已唯一地映射到基因组草图序列上，并参考了EMBL/GenBank文件中的位置。通过提供基因分型检测和功能预测，提高了数据的实用性。近期的数据结构扩展允许获取单倍型和基因型信息，并且一项新的举措（与BiSC和HUGO - MDI一起）旨在为广泛收集临床突变及相关的感兴趣的疾病表型创建一个中心存储库。
HGVbase (Human Genome Variation database; http://hgvbase.cgb.ki.se, formerly known as HGBASE) is an academic effort to provide a high quality and non-redundant database of available genomic variation data of all types, mostly comprising single nucleotide polymorphisms (SNPs). Records include neutral polymorphisms as well as disease-related mutations. Online search tools facilitate data interrogation by sequence similarity and keyword queries, and searching by genome coordinates is now being implemented. Downloads are freely available in XML, Fasta, SRS, SQL and tagged-text file formats. Each entry is presented in the context of its surrounding sequence and many records are related to neighboring human genes and affected features therein. Population allele frequencies are included wherever available. Thorough semi-automated data checking ensures internal consistency and addresses common errors in the source information. To keep pace with recent growth in the field, we have developed tools for fully automated annotation. All variants have been uniquely mapped to the draft genome sequence and are referenced to positions in EMBL/GenBank files. Data utility is enhanced by provision of genotyping assays and functional predictions. Recent data structure extensions allow the capture of haplotype and genotype information, and a new initiative (along with BiSC and HUGO-MDI) aims to create a central repository for the broad collection of clinical mutations and associated disease phenotypes of interest.