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Nucleic acids research
01 04, 2018;46 (D1): D944-D949.

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Shuhui Song, Dongmei Tian, Cuiping Li, Bixia Tang, Lili Dong, Jingfa Xiao, Yiming Bao, Wenming Zhao, Hang He, Zhang Zhang
Author Information
  1. Shuhui Song: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  2. Dongmei Tian: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  3. Cuiping Li: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  4. Bixia Tang: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  5. Lili Dong: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  6. Jingfa Xiao: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  7. Yiming Bao: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  8. Wenming Zhao: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  9. Hang He: School of Life Sciences, Peking University, Beijing 100871, China.
  10. Zhang Zhang: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
PMID: 29069473 DOI: 10.1093/nar/gkx986

Abstract

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes.

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MeSH Term

Access to Information
Animals
Animals, Domestic
Base Sequence
Big Data
Data Curation
Database Management Systems
Databases, Genetic
Forecasting
Genetic Variation
Genetics, Population
Genome
Genome, Human
Genotype
High-Throughput Nucleotide Sequencing
Humans
Plants
Species Specificity
User-Computer Interface
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC002026 (GVM)

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