GWAS Catalog数据库简介

GWAS Catalog

The NHGRI-EBI Catalog of published genome-wide association studies

EBI负责维护的一个收集已发表的GWAS研究的数据库

Catalog stats

• Last data release on 2019-09-24
• 4220 publications
• 107486 SNPs
• 157336 associations
• Genome assembly GRCh38.p12
• dbSNP Build 151
• Ensembl Build 96

基本的搜索方法

搜索表型：如breast carcinoma，会得到相关的非常规范的表型信息，EFO，就像GO一样，是一套表型分类规则。然后还会得到表型相关的基因。

搜索SNP：如rs7329174，会得到变异的详细信息，和对应的基因。

搜索人名：Yao，会得到相关的文献

搜索染色体位置：如2q37.1，Cytogenetic region

搜索基因：如HBS1L

搜索区域：如6:16000000-25000000

 

说是数据库，其实就是一个table，从这里下载，不过100MB

表里面有这些数据：

DATE ADDED TO CATALOG* +: Date a study is published in the catalog

PUBMEDID* +: PubMed identification number

FIRST AUTHOR* +: Last name and initials of first author

DATE* +: Publication date (online (epub) date if available)

JOURNAL* +: Abbreviated journal name

LINK* +: PubMed URL

STUDY* +: Title of paper

DISEASE/TRAIT* +: Disease or trait examined in study

INITIAL SAMPLE DESCRIPTION* +: Sample size and ancestry description for stage 1 of GWAS (summing across multiple Stage 1 populations, if applicable)

REPLICATION SAMPLE DESCRIPTION* +: Sample size and ancestry description for subsequent replication(