Back to Details

gnomad-database

Compare original and translation side by side

🇺🇸

Original

English
🇨🇳

Translation

Chinese

gnomAD Database

gnomAD 数据库

Prerequisites

前提条件

  1. uv
    : Read the 
    uv
    skill and follow its Setup instructions to ensure 
    uv
    is installed and on PATH.
  2. User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://gnomad.broadinstitute.org/policies and https://gnomad.broadinstitute.org/data#api, then (2) create the file recording the notification text and timestamp.
  1. uv
    ：阅读
    uv
    技能文档并遵循其设置说明，确保
    uv
    已安装并添加至PATH。
  2. 用户通知：若此技能目录中不存在LICENSE_NOTIFICATION.txt文件，则需(1) 显著提醒用户查看https://gnomad.broadinstitute.org/policies和https://gnomad.broadinstitute.org/data#api上的条款，然后(2) 创建该文件并记录通知文本和时间戳。

Core Rules

核心规则

  • Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the gnomAD API rate limits gracefully.
  • Notification: If this skill is used, ensure this is mentioned in the output.
  • 使用包装器：始终执行提供的辅助脚本来查询数据库，而非直接访问数据库。这些脚本会自动优雅地执行gnomAD API的速率限制。
  • 通知说明：若使用此技能，需在输出中提及这一点。

Utility Scripts

实用脚本

All scripts are located in the 
scripts/
subdirectory of this skill's installation directory. When running them, use the full absolute path to the script (e.g. 
/path/to/gnomad_database/scripts/get_variant_frequency.py
).
1. Variant Frequency. Retrieves global and ancestry-specific allele frequencies, homozygote counts, and Grpmax Filtering AF (faf95/faf99) for exome, genome, and total (exome+genome combined) data. The filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound of the 95% or 99% CI). Variant ID format must be 
chrom-pos-ref-alt
(e.g., 
1-55516888-G-GA
). Alternately, you may provide an 
rsID
.
bash
undefined
所有脚本均位于此技能安装目录的
scripts/
子目录中。运行时需使用脚本的完整绝对路径（例如
/path/to/gnomad_database/scripts/get_variant_frequency.py
）。
1. 变异频率：获取外显子组、基因组及总和（外显子组+基因组合并）数据的全球及特定祖先的等位基因频率、纯合子计数，以及Grpmax Filtering AF（faf95/faf99）。过滤等位基因频率（FAF）是最大可信遗传祖先组AF（95%或99%置信区间的下限）。变异ID格式必须为
chrom-pos-ref-alt
（例如
1-55516888-G-GA
）。此外，也可提供
rsID
。
bash
undefined

By variant ID:

通过变异ID：

uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json
uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json

By rsID (e.g., rs1800562):

通过rsID（例如rs1800562）：

uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json

**2. Gene Constraint.** Retrieves constraint metrics for a gene. The response
will explicitly contain `pli`, and the LOEUF score is represented by
`oe_lof_upper`.

```bash
uv run scripts/get_gene_constraint.py --gene {gene_symbol} --output {gene_symbol}_constraint.json
3. Region/Gene Variant Search. Finds all variants in a region or gene.
bash
undefined
uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json

**2. 基因约束**：获取某一基因的约束指标。响应结果将明确包含`pli`，而LOEUF分数由`oe_lof_upper`表示。

```bash
uv run scripts/get_gene_constraint.py --gene {gene_symbol} --output {gene_symbol}_constraint.json
3. 区域/基因变异搜索：查找某一区域或基因中的所有变异。
bash
undefined

By region:

通过区域：

uv run scripts/search_variants.py --chrom {chrom} --start {start} --end {end} --output region_variants.json
uv run scripts/search_variants.py --chrom {chrom} --start {start} --end {end} --output region_variants.json

By gene:

通过基因：

uv run scripts/search_variants.py --gene {gene_symbol} --consequence {pLoF|missense} --output {gene_symbol}_variants.json
undefined
uv run scripts/search_variants.py --gene {gene_symbol} --consequence {pLoF|missense} --output {gene_symbol}_variants.json
undefined

References

参考资料

Further documentation on the data: https://gnomad.broadinstitute.org/data#api More general database documentation: https://gnomad.broadinstitute.org/help
更多数据相关文档：https://gnomad.broadinstitute.org/data#api 更多数据库通用文档：https://gnomad.broadinstitute.org/help