Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research
Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research
复制标题
DOI：
10.1111/1755-0998.13269
复制
发表时间：
2020-10-27
影响因子：
7.7
通讯作者：
Deck, John
中科院分区：
文献类型：
--
作者：
Riginos, Cynthia;Crandall, Eric D.;Deck, John
基因数据代表了我们理解全球生物多样性的一个相对较新的前沿。理想情况下，这样的数据应该既包括基于DNA的生物基因类型，也包括对生物进行采样的生态环境。然而，大多数数据沉积的工具和标准都只关注遗传或生态属性。基因组观察站元数据库(GEOME：geome-db.org)为维护国际核苷酸序列数据库合作(INSDC)存储的遗传数据集与其相关生态元数据之间的联系提供了一个直观的解决方案。GEOME促进将原始遗传数据存入INSDCS序列读取档案，同时保持与GEOME数据库中保存的符合标准的生态元数据的持久链接。这种方法促进了可查找、可访问、可互操作和可重复使用的数据归档做法。此外，GEOME能够为大型协作小组提供数据管理解决方案，并加快从SRA批量检索遗传数据。接下来的文章描述了GEOME如何为分子生态学领域的研究人员实现真正开放的数据工作流程。
Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.