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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
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2020-10-08 , DOI: 10.1111/1755-0998.13269
Cynthia Riginos 1 , Eric D Crandall 2, 3 , Libby Liggins 4 , Michelle R Gaither 5 , Rodney B Ewing 6 , Christopher Meyer 7 , Kimberly R Andrews 8 , Peter T Euclide 9 , Benjamin M Titus 10 , Nina Overgaard Therkildsen 11 , Antonia Salces-Castellano 12 , Lucy C Stewart 13 , Robert J Toonen 14 , John Deck 15
Affiliation  

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.

中文翻译:

建立全球基因组观察站:使用 GEOME(基因组观察站元数据库)加快和改进用于生物多样性研究的遗传数据和元数据的存储和检索

遗传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领域。理想情况下,此类数据应包括基于生物体 DNA 的基因型和采样生物体的生态环境。然而,大多数数据存储工具和标准都只关注遗传或生态属性。基因组天文台元数据库(GEOME:geome-db.org)提供了一种直观的解决方案,用于维护国际核苷酸序列数据库协作(INSDC)存储的遗传数据集与其相关生态元数据之间的联系。GEOME 有助于将原始遗传数据存储到 INSDCs 序列读取存档 (SRA),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。这种方法有助于找到、可访问、可互操作和可重用的数据归档实践。此外,GEOME 可为大型协作组提供数据管理解决方案,并加快从 SRA 批量检索遗传数据的速度。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提供真正开放的数据工作流程。
更新日期:2020-11-04
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