Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
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DOI：
10.1093/gigascience/giac003
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发表时间：
2022-02-16
期刊：
影响因子：
9.2
通讯作者：
MacCannell DR
中科院分区：
文献类型：
--
作者：
Griffiths EJ;Timme RE;Mendes CI;Page AJ;Alikhan NF;Fornika D;Maguire F;Campos J;Park D;Olawoye IB;Oluniyi PE;Anderson D;Christoffels A;da Silva AG;Cameron R;Dooley D;Katz LS;Black A;Karsch-Mizrachi I;Barrett T;Johnston A;Connor TR;Nicholls SM;Witney AA;Tyson GH;Tausch SH;Raphenya AR;Alcock B;Aanensen DM;Hodcroft E;Hsiao WWL;Vasconcelos ATR;MacCannell DR
基因组流行病学公共卫生联盟（PHA4GE） （https://pha4ge.org）是一个全球联盟，积极致力于建立共识标准，记录和分享最佳做法，改善关键生物信息学工具和资源的可得性，并倡导公共卫生微生物生物信息学的更大开放性、互操作性、可及性和可重复性。面对当前的大流行，PHA4GE已经确定需要一个合适的、开源的SARS-CoV-2背景数据标准。因此，我们根据可协调的、公开的社区标准制定了SARS-CoV-2上下文数据规范包。该规范可以通过收集模板以及一系列协议和工具来实现，以支持序列数据和上下文信息的协调和提交到公共生物储存库。结构良好的、丰富的上下文数据可以增加价值，促进重用，并支持不同数据集的聚合和集成。采用拟议的标准和实践将更好地实现数据集和系统之间的互操作性，提高生成数据的一致性和实用性，并最终促进对SARS-CoV-2和COVID-19的新见解和新发现。该软件包现在由NCBI的生物样本数据库支持。
The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.
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影响因子：
64.5
作者：
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通讯作者：
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影响因子：
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Dugan VG;Emrich SJ;Giraldo-Calderón GI;Harb OS;Newman RM;Pickett BE;Schriml LM;Stockwell TB;Stoeckert CJ Jr;Sullivan DE;Singh I;Ward DV;Yao A;Zheng J;Barrett T;Birren B;Brinkac L;Bruno VM;Caler E;Chapman S;Collins FH;Cuomo CA;Di Francesco V;Durkin S;Eppinger M;Feldgarden M;Fraser C;Fricke WF;Giovanni M;Henn MR;Hine E;Hotopp JD;Karsch-Mizrachi I;Kissinger JC;Lee EM;Mathur P;Mongodin EF;Murphy CI;Myers G;Neafsey DE;Nelson KE;Nierman WC;Puzak J;Rasko D;Roos DS;Sadzewicz L;Silva JC;Sobral B;Squires RB;Stevens RL;Tallon L;Tettelin H;Wentworth D;White O;Will R;Wortman J;Zhang Y;Scheuermann RH
通讯作者：
Scheuermann RH
DOI：
10.1126/science.abf2946
发表时间：
2021-02-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
du Plessis L;McCrone JT;Zarebski AE;Hill V;Ruis C;Gutierrez B;Raghwani J;Ashworth J;Colquhoun R;Connor TR;Faria NR;Jackson B;Loman NJ;O'Toole Á;Nicholls SM;Parag KV;Scher E;Vasylyeva TI;Volz EM;Watts A;Bogoch II;Khan K;COVID-19 Genomics UK (COG-UK) Consortium;Aanensen DM;Kraemer MUG;Rambaut A;Pybus OG
通讯作者：
Pybus OG