Standardized metadata for human pathogen/vector genomic sequences.
Standardized metadata for human pathogen/vector genomic sequences.
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DOI：
10.1371/journal.pone.0099979
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Scheuermann RH
中科院分区：
文献类型：
--
作者：
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
高通量测序加速了数千种人类传染病病原体及其数十种载体的基因组序列的确定。这些数据的规模和范围使基因-表型关联研究能够确定病原体毒力和药物/杀虫剂耐药性的遗传决定因素，并使系统发育研究能够跟踪疾病暴发的来源和传播。为了最大限度地利用基因组序列用于这些目的，必须收集关于病原体/病媒分离特征的元数据，并以有组织、清晰和一致的格式提供。在这里，我们报告GSCID/BRC项目和样本应用标准的开发，该项目和样本应用标准由传染病基因组测序中心(GSCID)、传染病生物信息学资源中心(BRCs)和美国国家过敏和传染病研究所(NIAID)的代表开发，NIAID是美国国家卫生研究院(NIH)的一部分，通过与众多合作科学家的互动了解情况。它包括映射到其他数据标准倡议的术语，包括基因组标准联盟的最小信息(MIXS)和NCBI的生物样本/生物项目核对表和生物医学调查本体(OBI)。该标准包括关于样本的生物体或环境来源特征的数据域、关于样本隔离事件的时空信息、所分离病原体/病媒的表型特征以及项目领导和支持。通过将元数据字段建模为基于本体的语义框架，并重用现有的本体和最小信息核对表，应用标准可以被扩展以支持额外的特定于项目的数据字段，并与用可比标准表示的其他数据集成。所有正在进行的和未来的GSCID测序项目使用这一元数据标准，将在BRC资源和其他利用这些数据的储存库中提供这些数据的一致表示，使研究人员能够确定相关的基因组序列，并执行具有统计意义和生物相关性的比较基因组学分析。
High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.
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DOI：
10.1093/bioinformatics/bts718
发表时间：
2013-02-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Maguire E;González-Beltrán A;Whetzel PL;Sansone SA;Rocca-Serra P
通讯作者：
Rocca-Serra P
影响因子：
46.9
作者：
Smith, Barry;Ashburner, Michael;Lewis, Suzanna
通讯作者：
Lewis, Suzanna
影响因子：
46.9
作者：
Taylor, Chris F.;Field, Dawn;Sansone, Susanna-Assunta;Aerts, Jan;Apweiler, Rolf;Ashburner, Michael;Ball, Catherine A.;Binz, Pierre-Alain;Bogue, Molly;Booth, Tim;Brazma, Alvis;Brinkman, Ryan R.;Clark, Adam Michael;Deutsch, Eric W.;Fiehn, Oliver;Fostel, Jennifer;Ghazal, Peter;Gibson, Frank;Gray, Tanya;Grimes, Graeme;Hancock, John M.;Hardy, Nigel W.;Hermjakob, Henning;Julian, Randall K., Jr.;Kane, Matthew;Kettner, Carsten;Kinsinger, Christopher;Kolker, Eugene;Kuiper, Martin;Le Novere, Nicolas;Leebens-Mack, Jim;Lewis, Suzanna E.;Lord, Phillip;Mallon, Ann-Marie;Marthandan, Nishanth;Masuya, Hiroshi;McNally, Ruth;Mehrle, Alexander;Morrison, Norman;Orchard, Sandra;Quackenbush, John;Reecy, James M.;Robertson, Donald G.;Rocca-Serra, Philippe;Rodriguez, Henry;Rosenfelder, Heiko;Santoyo-Lopez, Javier;Scheuermann, Richard H.;Schober, Daniel;Smith, Barry;Snape, Jason;Stoeckert, Christian J., Jr.;Tipton, Keith;Sterk, Peter;Untergasser, Andreas;Vandesompele, Jo;Wiemann, Stefan
通讯作者：
Wiemann, Stefan
DOI：
10.1093/bioinformatics/btq415
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Rocca-Serra P;Brandizi M;Maguire E;Sklyar N;Taylor C;Begley K;Field D;Harris S;Hide W;Hofmann O;Neumann S;Sterk P;Tong W;Sansone SA
通讯作者：
Sansone SA
影响因子：
14.9
作者：
Pagani I;Liolios K;Jansson J;Chen IM;Smirnova T;Nosrat B;Markowitz VM;Kyrpides NC
通讯作者：
Kyrpides NC