Extending Standards for Genomics and Metagenomics Data: A Research Coordination Network for the Genomic Standards Consortium (RCN4GSC)
Tóm tắt
Through a newly established Research Coordination Network for the Genomic Standards Consortium (RCN4GSC), the GSC will continue its leadership in establishing and integrating genomic standards through community-based efforts. These efforts, undertaken in the context of genomic and metagenomic research aim to ensure the electronic capture of all genomic data and to facilitate the achievement of a community consensus around collecting and managing relevant contextual information connected to the sequence data. The GSC operates as an open, inclusive organization, welcoming inspired biologists with a commitment to community service. Within the collaborative framework of the ongoing, international activities of the GSC, the RCN will expand the range of research domains engaged in these standardization efforts and sustain scientific networking to encourage active participation by the broader community. The RCN4GSC, funded for five years by the US National Science Foundation, will primarily support outcome-focused working meetings and the exchange of early-career scientists between GSC research groups in order to advance key standards contributions such as GCDML. Focusing on the timely delivery of the extant GSC core projects, the RCN will also extend the pioneering efforts of the GSC to engage researchers active in developing ecological, environmental and biodiversity data standards. As the initial goals of the GSC are increasingly achieved, promoting the comprehensive use of effective standards will be essential to ensure the effective use of sequence and associated data, to provide access for all biologists to all of the information, and to create interdisciplinary opportunities for discovery. The RCN will facilitate these implementation activities through participation in major scientific conferences and presentations on scientific advances enabled by community usage of genomic standards.
Tài liệu tham khảo
Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glockner FO, Kottmann R, Angiuoli S, et al. Meeting report: the fifth Genomic Standards Consortium (GSC) workshop. OMICS 2008;12(2):109–113 PMID:18564915 doi:10.1089/omi.2008.A3B3
Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, Field D, Glockner FO. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS 2008;12(2):115–121 PMID:18479204 doi:10.1089/omi.2008.0A10
Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glockner FO, Cole J, Farris R, Schriml LM, De Vos P, et al. Laying the foundation for a Genomic Rosetta Stone: creating informationhubs through the use of consensus identifiers. OMICS 2008;12(2):123–127 PMID:18479205 doi:10.1089/omi.2008.0020
Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N, et al. Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS 2008;12(2):129–136 PMID:18416669 doi:10.1089/omi.2008.0016
Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glockner FO, Kolker E, Kowalchuk G, et al. Toward a standards-compliant genomic and metagenomic publication record. OMICS 2008;12(2):157–160 PMID:18564916 doi:10.1089/omi.2008.A2B2
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. Omics 2008; 12:137–141 PMID:18416670 doi:10.1089/omi.2008.0017
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S; Members of the RSBI Working Group. (2008) The first RSBI (ISA-TAB) workshop: “can a simple format work for complex studies?”. OMICS. 12(2):143–9 PMID 18447634 doi:10.1089/omi.2008.0019
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, et al., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotech. 2008; 26:889–896. PMID 18688244 doi:10.1038/nbt.1411
San Gil, I, Sheldon W, Schmidt T, Servilla M, Aguilar R, Gries C, Gray T, Field D, Cole J, Pan JY, Palanisamy G, Henshaw D, O’Brien M, Kinkel L, McMahon K, Kottmann R, Amaral-Zettler L, Hobbie J, Goldstein P, Guralnick RP, Brunt J, Michener WK.(2008) Defining linkages between the GSC and NSF’s LTER program: how the Ecological Metadata Language (EML) relates to GCDML and other outcomes. OMICS.12(2):151–6. PMID 18407745 doi:10.1089/omi.2008.0015