Data integration in microbial genomics ... - Jacobs University

More documents

Recommendations

Info

62 4. MIMARKS and sequencing contextual data, but extends them with further experimental contextual data such as PCR primers and conditions, or target gene name. For clarity and ease of use, all items within the MIMARKS checklist are presented with a value syntax description, as well as a clear definition of the item. Whenever terms from a specific ontology are required as the value of an item, these terms can be readily found in the respective ontology browsers linked by URLs in the item definition. Although this version of the MIMARKS checklist does not contain unit specifications, we recommend all units to be chosen from and follow the International System of Units (SI) recommendations. In addition, we strongly urge the community to provide feedback regarding the best unit recommendations for given parameters. Unit standardization across data sets will be vital to facilitate comparative studies in future. An Excel version of the MIMARKS checklist is provided on the GSC web site (). The MIxS environmental packages Fourteen environmental packages provide a wealth of environmental and epidemiological contextual data fields for a complete description of sampling environments. The environmental packages can be combined with any of the GSC checklists (Table 4.1 and Supplementary Results 2). Researchers within The Human Microbiome Project [Turnbaugh et al., 2007] contributed the host-associated and all human packages. The Terragenome Consortium contributed sediment and soil packages. Finally, ICoMM, Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites and the Max Planck Institute for Marine Microbiology contributed the water package. The MI- MARKS working group developed the remaining packages (air, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated and wastewater/sludge). The package names describe high-level habitat terms in order to be exhaustive. The miscellaneous natural or artificial environment package contains a generic set of parameters, and is included for any other habitat that does not fall into the other thirteen categories. Whenever needed, multiple packages may be used for the description of the environment. Examples of MIMARKS-compliant data sets Several MIMARKS-compliant reports are included in Supplementary
4.5. The MIMARKS checklist 63 Results 3. These include a 16S rRNA gene survey from samples obtained in the North Atlantic, an 18S pyrosequencing tag study of anaerobic protists in a permanently anoxic basin of the North Sea, a pmoA survey from Negev Desert soils, a dsrAB survey of Gulf of Mexico sediments and a 16S pyrosequencing tag study of bacterial diversity in the western English Channel (SRA accession no. SRP001108). Adoption by major database and informatics resources Support for adoption of MIMARKS and the MIxS standard has spread rapidly. Authors of this paper include representatives from genome sequencing centers, maintainers of major resources, principal investigators of large- and small-scale sequencing projects, and individual investigators who have provided compliant data sets, showing the breadth of support for the standard within the community. In the past, the INSDC has issued a reserved ‘barcode’ keyword for the CBOL7. Following this model, the INSDC has recently recognized the GSC as an authority for the MIxS standard and issued the standard with official keywords within INSDC nucleotide sequence records [Benson et al., 2008]. This greatly facilitates automatic validation of the submitted contextual data and provides support for data sets compliant with previous versions by including the checklist version as a keyword. GenBank accepts MIxS metadata in tabular format using the sequin and tbl2asn submission tools, validates MIxS compliance, and reports the fields in the structured comment block. The EBI-ENA Webin submission system provides prepared web forms for the submission of MIxS compliant data; it presents all of the appropriate fields with descriptions, explanations and examples, and validates the data entered. One tool that can aid submitting contextual data is MetaBar [Hankeln et al., 2010], a spreadsheet and web-based software, designed to assist users in the consistent acquisition, electronic storage and submission of contextual data associated with their samples in compliance with the MIxS standard. The online tool CDinFusion (http://www.megx.net/cdinfusion) was created to facilitate the combination of contextual data with sequence data, and generation of submission-ready files. The next-generation Sequence Read Archive (SRA) collects and dis-
Page 1:
Max Planck Institute for Marine Mic
Page 4 and 5:
List of abbreviations BLAST Basic L
Page 6 and 7:
Thesis abstract Deoxyribonucleic ac
Page 8 and 9:
4.2 Introduction . . . . . . . . .
Page 10 and 11:
2 1. Introduction syntax: data leve
Page 12 and 13:
4 1. Introduction used to derive ne
Page 14 and 15:
6 1. Introduction croorganisms thri
Page 16 and 17:
8 1. Introduction the middle at the
Page 18 and 19:
10 1. Introduction marker genes hel
Page 20 and 21: 12 1. Introduction what kind and wh
Page 22 and 23: 14 1. Introduction possibilities li
Page 24 and 25: 16 1. Introduction tual data acquis
Page 26 and 27: 18 1. Introduction Doug Wendel, Owe
Page 29 and 30: CHAPTER 2 METABAR A tool for consis
Page 31 and 32: 2.2. Background 23 molecular sequen
Page 33 and 34: 2.2. Background 25 printing of data
Page 35 and 36: 2.4. Results 27 KML export function
Page 37 and 38: 2.4. Results 29 Figure 2.3: Screens
Page 39 and 40: 2.5. Discussion 31 taking samples i
Page 41 and 42: 2.5. Discussion 33 Handlebar MetaBa
Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
Page 45: 2.6. Conclusion 37 RK advised progr
Page 48 and 49: 40 3. CDinFusion Genomic Standards
Page 50 and 51: 42 3. CDinFusion sortium (GSC), an
Page 52 and 53: 44 3. CDinFusion tiFASTA file with
Page 54 and 55: 46 3. CDinFusion offered the option
Page 56 and 57: 48 3. CDinFusion AMD Opteron TM pro
Page 58 and 59: 50 3. CDinFusion able separately an
Page 60 and 61: 52 3. CDinFusion and upload it with
Page 63 and 64: CHAPTER 4 MIMARKS The Minimum infor
Page 65 and 66: 4.2. Introduction 57 edge generatio
Page 67 and 68: 4.3. Development of MIMARKS 59 in t
Page 69: 4.4. Survey of published parameters
Page 73 and 74: 4.6. Conclusions and call for actio
Page 75 and 76: CHAPTER 5 MEGX.NET Integrated datab
Page 77 and 78: 5.3. New database structure and con
Page 79 and 80: 5.3. New database structure and con
Page 81 and 82: 5.4. User Access 73 5.4 User Access
Page 83 and 84: 5.4. User Access 75 tal context, co
Page 85: 5.5. Summary 77 access charge: Max
Page 88 and 89: 80 6. Domains of unknown function 6
Page 90 and 91: 82 6. Domains of unknown function F
Page 92 and 93: 84 6. Domains of unknown function p
Page 95 and 96: CHAPTER 7 SUMMARY AND DISCUSSION Th
Page 97 and 98: 7.2. GSC standards development 89 T
Page 99 and 100: 7.2. GSC standards development 91 o
Page 101 and 102: 7.4. In silico Hypothesis Generatio
Page 103: 7.5. Getting the most out of the da
Page 106 and 107: 98 8. Conclusion and outlook nities
Page 108 and 109: 100 8. Conclusion and outlook plina
Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
Page 114 and 115: 106 BIBLIOGRAPHY [Giovannoni et al.
Page 116 and 117: 108 BIBLIOGRAPHY [Kitano, 2002] Kit
Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
Page 120 and 121:
112 BIBLIOGRAPHY [Ramette, 2007] Ra
Page 122 and 123:
114 BIBLIOGRAPHY (2006). Microbial
Page 124 and 125:
116 BIBLIOGRAPHY [Williamson et al.
Page 127:
CHAPTER 9 ACKNOWLEDGEMENTS First, I
show all

Data integration in microbial genomics ... - Jacobs University

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?