Data integration in microbial genomics ... - Jacobs University

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90 7. Summary and discussion and descriptions using this web service. The standard development was a transparent and open process. The strength of the community-based standard development process is for sure that many people can contribute. The drawback is the slow pace with which this is done. This is due to frequent reiterations and a very eloborate decision making process. It took almost three years to publish this standard. Because many people and institutions all over the world were involved, this again increases the chance that it will be used by the community. A confusing fact about the MIxS standards is that they are intended to be minimal, which is also reflected in the names of the standards. The community-based development process, however, lead to the fact, that these standards are comprehensive rather than minimal. It is of course difficult to estimate which parameters are relevant and which are not. Of course not all parameters in the standards are mandatory. Users are confronted with long lists of parameters and need to decide which parameters to use and which not. This process might be overwhelming at first. For data integration and the contextualization of sequence data, it is a very important step forward that the MIMARKS standard is now published. However, the standards leave plenty of room for improvement. Currently, most of the MIxS parameters are free-text fields. To extract information out of these fields automatically, is not trivial, from a computational point of view [Hirschman et al., 2008]. All possible variations and ambiguities of natural language have to be taken into account to interpret the information in these fields correctly. Correct interpretation cannot be guaranteed. It is recommended to use SI units http://www.bipm.org/en/CGPM/db/11/12/ for measurements, though this is not strictly enforced. Controlled vocabularies or even ontology terms are, with the exception of the environmental ontology (EnvO) terms, not offered to the users. These are things that should be taken into account for the annually planned updates of the standard. Stability versus ’living standards’ It has to be noted that even though the MIxS standards are intended to be ’living standards’, it is very important from a programmer’s and user’s point of view to have stability. The planned annual refinement
7.2. GSC standards development 91 of the standard is in this respect a rather short frequency 2 . In order to have compatibility, consistency and function, stability is needed. Refinements should be done in a way that consistency and compatibility are not hampered. Still, a lot of implementation work needs to be done. Even though the basic mechanisms to store the data are present at the INSDC databases, validation routines have to be implemented. GenBank for example has enforced these routines for MIGS fields after they were available in June 2008, but not yet for MIMARKS. When this is all set, special tools need to be available for all kinds of use case scenarios. Adoption of MIxS standards Though the GSC is an open and democratic consortium the GSC members occupy mainly higher hierarchical positions in science. There are not many developers and users among the GSC members. Therefore, it can be observed that the MIxS standards are being propagated to the community ’top-down’ rather than ’bottom-up’, when professors or group leaders decide, their people should use the MIxS standards. Ultimately, life science journals and the INSDC database providers are in the position to require the deposition of contextual data along with publications. If the contextual data submission becomes a requirement the adoption will follow naturally. If these standards are adopted, it will be worthwhile to refine them ’bottom-up’. For this it would be a favourable approach to observe, what turns out to be best-practices. Tool developers and more importantly users should be asked for improvements. This could be done in surveys, by analyzing the scientific literature and last but not least by analyzing the data that accumulates in the INSDC. If for example a certain parameter is not used over a couple of years, it should be removed from a standard that is intended to be minimal 3 . If best practices are taken into account in the years to come, the chance of a wide impact will greatly increase. The MIxS tracker 2 If the standard that defines the winding of screws would be changed annually, it would be very hard for the industry to keep up with the production of standard-compliant screws and for the users it would be even harder to screw things together. The same holds true for software. 3 Something can be considered to be minimal, if no parts can be removed without loosing content.
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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4 1. Introduction used to derive ne
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6 1. Introduction croorganisms thri
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8 1. Introduction the middle at the
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10 1. Introduction marker genes hel
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12 1. Introduction what kind and wh
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14 1. Introduction possibilities li
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16 1. Introduction tual data acquis
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18 1. Introduction Doug Wendel, Owe
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CHAPTER 2 METABAR A tool for consis
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2.2. Background 23 molecular sequen
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2.2. Background 25 printing of data
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2.4. Results 27 KML export function
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2.4. Results 29 Figure 2.3: Screens
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2.5. Discussion 31 taking samples i
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2.5. Discussion 33 Handlebar MetaBa
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2.6. Conclusion 35 rine Microbiolog
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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 and 70: 4.4. Survey of published parameters
Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
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Page 75 and 76: CHAPTER 5 MEGX.NET Integrated datab
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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
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Page 106 and 107: 98 8. Conclusion and outlook nities
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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
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Data integration in microbial genomics ... - Jacobs University

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