The National Plant Genome Initiative Objectives for 2003-2008 (2002) / Chapter Skim
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6 Development of a National Strategy for Plant Bioinformatics
6 Development of a National Strategy for Plant Bioinformatics
Pages 41-50
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From page 41... ...
Making the data that are representative of the entire Kingdom of plant life available and usable to the scientific community is a major undertaking one that . requires a national strategy for plant bioinformatics.
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From page 42... ...
General databases wiD be needed to provide community services for the reference species, and they should be developed with community participation. The stewards of data and the creators of databases and tools should not act independently but should communicate and coordinate with each other and with public genome repositories to develop common platforms, standards, and interfaces.
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From page 43... ...
In general, it is neither desirable nor economically feasible to support separate databases for ad species; there must be other mechanisms, such as data warehousing for smaller projects in related community databases. In order for community databases to succeed, data maintenance needs to be recognized as a valid activity, and supported accordingly.
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From page 44... ...
As a data resource, these databases should be prepared to handle huge volumes of incoming data, annotate them automatically, present them to the research community in a timely fashion, work with the national data resources, and develop or adopt a curation model for the data. In addition, the databases must become a platform for comparative studies with data from related species, and their managers must recognize their responsibility as members of the larger genomics community.
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From page 45... ...
Development of a National Strategy for Plant Bioinformatics 45
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From page 46... ...
Relationship with national data repositories: Currently, community databases often incorporate data that are not validated, because including them can provide additional insights for users. However, these data often contain errors and are frequently asynchronous with data in the national public repositories (such as GenBank)
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From page 47... ...
Beyond the development of integrated information resources appropriate to the plant community, sophisticated analytical tools must be developed to handle the flow of large, multidimensional datasets and to allow biologists to analyze and interpret the data in an interactive fashion. Examples of this kind of specialized application are statistical analysis of microarrays, comparative sequence alignment and QTEs, and data mining.
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From page 48... ...
In the future, the development and maintenance of a genomics grid will allow many more investigators to participate in exploiting genomics data by making a vast array of data resources and computational tools generally available, thus leveling the playing field for biologic researchers. Like the databases themselves, algorithms, software, substantive scripts, and analytical methods developed and applied with support from the NPGI should be made freely available.
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From page 49... ...
Bioinformaticists who are responsible for community databases must be able to meet the projected demands of the community to incorporate increasingly diverse information into databases. There should be some support for database-design brainstorming sessions and for shortand long-term visits at a database or computing center (for example, to examine critical needs in new database construction or develop strategies for migration to improved hardware and software platforms)
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