National Collaboratories Applying Information Technology for Scientific Research (1993) / Chapter Skim
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4 BUILDING COLLABORATORIES FOR MOLECULAR BIOLOGY
4 BUILDING COLLABORATORIES FOR MOLECULAR BIOLOGY
Pages 41-55
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From page 41... ...
In addition several prototypes that support collaboration are in use now, and a mode! colIaboratory, the Worm Community System, illustrates a potential future direction for community information systems that support retrieval, analysis, and sharing of essential data and literature.
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From page 43... ...
However, the printed literature is no longer adequate for sharing such data, partly because of the economics of charges for the journal pages needed to print the long sequences, but largely because computer examination of the sequences is far more effective than human examination of the data on a printed page. As a result, it has become standard procedure for investigators to use sequence databases such as GenBank and mapping databases such as the Genome Data Base in their research and to submit new results to be incorporated into the databases.
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From page 44... ...
MedLine developed methods for electronic searching and retrieval of bibliographic information, GenBank developed methods for direct electronic data submission, and the Genome Data Base developed techniques for electronic checking of data by individuals at workstations distributed literally around the world. Each of these projects costs several million dollars per year to operate.
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From page 45... ...
Searching of the GenBank database rarely involves manually examining many sequences with a coarse search criterion; instead, an analysis program using some form of similarity matching is utilized. Because such analysis programs tend to be slow and the database is still relatively small, GenBank is
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From page 46... ...
A program available at no cost to scientists provides an interactive form for entering the sequence data and the appropriate annotations and then electronically mailing this information to the central archive. Individual researchers as well as large-scale sequencing projects submit data to GenBank, and essentially every sequence submitted is incorporated into the database.
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From page 47... ...
This 10-fold increase in production was made possible by leveraging the efforts of the entire genome research community. Electronic data publishing has also simplified collaboration with subscribers to other international databanks (e.g., the European Molecular Biology laboratory Data Library and the Database of Japan, each of which exchanges new entries daily via the Internet.
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From page 48... ...
Interrelating these sources is an essential component of genome research, largely because the available knowledge is now so incomplete. To obtain as much information as possible about the biological fimction of the genes they are studying, researchers consult and interrelate gene lists, genetic maps, DNA sequence data, formal and informal literature, and other sources of information.
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From page 49... ...
A complete analysis environment must enable analysis of the similarity of relationships among items not only within a single database, but also across multiple databases. To ensure that multiple sources can be easily interlinked, it is necessary to define a standard format for passing items between analysis programs.
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From page 50... ...
For example, both DNA sequence and protein sequence databases often mention the corresponding gene name for a given organism. These common names could be used automatically as points of interconnection if there were a standard nomencIature for naming genes.
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From page 51... ...
Adoption of a standard interface for passing data between analysis servers would greatly facilitate development of a complete analysis environment. For example, any server that manipulates DNA sequence data should be able to pass and return the same representation for a sequence.
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From page 52... ...
A complete electronic publishing environment will support entry of all the specific types of knowledge and publishing in all the different styles. With such a system, for example, an investigator will be able to run a program that enables interactive specification of a restriction map or preparation of a newsletter article and then automatically submits it to a central archive, which then automatically distributes it to the community.
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From page 53... ...
As the publishing system and the electronic community evolve, subsequent releases will support deeper knowledge semantics and begin to move toward a generic information infrastructure. OPPORTUNITIES TO ENHANCE RESEARCH Genome research in molecular biology has undergone a signif~cant revolution owing to the existence of archival databases such as MedLine, GenBank, and the Genome Data Base.
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From page 54... ...
Note that each of the items shown (literature, gene, map, sequence) comes originally from its own database, but the community information system enables navigation across all d~ese sources with single, uniform commands.
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From page 55... ...
Gel electrophoresis is a method of separating large molecules in an electric field, allowing DNA fragments differing by single bases to be readily separated. Combined with methods such as Sanger's dideoxynucleotide chain termination procedure, gel electrophoresis can produce ladders of DNA molecules from which DNA sequences can be determined.
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