Bioinformatics Converting Data to Knowledge (2000) / Chapter Skim
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Barriers to the Use of Databases
Barriers to the Use of Databases
Pages 11-16
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From page 11... ...
"The vast majority of databases are not actually accessible through the Internet right now," said Peter Karp, director of the Bioinformatics Research Group at SRI International in Menlo Park, California. If a database cannot be searched online, few researchers will take advantage of it even if, in theory, the information in it is publicly available.
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From page 12... ...
"We have many disciplines, many subfields," said Gio Wiederhold, of Stanford University's Computer Science Department, "and they are autonomous and must remain autonomous to set their own standards of quality and make progress in their own areas. We can't do without that heterogeneity." At the same time, however, "the heterogeneity that we find in all the sources inhibits integration." The result is what computer scientists call "the interoperability problem," which is actually not a single difficulty, but rather a group of related problems that arise when researchers attempt to work with multiple databases.
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From page 13... ...
There are also different data models: object-data models versus relational-data models versus ad hoc, invented-by-the-database-author data models. Daniel Gardner, of Cornell University, added, "it is interfaces, not uniformity, that can provide interoperability interfaces for data exchange and data-format description, interfaces to recognize data-model intersections, to exchange metadata and to parse queries." Wiederhold continued, "Another very important issue is the heterogeneity in user expertise.
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From page 14... ...
lust as the Internet connects a diverse set of geographically distributed locations, we have seen growth in a software infrastructure for connecting molecularbiology databases." Bioinformatics specialists have developed two broad approaches to integrating databases, each with its strengths and weaknesses. The first, which Karp referred to as the warehousing approach, combines a large number of individual databases in a single computer and lets outside users submit queries to that collection of databases.
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From page 15... ...
After the user formulates a question, a query processor transforms the question into individual queries sent to whichever of the various member databases might have information relevant to the original question. Later, the query engine receives and integrates the results of the individual queries and returns the results to the user.
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From page 16... ...
This will involve progress in multiple components of computer science and attention to the specific interests of biologists as data generators and users. It will also require biologists to present their needs in ways that excite database experts and other computer scientists to overcome the expertise scarcity noted by Karp.
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