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{bio,medical} informatics


Thursday, March 22, 2001

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find related articles. powered by google. ZDNet IBM Experiments With XML
"Besides the proposed query language, IBM has built an experimental "dataless" database system that gets the user the information needed from a variety of sources by breaking down a query into its parts. Each part is addressed to the database system or repository that can supply an answer, even though the data may reside in radically different systems and formats. When the results come back, they are assembled as one report or assembled view to the user."

"The system will be a "virtual database" or a federation of heterogeneous databases, and a pilot Discovery Link system has been in use for several months by pharmaceutical companies trying to research and manufacture new drugs.

"Pharmaceutical companies have the highest pain point" in trying to assemble diverse data, noted Jim Kleewein, developer of DataJoiner, an IBM predecessor product that extracts data from known sources. The drug companies are trying to combine information gleaned from the human genome, bio-informatic databases where human responses to chemical compounds are stored and new chemical interaction databases."
redux [03.11.01]
find related articles. powered by google. Health Informatics Europe Data warehouse deployment in pharmaceuticals increasing by 36% a year
"Research by Silico Research concludes that the deployment of data warehousing technology is widespread in the pharmaceutical, biotechnology and genomic sectors, with 77% of companies surveyed currently deploying at least one data warehouse somewhere in the R&D pipeline. Virtually all those who are not deploying data warehousing technology today expect to be doing so by 2004. This implementational build-out will combine with the fact that individual biopharmaceutical companies are deploying more warehouses across more functions to increase the number of warehouses in the sector by 36% a year and by 150% over the next three to four years."

"Today, data warehouse deployment is focused at the departmental level. "Companies believe, as a article of faith, that they should link scientists and researchers across the enterprise. How they go about doing this is another matter. We're seeing a lot of testing of federated and virtual warehouses and other middleware solutions but no clear answers so far", continued Emmett Power."

find related articles. powered by google. Peter Karp A Vision of DB Interoperation
"To realize the full potential of biological databases requires more than the interactive, hypertext flavor of database interoperation that is now so popular in the bioinformatics community. Interoperation based on declarative queries to multiple network-accessible databases will support analyses and investigations that are orders of magnitude faster and more powerful than what can be accomplished through interactive navigation. I present a vision of the capabilities that a query-based interoperation infrastructure should provide, and identify assumptions behind, and requirements of, this vision. I then propose an architecture for query-based interoperation that identifies a number of novel components of an information infrastructure for molecular biology. Those components include: A knowledge base that describes relationships among the conceptualizations used in different biological databases; a module that can determine what known DBs are relevant to a particular query; a module that can translate a query, or the results of a query, from one conceptualization to another; a family of DB drivers that provide uniform physical access to different DBMSs; a family of translators that can interconvert among different database schema languages; and a database that describes the network location and access methods for biological databases. A number of the components are translators because biological databases exhibit heterogeneity at several different levels, including the conceptual level, the data model, the query language, and data formats."

redux [02.28.01]
find related articles. powered by google. PENN Database Research Group K2/Kleisli and GUS: Experiments in integrated access to genomic data sources
"The integration of heterogeneous data sources and software systems is a major issue in the biomedical community and several approaches have been explored: linking databases, ``on-the-fly'' integration through views, and integration through warehousing. In this paper we report on our experiences with two systems that were developed at the University of Pennsylvania: an integration system called K2, which has primarily been used to provide views over multiple external data sources and software systems; and a data warehouse called GUS which downloads, cleans, integrates and annotates data from multiple external data sources. Although the view and warehouse approaches each have their advantages, there is no clear ``winner''. Therefore, users must consider how the data is to be used, what the performance guarantees must be, and how much programmer time and expertise is available to choose the best strategy for a particular application. Our experiences also point to some practical tips on how updates should be published by the community, and how XML can be used to facilitate the processing of updates in a warehousing environment."

redux [01.17.01]
find related articles. powered by google. The Collection of Computer Science Bibliographies Bibliography on Mediation, Database Integration, Database Interoperability and related topics
"personal bibliography on query mediation, database integration, database interoperability and related topics, concentrating on projects in genomic research. "


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Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.

BIOINFORMATICS IN THE 21st CENTURY

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