Tuesday, July 10, 2001

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"DoubleTwist, Inc. today announced that the genomic annotation XML format used to create its annotated human genome database is now freely available as an open standard to the life sciences community. AGAVE (Architecture for Genomic Annotation, Visualization and Exchange) allows users to manage, visualize and share annotations of genomic sequences using the document type definition (DTD) and associated tools available through www.agavexml.org."

"AGAVE was originally developed as part of DoubleTwist's bioinformatics architecture for high-throughput analysis of the human genome, which relies heavily on XML and Java technologies and tools. Central to AGAVE is a Java Object Model and a corresponding XML Document Type Definition (DTD) that facilitate data exchange, data integration and data transformation between components."

Agave.Org Introduction

"The design goals of AGAVE are to provide a comprehensive, extensible, open and readable markup language for genomic annotation. AGAVE is comprehensive because it can represent all the relevant biological data in public databases such as NCBI's GenBank, including the full sequence location format. It is extensible because it uses generic elements for computational results that can easily be used to capture results from new sequence annotation algorithms. Because AGAVE is XML-based, it is easy to use as an open standard for data storage and exchange. You can write programs to manipulate and extract genomic data using standard XML libraries, and you can easily transform data in the AGAVE format from and to other XML-based formats using tools such as XSLT (eXtensible Style Language Transformation). For example, you can easily transform data in GAME format to AGAVE format using XSLT templates. To aid readability, AGAVE focuses on biological data and uses standard biological terminology with a minimum of abbreviation."

GenomeWeb Incyte Outsources Genomics Knowledge Platform to Secant Technologies

"Recognizing that its Genomics Knowledge Platform has capabilities that exceed its own in-house research needs, Incyte Genomics awarded Secant Technologies an exclusive license to develop and market the data integration software platform, company officials said Monday."

"The platform, launched last November, provides tools for researchers to integrate and analyze a wide range of data, from gene sequence, expression, polymorphism, proteomic, and other functional data. The object model-based platform currently uses IBM's DiscoveryLink data integration software to integrate, or "federate," Incyte's multiple databases to make them appear to the user as a single source."

Yahoo! Finance Biomax Informatics AG Licenses the BioRS Integration and Retrieval Plus System to Millennium Pharmaceuticals, Inc

"Biomax Informatics AG announced today that Millennium Pharmaceuticals, Inc. (Nasdaq: MLNM - news) has licensed the BioRS(TM) Integration and Retrieval Plus System (version 4.0)"

""Millennium's unique approach to drug discovery and development is at the forefront of the industry," said Tim Clark, vice president, informatics at Millennium. "As a result, we are continuously evaluating software and technology products, and services that will help us enhance our productivity. We performed an extensive analysis of the BioRS system over several months and it proved to be a stable, comprehensive and efficient system. The speed and agility with which we assess drug targets in our gene-to-patient platform requires a system that can handle a broad spectrum of user scenarios for large data volumes. The BioRS system has the potential to meet our aggressive needs."

redux [03.22.01]
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]
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."