Abstract: We have built Drug2Gene, a knowledge base, which combines the compound/drug-gene/protein information from 19 publicly available databases. A key feature is our rigorous unification and standardization process which makes the data truly comparable on a large scale, allowing for the first time effective data mining in such a large knowledge corpus. As of version 3.2, Drug2Gene contains 4,372,290 unified relations between compounds and their targets most of which include reported bioactivity data. We extend this set with putative (i.e. homology-inferred) relations where sufficient sequence homology between proteins suggests they may bind to similar compounds. Drug2Gene provides powerful search functionalities, very flexible export procedures, and a user-friendly web interface... more

Abstract: Recently, several methods for analyzing phenotype data have been published, but only few are able to cope with data sets generated in different studies, with different methods, or for different species. We developed an online system in which more than 300 000 phenotypes from a wide variety of sources and screening methods can be analyzed together. Clusters of similar phenotypes are visualized as networks of highly similar phenotypes, inducing gene groups useful for functional analysis. This system is part of PhenomicDB, providing the world's largest cross-species phenotype data collection with a tool to mine its wealth of information... more

Abstract: The processing of breast specimens suspicious of ductal carcinoma in situ (DCIS) is hampered by the fact that DCIS is not regularly visible at the gross level. There is no general consensus as how to process those breast specimens. Suggestions lead from examination of the entire tissue sample with a special focus on the resection margins to algorithms such as cutting only those paraffin blocks containing calcifications... more

Abstract: Phenotypes are an important subject of biomedical research for which many repositories have already been created. Most of these databases are either dedicated to a single species or to a single disease of interest. With the advent of technologies to generate phenotypes in a high-throughput manner, not only is the volume of phenotype data growing fast but also the need to organize these data in more useful ways... more

Abstract: We have created PhenomicDB, a multi-species genotype/phenotype database by merging public genotype/phenotype data from a wide range of model organisms and Homo sapiens... more

"To know exactly what function has a gene is for us of essential importance. During the analysis of gene functions we collect enormous amount of data. Because of this we need optimal software tools." says Dr. Hans Kast, CEO BASF Plant Science GmbH. For this reason, the Microsoft Gold Certified Partner Metalife together with BASF Plant Science and their partners HP and Intel developed a cutting-edge software system, that helps the researchers to search and explore biological databases more efficiently... more (in German)

Looking to optimize the world?s largest fully integrated life sciences knowledge base, BASF Plant Science implemented Microsoft Windows® 2003, SQL Server 2005 Enterprise Edition, metalife trinity, Visual Studio® 2003 and 2005, and the Microsoft .NET Framework. These solutions allowed the company to combine semantic data integration, text mining and knowledge generation to help researchers activate, compare and analyze data from sources across various areas. The enterprise-wide aggregation of information and transformation into knowledge enabled BASF Plant Science to uniformly access and utilize all associated life sciences data. Metalife?s application, which can be easily enrolled on a large number of Windows clients, also drastically reduces administration expenses, by giving users easy-to-use and intuitive interfaces and complete control of tasks from database updates to user management...
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Metalife is helping researchers who are seeking new treatments and cures for a range of diseases. The company?s PhenomicDB database provides a central repository for genetic information from the Human Genome Project and similar efforts. As the success of Metalife?s database has grown, so has demand for support for concurrent, full-text searches against its database... more

You've seen DNA sequence databases for hundreds of species and protein sequence databases for probably an equal number. Interestingly, you've probably rarely, if ever, seen databases on phenotypes arising from these genes. This is an excellent reminder of how far molecular biology knowledge has progressed. Even 20 years ago, our knowledge of biology was far more focused on phenotype than on genotype. Phenotypes ARE important, however, and it is good to see databases like PhenomicDB providing online access links to phenotypes AND genotypes as information from the latter overwhelms that of the former... more

Intervet Innovation, a subsidiary of Intervet, operates a BioChemInformatics (BCI) division. BCI uses advanced computer modeling techniques to search for new animal medicines, but its existing infrastructure could not support the effective integration and analysis of internal and online research databases. Working with Microsoft Gold Certified Partner Metalife, the BCI division built a new high-performance computing infrastructure based on the 64-bit Microsoft Windows Server 2003 operating system and 64-bit Microsoft SQL Server 2000 database... more