BIOBASE GmbH has three fully owned daughter companies: BIOBASE Corporation in Beverly/Massachusetts, USA (since 2005), BIOBASE Databases India Pvt Ltd. in Bangalore, India (since 2006), and BIOBASE Japan K.K. in Yokohama, Japan (since 2007).
The company's databases provide manually curated content, collected and structured from peer-reviewed scientific primary publications.
The BIOBASE Knowledge Library (BKL) is an integrated database comprising the following modules:
TRANSFAC: Eukaryotic transcription factors, their genomic DNA-binding sites and DNA-binding profiles
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TRANSCompel: Transcription regulating composite elements
TRANSPro: Promoter sequences from a number of selected eukaryotic species
PathoDB: Pathologically relevant mutations in transcription factors and their binding sites
TRANSPATH: Signal transduction and metabolic pathways in mammalian species
YPD: The complete yeast proteome (protein reports for all known Saccharomyces cerevisiae proteins)
PombePD, MycopathPD: Proteomes of Schizosaccharomyces pombe and of pathological fungi
WormPD: The proteome of Caenorhabditis elegans
HumanPSD: The proteomes of human, mouse and rat [8]
GPCR-PD: G-protein coupled receptor reports
In addition, BIOBASE has developed the ExPlain system for the biological interpretation of gene expression and proteomics data by integrated functional, promoter and pathway analysis.
The "Gene Regulation Portal" offers a number of earlier revisions of company products free of charge to users from non-profit organizations.
A number of third-party products are also distributed by BIOBASE:
S/MARt DB: Scaffold/matrix attached regions (HZI Braunschweig)
BRENDA: The BRaunschweig ENzyme DAtabase (Technical University Braunschweig Enzymeta)
HGMD: The Human Gene Mutation Database (Cardiff University)
CI: Cell Illustrator for pathway simulations (Tokyo University/GNI, Tokyo)
In addition to these products, BIOBASE offers Knowledge process outsourcing (KPO) services. These may comprise the development and population of customized databases with specific contents, or systematic analyses of gene expression data.
Scientific projects/research
BIOBASE is a member of the following publicly funded research consortia, the first two of them being coordinated by BIOBASE (Alexander Kel):
Net2Drug: Integrated Labwork, Bio- and Cheminformatics technology for fighting breast cancer (9 partners; funded under EU6) https://web.archive.org/web/20110111035825/http://www.biobase.de/pages/index.php?id=437
Sysco: Combined experimental, bioinformatics and simulation approaches to analyze intracellular parasitism (8 partners; funded under EU6)
TRANSISTOR: Bioinformatics modeling of plant regulatory circuits (7 partners; Marie-Curie Project funded under EU6)
Valapodyn: Dynamic modeling of data on brain pathologies (7 partners; funded under EU6)
Eurodia: Potential targets for prevention and treatment of dysfunctional insulin secretion in type 2 diabetes (20 partners; funded under EU6)
Gen2Phen: Unified genotype-phenotype database (19 partners; funded under EU7)
LipidomicNet: Identification of targets for and biomarkers of energy overload diseases through lipid protein interactions (21 partners; funded under EU7);
GlobCell: Global scale analysis and prediction of human cellular behaviour in a complex environment (4 partners; funded by Eurotrans-Bio, ETB).
TCellTalk: (3 partners; funded by German Ministry of Research in the Forsys partnering program)
In addition, BIOBASE has entered research partnerships with
University Medicine of Georg August University of Göttingen, Göttingen, Germany (E. Wingender);
University of Tokyo, Tokyo, Japan (S. Miyano);
Windber Research Institute & Strategic Medicine, Inc, Windber/PA, USA (M. Liebman);
Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany;
Lawrence Berkeley National Laboratory, Berkeley/CA, USA (I. Dubchak)
