BIOBASE
Encyclopedia
BIOBASE is an international bioinformatics company headquartered in Wolfenbüttel
, Germany
. Its focus is on the generation, maintenance and licensing of databases in the field of molecular biology, and their related software platforms.
, Germany
, known today as the Helmholtz Research Centre for Infection Research. Of the four founders, three are still affiliated with the company (Edgar Wingender, Holger Karas, and Ingmar Reuter). The company is presently managed by Michael Tysiak (CEO/CFO) and Frank Schacherer (COO).
Rgw company's original product was the TRANSFAC
database, a platform for the description and analysis of gene regulatory events and networks. This was subsequently complemented by a number of smaller databases relevant to aspects of gene regulation, and by an early signaling pathway database (TRANSPATH). Bugunin 1999, TRANSPATH constituted the earliest signaling pathway database, alongside the Cell Signaling Network Database (CSNDB) curated by T. Takai.
By end of 1999, BIOBASE acquired venture capital from the IMH funds, now managed by Triginta Capital, by the MBG (Hannover; until 2007) and the tbg. In 2002, Intec W&G, Tokyo, Japan, invested in the company and remained a shareholder until 2005.
With this funding, in early 2005, the company acquired the databases produced by Incyte, Wilmington, Delaware, USA, which were operated at the time by Incyte's subsidiary, Proteome Inc in Beverly, MA. The early flagship of Proteome was the Yeast Proteome Database (YPD) there was complemented by a number of similar databases. Their latest achievement before the acquisition was the Human Proteome Survey Database (HumanPSD).
The BIOBASE Knowledge Library (BKL) is an integrated database comprising the following modules:
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:
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.
In addition, BIOBASE has entered research partnerships with
Wolfenbüttel
Wolfenbüttel is a town in Lower Saxony, Germany, located on the Oker river about 13 kilometres south of Brunswick. It is the seat of the District of Wolfenbüttel and of the bishop of the Protestant Lutheran State Church of Brunswick...
, Germany
Germany
Germany , officially the Federal Republic of Germany , is a federal parliamentary republic in Europe. The country consists of 16 states while the capital and largest city is Berlin. Germany covers an area of 357,021 km2 and has a largely temperate seasonal climate...
. Its focus is on the generation, maintenance and licensing of databases in the field of molecular biology, and their related software platforms.
History
The company was founded in 1997 as a spin-off from the German Research Centre for Biotechnology (GBF), BraunschweigBraunschweig
Braunschweig , is a city of 247,400 people, located in the federal-state of Lower Saxony, Germany. It is located north of the Harz mountains at the farthest navigable point of the Oker river, which connects to the North Sea via the rivers Aller and Weser....
, Germany
Germany
Germany , officially the Federal Republic of Germany , is a federal parliamentary republic in Europe. The country consists of 16 states while the capital and largest city is Berlin. Germany covers an area of 357,021 km2 and has a largely temperate seasonal climate...
, known today as the Helmholtz Research Centre for Infection Research. Of the four founders, three are still affiliated with the company (Edgar Wingender, Holger Karas, and Ingmar Reuter). The company is presently managed by Michael Tysiak (CEO/CFO) and Frank Schacherer (COO).
Rgw company's original product was the TRANSFAC
TRANSFAC
TRANSFAC is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites....
database, a platform for the description and analysis of gene regulatory events and networks. This was subsequently complemented by a number of smaller databases relevant to aspects of gene regulation, and by an early signaling pathway database (TRANSPATH). Bugunin 1999, TRANSPATH constituted the earliest signaling pathway database, alongside the Cell Signaling Network Database (CSNDB) curated by T. Takai.
By end of 1999, BIOBASE acquired venture capital from the IMH funds, now managed by Triginta Capital, by the MBG (Hannover; until 2007) and the tbg. In 2002, Intec W&G, Tokyo, Japan, invested in the company and remained a shareholder until 2005.
With this funding, in early 2005, the company acquired the databases produced by Incyte, Wilmington, Delaware, USA, which were operated at the time by Incyte's subsidiary, Proteome Inc in Beverly, MA. The early flagship of Proteome was the Yeast Proteome Database (YPD) there was complemented by a number of similar databases. Their latest achievement before the acquisition was the Human Proteome Survey Database (HumanPSD).
Subsidiaries
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)Products and services
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
- 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 UniversityCardiff UniversityCardiff University is a leading research university located in the Cathays Park area of Cardiff, Wales, United Kingdom. It received its Royal charter in 1883 and is a member of the Russell Group of Universities. The university is consistently recognised as providing high quality research-based...
) - CI: Cell Illustrator for pathway simulations (Tokyo University/GNI, Tokyo)
In addition to these products, BIOBASE offers Knowledge process outsourcing
Knowledge process outsourcing
Knowledge process outsourcing is a form of outsourcing, in which knowledge-related and information-related work is carried out by workers in a different company or by a subsidiary of the same organization, which may be in the same country or in an offshore location to save cost...
(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) 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 TokyoUniversity of Tokyo, abbreviated as , is a major research university located in Tokyo, Japan. The University has 10 faculties with a total of around 30,000 students, 2,100 of whom are foreign. Its five campuses are in Hongō, Komaba, Kashiwa, Shirokane and Nakano. It is considered to be the most prestigious university...
, Tokyo, Japan (S. Miyano); - Windber Research InstituteWindber Research InstituteWindber Research Institute or WRI is a private, non-profit biomedical research institute that is focused on women's health, cardiovascular disease and processes of aging, is located on Somerset Avenue in Windber, PA...
& 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);