BIOBASE

Infobox Company
name = BIOBASE GmbH
type = Private
foundation = Wolfenbuettel, Germany (1997)
location_city = Wolfenbuettel
location_country = EU
key_people = Michael Tysiak (CFO)
Edgar Wingender (CSO)
industry = Bioinformatics, databases, software, services
products = BIOBASE Knowledge Library, TRANSFAC, Proteome databases, ExPlain, See more complete product listing
services = Knowledge process outsourcing, custom curation, ExPlain analysis
num_employees = ~150 (2008)
slogan = Biology explained

BIOBASE is an international bioinformatics company headquartered in Wolfenbüttel, Germany. Its focus is on the generation, maintenance and licensing of biological databases and connected software platforms.

History

BIOBASE was founded in 1997 as spin-off of the German Research Centre for Biotechnology (GBF), Braunschweig, Germany, today known as Helmholtz Research Centre for Infection Research. Among the four founders, three are still affiliated with the company (Edgar Wingender, Holger Karas, and Ingmar Reuter). Michael Tysiak (CEO/CFO) and Edgar Wingender (President/CSO) manage the company. Originally, the company was mainly founded for further development and commercial exploitation of the TRANSFAC database. This was subsequently complemented by a number of smaller databases on gene regulation issues (see below, Products and services) as well as by an early signaling pathway database (TRANSPATH). Next to the Cell Signaling Network Database (CSNDB) by T. Takai, this was the earliest signaling pathway database provided to the community in 1999.

By end of 1999, BIOBASE acquired venture capital from the IMH funds, now managed by the Avida Group, by the MBG (Hannover; until 2007) and the tbg. In 2002, Intec W&G, Tokyo, Japan, was investing as well and stayed as shareholder until 2005.

Early 2005, BIOBASE acquired the database business from Incyte, Wilmington, Delaware, USA, which was operated by the subsidiary Proteome Inc in Beverly, MA. The early flagship of Proteome was the Yeast Proteome Database (YPD) which was then complemented by a number of other, similar databases. The latest achievement before the acquisition was the Human Proteome Survey Database (HumanPSD).

ubsidiaries

BIOBASE GmbH has three fully-owned daughter companies:
* BIOBASE Corporation in Beverly/Massachusetts, USA (since 2005) [ [http://findarticles.com/p/articles/mi_m0EIN/is_2005_Jan_18/ai_n8699647 BIOBASE acquires Proteome from Incyte] ]
* BIOBASE Databases India Pvte Ltd. in Bangalore, India (since 2006) [ [http://biospectrumindia.ciol.com/content/news/40611091.asp BIOBASE opens Bangalore office] ]
* BIOBASE Japan K.K. in Yokohama, Japan (since 2007) [ [http://www.reuters.com/article/pressRelease/idUS242892+24-Jan-2008+BW20080124 BIOBASE opens Yokohama office] ]

Products and services

All BIOBASE databases provide manually curated contents. BIOBASE staff is collecting and structuring the required data from peer-reviewed scientific primary publications.

The BIOBASE Knowledge Library (BKL) is an integrated database comprising the following modules: [Wingender E, Crass T, Hogan JD, Kel AE, Kel-Margoulis OV, Potapov AP (2007) Integrative content-driven concepts for bioinformatics "beyond the cell". J Biosci. 32:169-80. PMID: 17426389]

* TRANSFAC: Eukaryotic transcription factors, their genomic DNA-binding sites and DNA-binding profiles [Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34(Database issue):D108-10. PMID: 16381825]
* TRANSCompel: Transcription regulating composite elements
* TRANSPro: Promoter sequences for 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 [Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D, Michael H, Schwarzer K, Potapov A, Choi C, Kel-Margoulis O, Wingender E (2006) TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34(Database issue):D546-51. PMID: 16381929]
* YPD: The complete yeast proteome (protein reports for all known Saccharomyces cerevisiae proteins) [Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI (2001). YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 29:75-9. PMID: 11125054]
* PombePD, MycopathPD: Proteomes of Schizosaccharomyces pombe and of pathological fungi [Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI (2001). YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 29:75-9. PMID: 11125054]
* WormPD: The proteome of Caenorhabditis elegans [Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI (2001). YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 29:75-9. PMID: 11125054]
* HumanPSD: The proteomes of human, mouse and rat [8]
* GPCR-PD: G-protein coupled receptor reports [Hodges PE, Carrico PM, Hogan JD, O'Neill KE, Owen JJ, Mangan M, Davis BP, Brooks JE, Garrels JI (2002) Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Res. 2002 Jan 1;30(1):137-41. PMID: 11752275]

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 for users from non-profit organizations.

A number of third-party products are distributed by BIOBASE as well:

* S/MARt DB: Scaffold/matrix attached regions (HZI Braunschweig) [Liebich I, Bode J, Frisch M, Wingender E (2002) S/MARt DB: a database on scaffold/matrix attached regions. Nucleic Acids Res. 30:372-4. PMID: 11752340]
* BRENDA: The BRaunschweig ENzyme DAtabase (Technical University Braunschweig/enzymeta) [ [http://fileserver.bioinfo.nat.tu-bs.de/bioinf/ Department of Bioinformatics and Biochemistry - Technical University of Braunschweig Germany ] ] [ [http://www.enzymeta.de/ enzymeta ] ]
* HGMD: The Human Genome Mutation Database (University of Cardiff) [ [http://www.hgmd.cf.ac.uk/ac/index.php HGMD® home page ] ]
* CI: Cell Illustrator for pathway simulations (Tokyo University/GNI, Tokyo) [ [http://www.csml.org/tools/cell-illustrator/ Cell System Markup Language (CSML) - Cell Illustrator ] ] http://www.cellillustrator.com/new_version] ]

Besides these products, BIOBASE offers Knowledge process outsourcing (KPO) services. These may comprise development and population of customized databases with specific contents, or systematic analyses of gene expression data.

cientific projects/Research

BIOBASE is a member of the following publicly funded research consortia, the first two of them being coordinated by BIOBASE (Alexander Kel): [ [http://europabio.euproject.eu/index.php/kb_3121/oe_1212/oe.html EU Projects at BIOBASE] ]

* 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 [ [http://findarticles.com/p/articles/mi_m0EIN/is_2007_March_27/ai_n18767478 Net2Drug] ]
* Sysco: Combined experimental, bioinformatics and simulation approaches to analyze intracellular parasitism (8 partners; funded under EU6) [ [http://www.biobase.de/pages/index.php?id=438 BIOBASE Biological Databases: SysCo - Functional Analysis ] ] [ [http://europabio.euproject.eu/index.php/kb_3121/io_610/io.html Home - Systematic functional analysis of intracellular parasitism as a model of genomes conflict ] ]
* TRANSISTOR: Bioinformatics modeling of plant regulatory circuits (7 partners; Marie-Curie Project funded under EU6) [ [http://www.biobase.de/pages/index.php?id=transistor BIOBASE Biological Databases: TRANSISTOR ] ]
* 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) [ [http://www.geneticsandhealth.com/2008/01/22/gen2phen-web-based-project-to-capture-health-disease-genetic-knowledge/ Gen2Phen] ]
* LipidomicNet: Identification of targets and biomarkers for 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 University of Göttingen, Göttingen, Germany (E. Wingender);
* Tokyo University 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; [Kel AE, Niehof M, Matys V, Zemlin R, Borlak J. (2008) Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context. Genome Biol. 9:R36. PMID: 18291023]
* Lawrence Berkeley National Laboratory, Berkeley/CA, USA (I. Dubchak); [Minovitsky S, Stegmaier P, Kel A, Kondrashov AS, Dubchak I (2007) Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics. 8:378. PMID: 17945028]

ee also

* Gene expression
* Bioinformatics
* Bioinformatics companies

References

External links

* [http://www.biobase-international.com Official website]
* [http://www.gene-regulation.com Gene Regulation Portal]
* [http://www.helmholtz-hzi.de/en/ Helmholtz Research Centre for Infection Research Official website]