User:Onemunk/BIOBASE

+++++ Under Construction ++++++++

BIOBASE Biological Databases GmbH

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).

Subsidiaries

BIOBASE GmbH has three fully-owned daughter companies:
 * BIOBASE Corporation in Beverly/Massachusetts, USA (since 2005)[1]
 * BIOBASE Databases India Pvte Ltd. in Bangalore, India (since 2006) [2]
 * BIOBASE Japan K.K. in Yokohama, Japan (since 2007) [3]

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: [4]


 * TRANSFAC: Eukaryotic transcription factors, their genomic DNA-binding sites and DNA-binding profiles [5]
 * 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 [6]
 * YPD: The complete yeast proteome (protein reports for all known Saccharomyces cerevisiae proteins) [7]
 * PombePD, MycopathPD: Proteomes of Schizosaccharomyces pombe and of pathological fungi [7]
 * WormPD: The proteome of Caenorhabditis elegans [7]
 * HumanPSD: The proteomes of human, mouse and rat [8]
 * GPCR-PD: G-protein coupled receptor reports [8]

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” www.gene-regulation.com 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) [9]
 * BRENDA: The BRaunschweig ENzyme DAtabase (Technical University Braunschweig / enzymeta) http://fileserver.bioinfo.nat.tu-bs.de/bioinf/; http://www.enzymeta.de/
 * HGMD: The Human Genome Mutation Database (University of Cardiff) http://www.hgmd.cf.ac.uk/ac/index.php
 * CI: Cell Illustrator for pathway simulations (Tokyo University / GNI, Tokyo) http://www.csml.org/tools/cell-illustrator/; http://www.cellillustrator.com/new_version

Besides these products, BIOBASE offers KPO (Knowledge process outsourcing) services. These may comprise 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): [10]


 * 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 [11]
 * 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, http://europabio.euproject.eu/index.php/kb_3121/io_610/io.html
 * TRANSISTOR: Bioinformatics modeling of plant regulatory circuits (7 partners; Marie-Curie Project funded under EU6) http://www.biobase.de/pages/index.php?id=transistor
 * Valapodyn: Dynamic modeling of data on brain pathologies (7 partners; funded under EU6) http://www.valapodyn.eu/
 * Eurodia: Potential targets for prevention and treatment of dysfunctional insulin secretion in type 2 diabetes (20 partners; funded under EU6) http://www.eurodia.info/
 * Gen2Phen: Unified genotype-phenotype database (19 partners; funded under EU7) http://gen2phen.org/ [12]
 * 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).
 * CellTalk: (x 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),http://www.bioinf.med.uni-goettingen.de/
 * Tokyo University University of Tokyo, Tokyo, Japan (S. Miyano) http://bonsai.ims.u-tokyo.ac.jp/
 * Windber Research Institute Windber_Research_Institute & Strategic Medicine, Inc, Windber/PA, USA (M. Liebman) http://www.wriwindber.org/
 * Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany http://www.item.fraunhofer.de/english/index.html [13]
 * Lawrence Berkeley National Laboratory, Berkeley/CA, USA (I. Dubchak) http://www.wriwindber.org/ [14]

See also * Bioinformatics * Bioinformatics companies * Gene expression

References

(some of our own press releases; own review articles such as that in J. Biosci. and the upcoming one in Briefings Bioinform.; some of our original scientific papers, preferably those in Open Access journals; also some early papers of the Proteome team)

[1] BIOBASE acquires Proteome from Incyte: http://findarticles.com/p/articles/mi_m0EIN/is_2005_Jan_18/ai_n8699647

[2] BIOBASE opens Bangalore office: http://biospectrumindia.ciol.com/content/news/40611091.asp

[3] BIOBASE opens Yokohama office: http://www.reuters.com/article/pressRelease/idUS242892+24-Jan-2008+BW20080124

[4] 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.

[5] 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. [6] 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.

[7] 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.

[8] 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.

[9] 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.

[10] EU Projects at BIOBASE: http://europabio.euproject.eu/index.php/kb_3121/oe_1212/oe.html

[11] Net2Drug: http://findarticles.com/p/articles/mi_m0EIN/is_2007_March_27/ai_n18767478

[12] Gen2Phen: http://www.geneticsandhealth.com/2008/01/22/gen2phen-web-based-project-to-capture-health-disease-genetic-knowledge/

[13] 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.

[14] 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.

External links
 * Official corporate website
 * Gene Regulation Portal

Disambiguation page:

BIOBASE

BIOBASE, a bioinformatics company http://www.biobase-international.com/

BIOBASE, a bibliographic database from Elsevier http://www.elsevier.com/wps/find/bibliographicdatabasedescription.cws_home/600715/description#description