BIOBASE (company)
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.
History
The company was founded in 1997 as a spin-off from the German Research Centre for Biotechnology (GBF), Braunschweig, 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).
Subsidiaries
BIOBASE GmbH has three fully owned daughter companies: BIOBASE Corporation in Beverly/Massachusetts, USA (since 2005),[1] BIOBASE Databases India Pvt Ltd. in Bangalore, India (since 2006),[2] and BIOBASE Japan K.K. in Yokohama, Japan (since 2007) [3]
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:[4]
- TRANSFAC: Eukaryotic transcription factors, their genomic DNA-binding sites and DNA-binding profiles [5]
- 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 [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" 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.
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):[15]
- 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 [16]
- Sysco: Combined experimental, bioinformatics and simulation approaches to analyze intracellular parasitism (8 partners; funded under EU6) [17][18]
- TRANSISTOR: Bioinformatics modeling of plant regulatory circuits (7 partners; Marie-Curie Project funded under EU6) [19]
- 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) [20]
- 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;[21]
- Lawrence Berkeley National Laboratory, Berkeley/CA, USA (I. Dubchak);[22]
See also
References
- ^ BIOBASE acquires Proteome from Incyte
- ^ BIOBASE opens Bangalore office
- ^ BIOBASE opens Yokohama office
- ^ Wingender, E; Crass, T; Hogan, JD; Kel, AE; Kel-Margoulis, OV; Potapov, AP (2007). "Integrative content-driven concepts for bioinformatics "beyond the cell"". Journal of Biosciences 32 (1): 169–80. PMID 17426389.
- ^ Matys, V; Kel-Margoulis, OV; Fricke, E; Liebich, I; Land, S; Barre-Dirrie, A; Reuter, I; Chekmenev, D et al. (2006). "TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes". Nucleic Acids Research 34 (Database issue): D108–10. doi:10.1093/nar/gkj143. PMC 1347505. PMID 16381825. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1347505.
- ^ Krull, M; Pistor, S; Voss, N; Kel, A; Reuter, I; Kronenberg, D; Michael, H; Schwarzer, K et al. (2006). "TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations". Nucleic Acids Research 34 (Database issue): D546–51. doi:10.1093/nar/gkj107. PMC 1347469. PMID 16381929. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1347469.
- ^ a b c Costanzo, MC; Crawford, ME; Hirschman, JE; Kranz, JE; Olsen, P; Robertson, LS; Skrzypek, MS; Braun, BR et al. (2001). "YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information". Nucleic Acids Research 29 (1): 75–9. doi:10.1093/nar/29.1.75. PMC 29810. PMID 11125054. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=29810.
- ^ Hodges, PE; Carrico, PM; Hogan, JD; O'Neill, KE; Owen, JJ; Mangan, M; Davis, BP; Brooks, JE et al. (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 Research 30 (1): 137–41. doi:10.1093/nar/30.1.137. PMC 99168. PMID 11752275. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=99168.
- ^ Liebich, I; Bode, J; Frisch, M; Wingender, E (2002). "S/MARt DB: a database on scaffold/matrix attached regions". Nucleic Acids Research 30 (1): 372–4. doi:10.1093/nar/30.1.372. PMC 99064. PMID 11752340. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=99064.
- ^ Department of Bioinformatics and Biochemistry - Technical University of Braunschweig Germany
- ^ enzymeta
- ^ HGMD home page
- ^ Cell System Markup Language (CSML) - Cell Illustrator
- ^ [1]
- ^ EU Projects at BIOBASE
- ^ Net2Drug
- ^ BIOBASE Biological Databases: SysCo - Functional Analysis
- ^ Home - Systematic functional analysis of intracellular parasitism as a model of genomes conflict
- ^ BIOBASE Biological Databases: TRANSISTOR
- ^ Gen2Phen
- ^ 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 biology 9 (2): R36. doi:10.1186/gb-2008-9-2-r36. PMC 2374721. PMID 18291023. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2374721.
- ^ 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. doi:10.1186/1471-2164-8-378. PMC 2176071. PMID 17945028. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2176071.
External links