MatrixDB is a

biological database Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genom ...

focused on molecular interactions between

extracellular This glossary of biology terms is a list of definitions of fundamental terms and concepts used in biology, the study of life and of living organisms. It is intended as introductory material for novices; for more specific and technical definitions ...

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respondi ...

and

polysaccharides Polysaccharides (), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with w ...

. MatrixDB takes into account the multimeric nature of the extracellular proteins (for example, collagens, laminins and thrombospondins are multimers). The database was initially released in 2009 and is maintained by the research group of Sylvie Ricard-Blum at UMR5246,

Claude Bernard University Lyon 1 Claude Bernard University Lyon 1 (french: link=no, Université Claude-Bernard Lyon 1, UCBL) is one of the three public universities of Lyon, France. It is named after the French physiologist Claude Bernard and specialises in science and technol ...

. MatrixDB is linked with

UniGene UniGene was a NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that appear to stem from the same transcription locus (i.e. gene or expressed pseudogene). Informat ...

and the

Human Protein Atlas The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectromet ...

. It also allows users to build customised tissue- and disease-specific interaction networks, which can be further analysed and visualised using

Cytoscape Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available f ...

or Medusa. MatrixDB is an active member of the International Molecular Exchange Consortium (IMEx), a group of the major public providers of interaction data. Other participating databases include the Biomolecular Interaction Network Database (BIND), IntAct, the Molecular Interaction Database (MINT), MIPS, MPact, and BioGRID. The databases of IMEx work together to prevent duplications of effort, collecting data from non-overlapping sources and sharing the curated interaction data. The IMEx consortium also worked to develop the

HUPO The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. The organization was launched in February 2001, and it promotes ...

PSI Psi, PSI or Ψ may refer to: Alphabetic letters * Psi (Greek) (Ψ, ψ), the 23rd letter of the Greek alphabet * Psi (Cyrillic) (Ѱ, ѱ), letter of the early Cyrillic alphabet, adopted from Greek Arts and entertainment * "Psi" as an abbreviation ...

-MI XML standard format for annotating and exchanging interaction data. MatrixDB includes interaction data extracted from the literature by manual curation and offers access to relevant data involving extracellular proteins provided by IMEx partner databases through the PSICQUIC webservice, as well as data from the

Human Protein Reference Database The Human Protein Reference Database (HPRD) is a protein database accessible through the Internet. It is closely associated with the premier Indian Non-Profit research organisation Institute of Bioinformatics (IOB), Bangalore. This database is a ...

References

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External links

* http://matrixdb.univ-lyon1.fr * http://www.icbms.fr/aspe Biological databases Polysaccharides