DASMI: exchanging, annotating and assessing molecular interaction data

Abstract

Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.Results: We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.Availability: The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/.Contact: mario.albrecht@mpi-inf.mpg.deSupplementary information: Supplementary data and all figures in color are available at Bioinformatics online.

Discovering cellular protein‐protein interactions: Technological strategies and opportunities

“…59 Furthermore, databases that mainly contain in silico predicted complexes will contain more false positives than manually curated ones, but many of the larger databases allow the selection of subsets that are more suited for the evaluated technologies or have a specific throughput. Several databases also exist that aggregate and consolidate data from all the other databases, [282][283][284][285][286] facilitated by the wide adoption of unified formatting standards. 287,288 Although these aggregated databases give a more complete view of all possible interactions, they still have clear biases.…”

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

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Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology

“…Proteomic data has been used in the development of various software utilities used in the analyses of genomic and proteomic data. PPI data from HPRD has been used in several interactomebased biological network visualization tools such as DASMIweb [51,52], DynaMod [53], PATIKAweb [54], POINeT [55], SubExtractor [56], NASCENT [57], ConsensusPathDB [58], VisANT [59], Genes2Networks [60], Cerebral [61,62], BioNetBuilder [62], COXPRESdb [63], STRING 8 [64], and UniHI [65]. Proteomic information from HPRD has been utilized in the functional analysis of an integrin adhesome network [66].…”