DASMiner: discovering and integrating data from DAS sources.

BMC Systems Biology
Diogo F T VeigaJonas S Almeida

Abstract

DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources. We developed DASMiner, a Matlab toolkit for querying DAS data sources that enables creation of integrated biological models using the information available in DAS-compliant repositories. DASMiner is composed by a browser application and an API that work together to facilitate gathering of data from different DAS sources, which can be used for creating enriched datasets from multiple sources. The browser is used to formulate queries and navigate data contained in DAS sources. Users can execute queries against these sources in an intuitive fashion, without the need of knowing the specific DAS syntax for the particular source. Using the source's metadata provided by the DAS Registry, the browser's layout adapts to expose only the set of commands and coordinate systems supp...Continue Reading

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Citations

Sep 21, 2010·Briefings in Bioinformatics·Tomas Klingström, Dariusz Plewczynski
Jun 11, 2014·BMC Bioinformatics·Sean R Wilkinson, Jonas S Almeida

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Datasets Mentioned

BETA
GM06990

Methods Mentioned

BETA
pull-down
ChIP-chip
acetylation

Software Mentioned

executeDASCommand
histonesPlots
Bioinformatics toolbox
DASMiner
Windows
Dasobert
IntAct
Proserver
Linux
HomoMint

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