This facilitates identification of redundant interaction records (and interactors) at search time regardless of the protein accession system used to construct a query. The iRefIndex uses a unique consolidation process: each interactor's amino acid sequence and taxonomy identifier are used to assign a universally accessible hash-key to each distinct interactor and interaction. The interaction reference index (iRefIndex) consolidates protein interaction data from ten databases including BIND, BioGRID ,CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. The plug-in uses a number of strategies that will be of interest to other plug-in developers. Tools are provided to facilitate a range of tasks from a simple search to knowledge discovery. The plug-in provides access to a consolidated data set in a uniform accession space while remaining faithful to the underlying source data. The iRefScape plug-in will be of interest to advanced users of interaction data. Finally, a synchronized adjacency-matrix view facilitates visualization of relationships between sets of user defined groups. Searching for interactions between sets of proteins is supported and specifically includes searches on disease-related genes found in OMIM. Overlapping evidence is presented using a multi-graph and a bi-partite representation is used to distinguish binary and n-ary source data. Node colours and features supply information about search result provenance. Multiple node and edge features support data filtering and mining. A uniform accession space is used to limit redundancy and support search expansion and searching on multiple accession types. We show how these factors impact on data-mining tasks and how our solutions resolve them in a simple and efficient manner. The iRefScape plug-in for the Cytoscape graphical viewer addresses these challenges. These phenomena were quantified in our previous studies. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys.
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