Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies

Abstract

FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft’s PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.

DruGeVar: An Online Resource Triangulating Drugs with Genes and Genomic Biomarkers for Clinical Pharmacogenomics

“…This application offers useful tools for querying large datasets in multiple ways and in a very dynamic and user-friendly manner. The entire system architecture is based on a 3-tier client-server model, as described previously in FINDbase worldwide database for clinically relevant genomic variation allele frequencies [6]. …”

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

“…Contrary to the previous FINDbase data content updates in 2010 (9) and 2013 (10), the recent (2014–2016) update did not only include data curation, update and correction, where necessary, but also extensive data enrichment in all three data modules.…”

“…In the last FINDbase update, we have built a new module for rare genetic disease summaries (10), in which we migrated all genetic disease summary data collection from five previously developed NEGDBs (Hellenic, Lebanese, Cypriot, Egyptian and Moroccan). Based on this functionality, and given that the component services of all three modules homogeneously follow the Service Oriented Architecture (SOA; 13) and are built around the same data visualization tool (PivotViewer; http://www.microsoft.com/silverlight/pivotviewer), we have decided to (i) completely restructure and upgrade the previous version of the ETHNOS software (2), to include improved data submission, querying and curation functionalities, standing as an ‘off-the-shelf’ web application that would allow the development of new NEGDBs, (ii) exploit the entire FINDbase data content, subdivided into 3 modules, to migrate the entire FINDbase data collection to establish 90 individual ETHNOS -based NEGDBs in all 5 continents (Table 1).…”

The Genomic Medicine Alliance: A Global Effort to Facilitate the Introduction of Genomics into Healthcare in Developing Nations

“…The result is that the ETHNOS software supports, in its present format, the development of National Genetic databases [Papadopoulos et al, 2014], based on the data warehouse principle and pre-existing guidelines . These databases will be assigned to senior human geneticists in the corresponding populations in order to coordinate their curation and stimulate data enrichment and expansion.…”