CliniPhenome: a clinical and phenotypic data warehouse

Dipankar Sengupta, Didier Croes, Mary-Louise Bonduelle, Ann Nowe, Sonia Van Dooren

Research output: Unpublished contribution to conferenceOther

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Abstract

Project BRiDGEIris (http://bridgeiris.ibsquare.be/) aimed to develop a big data platform that can be used for sharing genomic and clinical data, and support discovery studies in clinical genomics. A part of this goal was attained by the proposal and development of CliniPhenome, having a generalized clinical schema design along with a merged ontology that supports cross-referencing. Also, introduction of the controlled vocabulary and data structure answers to the prevalent problem of plain text storage in the existing clinical databases, causing impediment during data analysis.
CliniPhenome is a web based application coupled to a database, developed primarily for the collection of data for patient's being analyzed for Cardiac Arrhythmia Syndromes and Prenatal analysis, but also supports for other diseases. A user needs to be registered in CliniPhenome to access its utilities. There are three user types in CliniPhenome based on the "Label Based Access", and defined as per the Health Level 7 (HL7) Healthcare Privacy Guidelines. Its application interface provides an interactive platform with varied usage features depending on the user type, like, a privileged user, can insert data along with clinical measures (obtained from varied diagnostic processes) or can access the clinical history of a patient. Furthermore, based on the provided observations, a patient can be annotated against the combination of phenotype ontology's - HPO, OMIM, Orphanet; and clinical ontology - SNOMED. Another key component of CliniPhenome is the data migration utility, that supports exchange of de-identified information, among the participating hospital/centres in an XML/JSON file structure. Furthermore, there are API's that integrates it with HIGHLANDER (Genomic db) database and analytical tools like DiGeST (gene/variant ranking).
CliniPhenome (http://bridgeiris.ulb.ac.be/cliniphenome/) has been developed in PHP (CodeIgniter Web MVC framework), MySQL (version 5.5) and runs on an Apache server.
Original languageEnglish
Pages1-2
Publication statusPublished - 13 Apr 2016
EventBeMGI 2016 Annual Meeting: From predisposing germline and somatic variants to disease-driving mechanisms - UCL Brussels Campus, Brussels, Belgium
Duration: 13 Apr 201613 Apr 2016

Presentation

PresentationBeMGI 2016 Annual Meeting
CountryBelgium
CityBrussels
Period13/04/1613/04/16

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