A web portal for management of biological data and applications

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Presentation transcript:

A web portal for management of biological data and applications Matteo Gnocchi, Alessandro Orro, Davide Di Pasquale, Luciano Milanesi Institute for Biomedical Technologies – CNR, Segrate, Italy

Outline introduction motivation architecture ported tools genotype management system phenotype management system web portal xml-rpc interface liferay web interface genetic analysis linkage analysis

Introduction Motivations management of huge amount of data coming from a molecular biology laboratory availability of many tools for data analysis home made heterogeneous (formats and interfaces) not integrated in any framework

Introduction implementation of a web-based application for resources integration technologies ad-hoc solution based on xml-rpc liferay main field data management of data coming from genetics laboratory medical genetics studies (association studies, linkage analysis)

Architecture

Ported tools genotypes data management local database for gene annotation UCSC, www.genome.ucsc.edu phenotype data management statistical aplpications in development . . . linkage analysis

Genotypes data management management of data coming from ht genotyping platforms (Illumina, Affymetrix) postgresql + python (scripts)

Genotypes data management data representation

Genotypes data management main features (bmc bioinformatics, 26 march 2008) some LIMS features users/projects samples (by projects) metadata (chips) genotypes manipulation data import/exports most important input formats (ped, map, ...) standard data from Affymetrix and Illumima interface only command line

Genotypes data management python API metadata getAvailChips() getChipInfo(chipname: string) dataset management getDatasets(project: string) newDatasset(name: string, project: string) user/permissions/groups/ projects addUser, addGroup, addProject delUser, ... etc.

Web portal middleware porting of the API interface to RPC-XML interface porting the command line application to XML-RPC

Web portal portal implementation of a liferay based portal user management mapping portal user <-> appl user applications as portlets a resizable and independent windows into the portal that implement a single application each portlet uses one or more web services in order to accomplish its task

Web portal

Web portal

Phenotype management phenotype: every info of a sample (patient) related to his clinical/demographics/medical status heterogeneous data treatment temporal reference management software metadata : defining new phenotypes insert/delete/edit of phenotype value import/export based on mysql + python cmdline interface -> xml-rpc

Phenotype management

Phenotype management

Data analysis Genotype/Phenotype can be combined together and analyzed with many tools case/control (association) Linkage analysis Quality control Stratification analysis computation No computational intensive -> xml-rpc Linkage analysis -> glite

Linkage analysis Linkage Analysis is a genetic analysis that permits the discovery of genetic correlations in complex diseases following their transmission through family generations.

Linkage analysis

conclusions The application developed represents an easy way to interact with the various biological data and informationcase/control (association) Liferay and Xml-rpc Future works Interaction with HP computing infrastructures XML-RPC –> WSDL (compatibility with WF systems)

thank you for your attention