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Building a European distributed clinical data mining ... - Debugit

Building a European distributed clinical data mining ... - Debugit

Data warehousing is a

Data warehousing is a centralised approach that stores all the data of the sharingsites into one central database. In this approach, a unified data model is defined in orderto accommodate all the information contained in the source sites. In addition, wrappersare created for each participant site in order to upload and manage the local data, sothat it fits into the central database schema. Then, all the queries can be easilysubmitted centrally. Some projects using this approach are the Genome Database (IGD)project, ATLAS, BioWarehouse, and BioDWH.High performance can be considered as one of the highest advantages of thissystem. In addition, it allows the user to modify and annotate the data since this is areplica, not the production database. There exist also other well-known techniques tobuild dynamic and online data navigation (OLAP) functionalities upon datawarehouses that could serve the users for their data analyses.This well-known industrial approach to data integration has proven to be efficientfor relatively simple industrial contexts. In life science, with its fast evolvingknowledge domain as well as the complexity of domain data models, this approach isless widely used due to the cost of data model updates in the central data stores, and tothe additional risk of data exposure it leads to.b) View IntegrationView integration is a decentralised approach where source data is kept only in thesource site. A single view around all the databases that share information within thesystem is created. Queries are converted into a common query language that is laterhandled by a mediator. The mediator identifies the sources that need to be accessed toretrieve the result. Then, it splits the query in many sub queries that are passed towrappers. Those will transform their sub queries into the local language using mappingrules metadata, and access the data. After the data is fetched from the different sources,the result is globally integrated and returned to the user. HEMSYS [8] and TAMBIS[9] are examples of systems that follow this approach. Ontologies are usually used forview integration to help in aligning different data sources into a global concept of thedata. The system can use either integration with a global ontology as in SIMS [10],where each source references the same domain ontology; or local ontology as inKRAFT [11].When view integration is used, the data is always up to date and there is a relativedecoupling from the data sources to the integration system. In the downside, usually theperformance is not good since the loading of the data is on-demand and relies on theunderlying network performance.c) Others approachesIn the link integration approach, entries in a data source, usually a web page, arelinked to other entries in another data sources via the integration system. SRS, one ofthe most used integration systems, follows this approach. Entrez and Integr8 are otherexamples.Mashups are a Web 2.0 idea beginning to take hold in the life sciences. Mashupsprovide means to take data from more than one web-based resource and make a newweb application. An example is the use of Google Earth to track the global spread ofavian flu. Mashup development framework such as Google Mashup Editor, Microsoft’sPopfly and Yahoo! Pipes speed up the development of mashups.

Figure 3. DebugIT CDR architecture.(acronyms: see table 1)5. Dealing with rules, information and knowledgeAnother very important challenge is the ability to formalize existing rules, guidelinesand other types of medical knowledge within a knowledge repository, which will holdnew acquired knowledge. A very short example is given hereafter. Manually-generatedrules are based on clinical guidelines provided by healthcare institutions. Typicalrecommendations are useful to prescribe the most appropriate antibiotic, according todifferent parameters, such as costs, benefits, adverse effects, as well as the risk ofresistance development. As case study, we started investigating guidelines for thegeriatrics (cf. Table 1) and the surgery services from the University Hospitals ofGeneva (HUG).Table 1. Slightly simplified sample of the guidelinesPathologies Pathogenic agents Antibiotics Alternatives Treatment durationCholecystitisGastroenteritisEnterobacteriaceaeEnterococcusClostridium spCampylobacterSalmonellaE. ColiShigella (rare)ceftriaxone1 g/24h iv +metronidazole500 mg/8h ivciprofloxacine500 mg/12h poamoxi./clav.1,2 g/8h ivco-trimoxazole forte(160mg TMP/ 800mgSMX)/12h po &clarithromycine500 mg/12h po10-14 days5-10 days

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