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RIMBAA: IBM RIMon Hypergenes

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During the January 2010 WGM the RIMon product was presented. Below an excerpt from the minutes:

  • RIMBAA Product presentation: RIMBAA Aspects of the DB2 PureXML database. Amnon Shabo (IBM) presents: "research effort developing a data warehouse (RIMon) that is based on the RIM". See http://www.ringholm.de/persist/20100118_RIMBAA_IBM_Hypergenes_BII.PDF for the presentation.
    • Core aspect: BII - Biomedical Information Infrastructure, contains general purpose data warehouse. Called RIMon (RIM based XML storage); querying supported by XQuery. Support export to datamarts using RDF definitions (datamart could be peristed in relational format).
    • Received v3 instances are RIMified (mapped to generic RIM classes); allows for creation of Rimified queries for decision support. Archived instances are "RIM ITS" (an in-company own version thereof) based, with preserved clone names.
    • Lesson learned: XQuery too complex for most researchers. Lead to the creation of datamarts.

See also:

  1. From the RIMBAA 201105 Minutes Orlando
  2. Hybrid approaches to RIMBAA (Amnon Shabo, see http://www.hl7.org/documentcenter/public/wg/java/20110517_IBM_Hypergenes.pdf for his slides)
    • Amnon Shabo presented the IBM research project on human genomics. They collect genotypes including genome-wide scan of each subject and they also collect phenotypes. The data is in a hybrid warehouse with RIM-based database for clinical data snd relational database for the genomic data (1M SNP/subject). They are able to find new correlations between genotype and phenotypes, and if the correlation is already known, they can be used in decision support. For example, a given genotype may suggest drug resistance for a given patient and conditon. The system can warn the clinician not to prescribe it - based on the genotype. The RMIM's used for the warehouse XML database are the Pedigree and Genetic Variation (of HL7 Clinical Genomic Domain) and CDA. These RMIM's were constrained to meet the project requirements. The constrained RMIM's were interrelated under one infromation model that govern the warehouse XML database.
    • Native-XML RIMBAA for semantic warehousing with XQUERY exploration. Exported data marts in RDF or relational formats for analytics and optimization. RDF-based promotion layer facilitates the definition of data marts. Data mart schemas are user-defined and mapped to the XML warehouse and/or promotion layer.
      • Stage data as is fully-indexed XML and not as blob
      • Separate databases for normal-data and mass-data (e.g. genotype data)
      • MDHT tool used to create templates with UML/OCL.
      • XML in generic layer = core model, query using XQuery.
      • IHE QED implemented and tested on Connecthathon, QED connected to RIM database (XML, RIMon)