1 / 14

WP3.2: Mobility Brokerage Service

WP 4: ( Data Interoperability and Management). WP3.2: Mobility Brokerage Service. WP4: Data Interoperability and Management. Presentation: Victor Maojo UPM. GOALS. To detect existing gaps and opportunities for BMI research on: Ontologies and Data models Heterogeneous Database integration

quon-owens
Download Presentation

WP3.2: Mobility Brokerage Service

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. WP 4: (Data Interoperability and Management) WP3.2: Mobility Brokerage Service WP4: Data Interoperability and Management Presentation: Victor MaojoUPM

  2. GOALS • To detect existing gaps and opportunities for BMI research on: • Ontologies and Data models • Heterogeneous Database integration • Security • To find the adequate methods and tools to solve specific issues that might appear in the rest of the WPs.

  3. STATE OF THE ART WP3.2: Mobility Brokerage Service SoA document publicly available

  4. ON-GOING WORK FOR WP4 • Phenotype data model • Development of PML (Polymorphism Markup Language) • Involvement in developing standards for the systems biology community (graphical notation and ontologies for pathways, at www.sbgn.org) • Updating ontology language representations to OWL • Using ontologies for database homogeneization • Privacy-enhanced data storage for the pilots

  5. PHENOTYPE DATA MODEL HGVbase-G2P 2006-... PHENOTYPE Unique entry ID General Specific Name Category Disease Area Method Sub-Phenotype IDs Free Text Citations Keywords Name Attribute Value Units Qualifiers ...based upon a core entity-attribute-value (EAV) triplet model, adaptedto enable any depth, breadth, or type of phenotype to be represented ...envisage a 'dynamic' ontology system

  6. ONTOFUSION + Data mining Ontofusion + Preprocessing Results Inconsistencies Ontology-based model for database integration and mining

  7. OntoDataClean Integration at an Instance level • An Ontology as a framework to identify inconsistencies • Terminology • Scale • Format • Patterns • Missing Values • … • automatic homogenization of databases

  8. PREPROCESSING ONTOLOGY OntoDataClean Order Source DB Fields Data Source Cleaning Model URL Missing Values Format Scale Pattern Duplicate Rule Data Type Synonym Expression String Regular Expression Synonym Database Values Replacement URL Name Condition Detection Transformation Preferred Name Missing Value Ranges Condition Representative Values Average Column Replacement Schema of the OntoDataClean Preprocessing Ontology Representative Values Most Frequently Replacement Condition Value Ranges Row Removal String Replacement

  9. HOMOGENIZATION RESULTS XML Tabulated text format

  10. RESULTS: BMI papers Three papers “in press” in major Biomedical Informatics journals (Computers in Biology and Medicine, Journal of Biomedical Informatics, Methods of Information in Medicine)

  11. LINKS TO WP 6.2 • Synonym tool • Workflow with XML input and output files for supporting systems biology research • Pathway representation

  12. INFORMA PROPOSAL Current Pending Roberto Ricci - Informa INFOBIOMED: WP4 (DATA INTEROPERABILITY AND MANAGEMENT) • Proposal of a BMI demonstrator focused on the integration of viral genomics with clinical data in HIV infection • Create a new public DB by integrating ARCA with genotype-response DBs, host data and other publicly available resources • Develop a dedicated web site and a platform for data flow and linking

  13. LINKS WITH 6.3 (ACTA) Data Data • Information • - Clinical • Genetic • Environment (2) (1) (3) DWH XML files (5) (6) DATA MINING (Results) Visualization (4) External Databases SNPs, etc

  14. SUMMARY: EFFORTS WITH PILOTS WP4 6.2 6.3 6.4 Proposed after 1st review End of 2006 (2007?)

More Related