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EDRN Biomarker Database

EDRN Biomarker Database. Curation Web Interface and Model. EDRN Informatics Goals and Principles Applicable to the Biomarker Database. Develop a knowledge system that links together EDRN data assets into a virtual data system based on common data elements

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EDRN Biomarker Database

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  1. EDRN Biomarker Database Curation Web Interface and Model

  2. EDRN Informatics Goals and PrinciplesApplicable to the Biomarker Database • Develop a knowledge system that links together EDRN data assets into a virtual data system based on common data elements • Establish an EDRN bioinformatics program that promotes the use of a common informatics infrastructure by EDRN sites.  • Provide an infrastructure for capturing EDRN biomarkers and validation study results and a mechanism for distribution • Define data and software standards for EDRN informatics systems • Collaborate with both EDRN and non-EDRN sites on informatics. • Enable tools that support scientific inquiry both within and across databases and data sets.

  3. Relationship to EKE • The Biomarker Database provides a means for capturing relationships between the many elements of Biomarker research, including publications, studies (protocols), and resources. • Available element attributes and relationships flow directly from the EKE Ontology / CDEs

  4. BMDB Data Model

  5. Biomarker Name Type Description QAState Security Biomarker-Organ Description Sens. Min/Max/Comment Spec. Min/Max/Comment NPV Min/Max/Comment PPV Min/Max/Comment Phase QAState Element Attributes • Study • DMCC_ID • isEDRN • Title • Abstract • Bio. Pop. Char. • B.P.C. Desc. • Design • Design Desc. • Study Type • Publication • PubMed ID (opt) • Title • Author • Journal • Date Published • Resource • URL • Description

  6. DMCC-JPL-NCI Coordination RDF Export Compass BMDB The Biomarker Database regularly “scrapes” the DMCC Protocol website, updating its internal database. The information is then available for association with other BMDB data elements by a curator. Finally, curated, peer-reviewed BMDB data is made available to the public via the EDRN Public Portal. Public Portal

  7. Curation Process Curators add detail to attributes and…

  8. Curation Process 2 … capture relationships between elements

  9. Current Status • Biomarker Entry • Soliciting information from the PIs • Currently curating relationships between biomarkers, studies (protocols), publications, and external resources • Interface refinements • Interface evolving as feedback flows in from curation process

  10. Next Steps • Increased curation activity • Tighter integration between DMCC-JPL • Move away from “scraping” towards a defined (RDF?) interface for data retrieval • Incorporate DMCC Publication data into the BMDB • Provide Reporting / Metrics • System-wide and by Collaborative Group

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