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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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Edrn biomarker database

EDRN Biomarker Database

Curation Web Interface and Model

Edrn informatics goals and principles applicable to the biomarker database

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.

Relationship to eke

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

Bmdb data model

BMDB Data Model

Element attributes









Sens. Min/Max/Comment

Spec. Min/Max/Comment

NPV Min/Max/Comment

PPV Min/Max/Comment



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

Dmcc jpl nci coordination

DMCC-JPL-NCI Coordination

RDF Export



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

Curation process

Curation Process

Curators add detail to attributes and…

Curation process 2

Curation Process 2

… capture relationships between elements

Current status

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

Next steps

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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