EDRN Biomarker Database

Curation Web Interface and Model

• 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.

EDRN Informatics Goals and PrinciplesApplicable to the Biomarker Database

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

Element Attributes• 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

• 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

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.

RDF Export

Public Portal

BMDBCompass

Curation Process

Curators add detail to attributes and…

Curation Process 2

… capture relationships between elements

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• 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