Post on 19-Jan-2016
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