aug. 20, 2009edrn @ jpl, socalbsi '091 the power of bioinformatics tools in cancer research...

Aug. 20, 2009 EDRN @ JPL, SoCalBSI '09 1

The power of bioinformatics tools in

cancer researchEarly Detection Research Network, JPL

Mentors: Dr. Chris Mattmann, Andrew Hart

Andrew ClarkSouthern California Bioinformatics

Summer Institute, 2009


Agenda Introduction

Biomarkers and cancer research

Early Detection Research Network (EDRN)

The NCI & JPL EDRN Infrastructure

Project objective eCAS Curator additions

The eCAS Catalog and Archive

Service Data curation

Architectural & design considerations Software engineering Meta-data processing

Results & conclusions

Acknowledgements


Introduction

Biomarkers and cancer researchConstant research is underway to

discover and identify reliable biomarkers of cancer in the human body.

What is a biomarker?“A biological molecule found in blood, other

body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease.”

source: http://www.cancer.gov/dictionary/?searchTxt=biomarker

http://www.cancer.gov/dictionary/?searchTxt=biomarker


Biomarker research

The more information that is collected and shared between research sites and medical laboratories:The more effective diagnosis will become. The more specialized treatments can be

devised to minimize the devastating effects of cancer on its host.


The Early Detection Research Network

The NCI is concerned with managing biomarker research data and disseminating information to the public.

Formed the EDRN in 1999 “to provide up-to-date information on

biomarker research” to the scientific and medical communities and to the general public.

source: http://edrn.nci.nih.gov/about-edrn

http://edrn.nci.nih.gov/about-edrn


The Jet Propulsion Laboratory

FFRDC, operated by Cal-Tech, for NASAJPL’s technology for cataloging and

managing extremely large sets of data provided the underlying infrastructure needed by the EDRN to accomplish its own mission.


The EDRN Infrastructure

My mentors, Dr. Chris Mattmann and Andrew Hart, and their team continue ongoing development of the underlying software grid.

JPL software engineers work with bioinformatics experts to develop the public interface to the EDRN, a web-based portal available to the general public:

http://edrn.nci.nih.gov

http://edrn.nci.nih.gov/


Project objective

Overall:To participate as a bioinformatics

software engineer at JPL. To contribute to the EDRN software

infrastructure.Specifically:

Improve the functionality of the eCAS Curator.


EDRN Catalog and Archive Service

JPL software customized for cataloging and archiving biomarker data, including specimen details, specimen images and related information.

A

B

C

EDRNStagingServer

EDRNPublicPortal

WWW

Research data

2. Curation-Meta-data edits-Pub. survey & cross reference-Expert review

1. Data Ingestion 3. Product Release

Pre-release data

Released dataxmlDataset meta-data

Curator


eCAS data curationData ingested from research sites

undergoes a curation phase before its publication to the public portal.

A

B

C

EDRNStagingServer

EDRNPublicPortal

WWW

Research data



Pre-release data


Curator


eCAS CuratorThe curation activities would benefit

from additional software tools as part of the overall eCAS workflow.

A

B

C

EDRNStagingServer

EDRNPublicPortal

WWW

Research data



Pre-release data


Curator


Architectural & design considerations

Software engineering:EDRN tools are primarily web applicationsDesign and integrate modular

components Meta-data management:

Meta-data: information that describes the content of other information.

Meta-data management is crucial to the data curation and the operation of the EDRN system.


Data curation with eCAS

A

B

C

EDRNStagingServer

EDRNPublicPortal

WWW

Research data



Pre-release data


Curator

Internal EDRN policy files contain meta-data definitions and configuration details that describe the dataset expected from each research site.

1



A

B

C

EDRNStagingServer

EDRNPublicPortal

WWW

Research data



Pre-release data


Curator

Curators edit and revise dataset meta-data to make the final product records complete and accurate.

2



A

B

C

EDRNStagingServer

EDRNPublicPortal

WWW

Research data



Pre-release data


Curator

Accepted data made available through web portal. Meta-data definitions provide searchable fields and descriptions of dataset contents to portal users.

3


. . .

A dataset policy file


Dataset meta-data configuration


Curator tool

Browser based meta-data editor.


Curator tool

Selecting datasets formetadata editing

Metadata items retrieved from backend.


Results and conclusions

Final resultMeta-data management tool

integrated with the eCAS and curation functionality incorporated into the workflow.


Conclusion

The goal of software engineering in bioinformatics should be to:support scientists’ activities facilitate better research and

collaborationsimplify/bring clarity to complex tasks


Conclusion

The combined effectiveness of software tools and expert curation make the EDRN a more powerful

scientific resource that helps drive progress in biomarker research.


Acknowledgements

Thanks to my mentors and supporters at JPL: Chris Mattmann, Andrew Hart

Thanks to the SoCalBSI faculty and staff: Dr. Momand, Drs. Johnston, Dr. Sharp, Dr. Warter-

Perez, Ronnie Cheng

Thanks to the SoCalBSI funding sources: The National Science Foundation The National Institutes of Health Economic and Workforce Development

aug. 20, 2009edrn @ jpl, socalbsi '091 the power of bioinformatics tools in cancer research...

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