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The EDRN knowledge environment: an open source, scalable informatics platform for biological sciences research

Crichton, Daniel and Mahabal, Ashish and Anton, Kristen and Cinquini, Luca and Colbert, Maureen and Djorgovski, S. George and Kincaid, Heather and Kelly, Sean and Liu, David (2017) The EDRN knowledge environment: an open source, scalable informatics platform for biological sciences research. In: Micro- and Nanotechnology Sensors, Systems, and Applications IX. Proceedings of SPIE. No.10194. Society of Photo-Optical Instrumentation Engineers (SPIE) , Bellingham, WA, Art. No. 101942A. ISBN 9781510608894. https://resolver.caltech.edu/CaltechAUTHORS:20190828-141822439

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Abstract

We describe here the Early Detection Research Network (EDRN) for Cancer’s knowledge environment. It is an open source platform built by NASA’s Jet Propulsion Laboratory with contributions from the California Institute of Technology, and Giesel School of Medicine at Dartmouth. It uses tools like Apache OODT, Plone, and Solr, and borrows heavily from JPL’s Planetary Data System’s ontological infrastructure. It has accumulated data on hundreds of thousands of biospecemens and serves over 1300 registered users across the National Cancer Institute (NCI). The scalable computing infrastructure is built such that we are being able to reach out to other agencies, provide homogeneous access, and provide seamless analytics support and bioinformatics tools through community engagement.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1117/12.2263842DOIArticle
ORCID:
AuthorORCID
Mahabal, Ashish0000-0003-2242-0244
Djorgovski, S. George0000-0002-0603-3087
Additional Information:© 2017 Society of Photo-Optical Instrumentation Engineers (SPIE). We acknowledge the EDRN grant from NIH (82-16333), and the support from JPL Center for Data Science and Technology. AAM and SGD also acknowledge support from the Center for Data-Driven Discovery at Caltech, and from the Ajax Foundation.
Funders:
Funding AgencyGrant Number
NIH82-16333
JPLUNSPECIFIED
CaltechUNSPECIFIED
Ajax FoundationUNSPECIFIED
Subject Keywords:Data Science, Knowledge Environment, Cancer, Open Source, Apache OODT, Common Data Elements, Biomarker, Ontology
Series Name:Proceedings of SPIE
Issue or Number:10194
Record Number:CaltechAUTHORS:20190828-141822439
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190828-141822439
Official Citation:Daniel Crichton, Ashish Mahabal, Kristen Anton, Luca Cinquini, Maureen Colbert, S. George Djorgovski, Heather Kincaid, Sean Kelly, and David Liu "The EDRN knowledge environment: an open source, scalable informatics platform for biological sciences research", Proc. SPIE 10194, Micro- and Nanotechnology Sensors, Systems, and Applications IX, 101942A (18 May 2017); https://doi.org/10.1117/12.2263842
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:98320
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:28 Aug 2019 21:36
Last Modified:03 Oct 2019 21:39

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