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Crowd-Assisted Deep Learning (CrADLe) Digital Curation to Translate Big Data into Precision Medicine

Award Number: U01LM012675
ORGANIZATION: NATIONAL LIBRARY OF MEDICINE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/01/2017
PERIOD OF PERFORMANCE END DATE: 07/31/2022

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Crowd-Assisted Deep Learning (CrADLe) Digital Curation to Translate Big Data into Precision Medicine - PROJECT SUMMARY/ABSTRACT The NIH and other agencies are funding high-throughput genomics (‘omics) experiments that deposit digital samples of data into the public domain at breakneck speeds. This high-quality data measures the ‘omics of diseases, drugs, cell lines, model organisms, etc. across the complete gamut of experimental factors and conditions. The importance of these digital samples of data is further illustrated in linked peer-reviewed publications that demonstrate its scientific value. However, meta-data for digital samples is recorded as free text without biocuration necessary for in-depth downstream scientific inquiry. Deep learning is revolutionary machine intelligence paradigm that allows for an algorithm to program itself thereby removing the need to explicitly specify rules or logic. Whereas physicians / scientists once needed to first understand a problem to program computers to solve it, deep learning algorithms optimally tune themselves to solve problems. Given enough example data to train on, deep learning machine intelligence outperform humans on a variety of tasks. Today, deep learning is state-of-the-art performance for image classification, and, most importantly for this proposal, for natural language processing. This proposal is about engineering Crowd Assisted Deep Learning (CrADLe) machine intelligence to rapidly scale the digital curation of public digital samples. We will first use our NIH BD2K-funded Search Tag Analyze Resource for Gene Expression Omnibus (STARGEO.org) to crowd-source human annotation of open digital samples. We will then develop and train deep learning algorithms for STARGEO digital curation based on learning the associated free text meta-data each digital sample. Given the ongoing deluge of biomedical data in the public domain, CrADLe may perhaps be the only way to scale the digital curation towards a precision medicine ideal. Finally, we will demonstrate the biological utility to leverage CrADLe for digital curation with two large- scale and independent molecular datasets in: 1) The Cancer Genome Atlas (TCGA), and 2) The Accelerating Medicines Partnership-Alzheimer’s Disease (AMP-AD). We posit that CrADLe digital curation of open samples will augment these two distinct disease projects with a host big data to fuel the discovery of potential biomarker and gene targets. Therefore, successful funding and completion of this work may greatly reduce the burden of disease on patients by enhancing the efficiency and effectiveness of digital curation for biomedical big data.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2023 ( Subtotal = -$2 )
2023	2020	THE UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Medical Library Assistance	000	5	11/28/2022	NON-COMPETING CONTINUATION	-$2
														Subtotal = -$2

Issue Date FY: 2021 ( Subtotal = $0 )
2021	2020	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Medical Library Assistance	000	5	10/19/2020	NON-COMPETING CONTINUATION	$0
2021	2020	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Medical Library Assistance	001	5	1/27/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2020 ( Subtotal = $428,713 )
2020	2020	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Medical Library Assistance	004	5	7/31/2020	NON-COMPETING CONTINUATION	$467,177
2020	2019	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Medical Library Assistance	003	4	5/5/2020	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$1
2020	2019	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CNTRL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Medical Library Assistance	001	4	2/11/2020	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$375,751
2020	2019	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Medical Library Assistance	002	3	5/5/2020	NON-COMPETING CONTINUATION	-$1
2020	2019	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Medical Library Assistance	000	3	2/10/2020	NON-COMPETING CONTINUATION	-$414,215
														Subtotal = $428,713

Issue Date FY: 2019 ( Subtotal = $529,266 )
2019	2019	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Medical Library Assistance	000	3	7/16/2019	NON-COMPETING CONTINUATION	$529,266
														Subtotal = $529,266

Issue Date FY: 2018 ( Subtotal = $545,116 )
2018	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 420	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Medical Library Assistance	000	2	7/19/2018	NON-COMPETING CONTINUATION	$545,116
														Subtotal = $545,116

Issue Date FY: 2017 ( Subtotal = $548,068 )
2017	2017	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Medical Library Assistance	000	1	7/12/2017	NEW	$548,068
														Subtotal = $548,068

Grand Total All Awards = $2,051,161

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Crowd-Assisted Deep Learning (CrADLe) Digital Curation to Translate Big Data into Precision Medicine

Award Number: U01LM012675

ORGANIZATION: NATIONAL LIBRARY OF MEDICINE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 08/01/2017

PERIOD OF PERFORMANCE END DATE: 07/31/2022

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