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Image-guided Biocuration of Disease Pathways From Scientific Literature

Award Number: R01LM013392
ORGANIZATION: NATIONAL LIBRARY OF MEDICINE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 05/01/2020
PERIOD OF PERFORMANCE END DATE: 02/28/2025

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Image-guided Biocuration of Disease Pathways From Scientific Literature - Realization of precision medicine ideas requires an unprecedented rapid pace of translation of biomedical discoveries into clinical practice. However, while many non-canonical disease pathways and uncommon drug actions, which are of vital importance for understanding individual patient-specific disease pathways, are accumulated in the literature, most are not organized in databases. Currently, such knowledge is curated manually or semi-automatically in a very limited scope. Meanwhile, the volume of biomedical information in PubMed (currently 28 million publications) keeps growing by more than a million articles per year, which demands more efficient and effective biocuration approaches. To address this challenge, a novel biocuration method for automatic extraction of disease pathways from figures and text of biomedical articles will be developed. Specific Aim 1: To develop focused benchmark sets of articles to assess the performance of the biocuration pipeline. Specific Aim 2: To develop a method for extraction of components of disease pathways from articles’ figures based on deep-learning techniques. Specific Aim 3: To develop a method for reconstruction of disease-specific pathways through enrichment and through graph neural network (GNN) approaches. Specific Aim 4: To conduct a comprehensive evaluation of the pipeline. The overarching goal of this project is to develop a computer-based automatic biocuration ecosystem for rapid transformation of free-text biomedical literature into a machine-processable format for medical applications. The overall impact of the proposed project will be to significantly improve health outcomes in individualized patient cases by efficiently bringing the latest biomedical discoveries into a precision medicine setting. It will especially benefit cancer patients for which up-to-date knowledge of newly discovered molecular mechanisms and drug actions is critical.


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: 2025 ( Subtotal = $0 )
2025	2023	UNIVERSITY OF MISSOURI SYSTEM	121 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	000	4	5/12/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $316,361 )
2023	2023	UNIVERSITY OF MISSOURI SYSTEM	121 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	000	4	2/8/2023	NON-COMPETING CONTINUATION	$316,361
														Subtotal = $316,361

Issue Date FY: 2022 ( Subtotal = $312,528 )
2022	2022	UNIVERSITY OF MISSOURI SYSTEM	316 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	000	3	3/3/2022	NON-COMPETING CONTINUATION	$312,528
														Subtotal = $312,528

Issue Date FY: 2021 ( Subtotal = $313,018 )
2021	2021	UNIVERSITY OF MISSOURI SYSTEM	316 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	002	2	5/14/2021	NON-COMPETING CONTINUATION	$15,651
2021	2021	UNIVERSITY OF MISSOURI SYSTEM	316 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	001	2	2/22/2021	NON-COMPETING CONTINUATION	$297,367
2021	2020	UNIVERSITY OF MISSOURI SYSTEM	316 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	000	1	12/23/2020	NEW	$0
														Subtotal = $313,018

Issue Date FY: 2020 ( Subtotal = $313,495 )
2020	2020	UNIVERSITY OF MISSOURI SYSTEM	316 UNIVERSITY HALL	COLUMBIA	MO	65211	BOONE	USA	Medical Library Assistance	000	1	4/23/2020	NEW	$313,495
														Subtotal = $313,495

Grand Total All Awards = $1,255,402

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Image-guided Biocuration of Disease Pathways From Scientific Literature

Award Number: R01LM013392

ORGANIZATION: NATIONAL LIBRARY OF MEDICINE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 05/01/2020

PERIOD OF PERFORMANCE END DATE: 02/28/2025

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