Sunday, November 24, 2024 11/24/2024

UniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's Disease

Award Number: U24HG007822
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Project Summary Text Mining and Large Language Models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's Disease Alzheimer’s Disease (AD) is a common and devastating neurodegenerative disorder that currently has no effective treatment. Many genetic variants associated with AD have been identified and, in some cases, the molecular and clinical consequences of these variants have been elucidated and reported in the scientific literature. As the premier resource for protein sequence and function information, UniProt is in an ideal position to curate and disseminate this AD variant information to support research on novel therapies. Here, we propose to use a combination of text mining strategies, including our previously developed relation extraction tool eMIND, which captures information about the functional impact of variants in AD, as well as a cutting edge GPT Large Language Model (LLM), to enable high-throughput curation of variants of high interest to the AD community. We have previously developed eMIND, a transformer-based text mining system that extracts relations between AD variants and functional impacts from the literature, and have demonstrated that it has good performance on a selected set of AD-related abstracts. In this work, we will develop a pipeline to automatically process PubMed abstracts at full-scale using eMIND and output variant-impact relations as well as the abstracts and individual sentences from which they were derived. This information will be used in conjunction with the LLM for several purposes. First, we will use the LLM to create natural language summaries of the impact of AD-related variants based on sentences and abstracts identified by eMIND (Aim 1). By focusing the LLM on text already flagged as relevant by eMIND, we will increase accuracy while taking advantage of the LLM’s ability to synthesize information across sentences from multiple papers and produce a highly readable product. All summaries will be manually evaluated by expert curators. Next, we will develop a set of high-confidence variant-impact relations that can be used in applications, such as knowledge graph representation and learning, that require information in a structured format (Aim 2). We will use the LLM in two ways: (i) to assess the validity of the relations extracted by eMIND and (ii) to extract relations de novo from eMIND-positive sentences and abstracts. The results of both approaches will be manually assessed and compared. Finally, the most relevant relations and summaries of the functional impact of AD-related variants obtained in Aim 1 and Aim 2 will be made available to users through the UniProt API and website (Aim 3). We will seek feedback from the AD community about the quality and presentation of the information. Taken together, this work will enable scalable curation of AD variant information of high value to the AD community and serve as a model for a fully automated variant annotation workflow that can be generalized to other diseases.


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: 2024 ( Subtotal = $5,682,070 )
2024	2024	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG				DEU	Human Genome Research	000	11	7/18/2024	NON-COMPETING CONTINUATION	$5,357,980
2024	2024	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG				DEU	Human Genome Research	001	11	8/12/2024	SUPPLEMENT FOR EXPANSION	$324,090
														Subtotal = $5,682,070

Issue Date FY: 2023 ( Subtotal = $5,934,121 )
2023	2023	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG				DEU	Human Genome Research	000	10	6/2/2023	NON-COMPETING CONTINUATION	$5,934,121
														Subtotal = $5,934,121

Issue Date FY: 2022 ( Subtotal = $6,399,655 )
2022	2022	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	003	9	7/12/2022	NON-COMPETING CONTINUATION	$5,690,000
2022	2022	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	005	9	8/1/2022	SUPPLEMENT FOR EXPANSION	$198,000
2022	2022	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	004	9	7/21/2022	NON-COMPETING CONTINUATION	$260,675
2022	2022	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	006	9	8/2/2022	SUPPLEMENT FOR EXPANSION	$250,980
2022	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	000	8	2/16/2022	COMPETING CONTINUATION	$64,665
2022	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	002	8	3/23/2022	COMPETING CONTINUATION	$0
2022	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	001	7	2/16/2022	SUPPLEMENT FOR EXPANSION	-$64,665
														Subtotal = $6,399,655

Issue Date FY: 2021 ( Subtotal = $5,750,000 )
2021	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	006	8	9/22/2021	COMPETING CONTINUATION	$783,173
2021	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	004	7	9/16/2021	SUPPLEMENT FOR EXPANSION	$0
2021	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	002	7	5/13/2021	SUPPLEMENT FOR EXPANSION	$1,916,827
2021	2021	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	005	8	9/17/2021	COMPETING CONTINUATION	$3,050,000
2021	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	003	7	9/15/2021	NON-COMPETING CONTINUATION	$0
2021	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	001	7	5/13/2021	NON-COMPETING CONTINUATION	$0
2021	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	000	7	4/15/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $5,750,000

Issue Date FY: 2020 ( Subtotal = $6,058,651 )
2020	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	002	7	6/30/2020	SUPPLEMENT FOR EXPANSION	$318,651
2020	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	001	7	6/24/2020	NON-COMPETING CONTINUATION	$5,740,000
2020	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	003	7	9/15/2020	NON-COMPETING CONTINUATION	$0
2020	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	004	7	9/16/2020	NON-COMPETING CONTINUATION	$0
2020	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	000	6	4/10/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $6,058,651

Issue Date FY: 2019 ( Subtotal = $6,369,881 )
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	003	6	9/20/2019	SUPPLEMENT FOR EXPANSION	$453,902
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	004	6	9/24/2019	SUPPLEMENT FOR EXPANSION	$13,980
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	000	5	2/14/2019	SUPPLEMENT FOR EXPANSION	$67,499
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	002	6	8/29/2019	NON-COMPETING CONTINUATION	$400,000
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	001	6	6/7/2019	NON-COMPETING CONTINUATION	$5,434,500
														Subtotal = $6,369,881

Issue Date FY: 2018 ( Subtotal = $6,555,617 )
2018	2018	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	003	5	9/6/2018	SUPPLEMENT FOR EXPANSION	$512,695
2018	2018	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	001	5	8/22/2018	COMPETING CONTINUATION	$412,999
2018	2018	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	002	5	9/6/2018	COMPETING CONTINUATION	$0
2018	2018	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	004	5	9/22/2018	COMPETING CONTINUATION	$142,922
2018	2018	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	000	5	5/31/2018	COMPETING CONTINUATION	$5,487,001
														Subtotal = $6,555,617

Grand Total All Awards = $42,749,995

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UniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's Disease

Award Number: U24HG007822

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

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