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WormBase: a core data resource for C. elegans and other nematodes

Award Number: U24HG002223
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 07/20/2000
PERIOD OF PERFORMANCE END DATE: 06/30/2028

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WormBase: a core data resource for C. elegans and other nematodes - Project Summary We will continue to develop WormBase, a broadly and often daily-used knowledgebase of information about the C. elegans genome, genes, sequence features, gene function, gene interactions, and related information. C. elegans is a premier research organism with about 1500 registered laboratories worldwide who use the short generation time, complete genome, efficient genome editing, defined anatomy and neuroanatomy to study a wide range of biomedical and fundamental topics. WormBase also curates, stores, and displays information about nine other nematode genomes of biomedical importance. We will continue to develop necessary ontologies and gene nomenclature to support systematic annotation of the genome and gene function and expression. After 20 years of independent infrastructure development, we will now use the Alliance of Genome Resources infrastructure for data ingest, storage, efficient curation, and presentation via download, API, and web portal. We will complete the migration of the software infrastructure by the second year. This project will focus on curation of genome scale datasets and individual experiments from the literature as well as storage and display of C. elegans- or nematode-specific data. A major challenge is the increased published data and datasets and decreased staff, which we will proactively address by streamlining and making our systems more automated and high throughput. Our main strategies for scaling curation are by increased automation, namely machine learning (ML) and artificial intelligence (AI); and by community input powered by ML/AI, also incentivized by microPublication-based reviews of pathways and genes. As we are trying to scale, while maintaining our very high-quality data collection (which is re-used by many other bioinformatic resources), professional biocurators with a deep understanding of the biology and researchers needs will increasingly focus on data modeling, quality control, development and training of automated systems, and supporting community curation. We will curate information directly tied to nucleic acid sequence including the genome sequence; sequence features such as gene structure models, regulatory regions, variants, sequence-based reagents, genome-scale experiments; and gene expression including reporter gene assays and RNA-seq, sc-RNA-seq. We will curate information centered on gene function including phenotype of variants and perturbations, disease models, genetic and physical interactions, Gene Ontology (GO) annotations, and pathways using GO-Causal Activity Models. After we transition computational infrastructure to the Alliance, we will continue to curate datasets unique to C. elegans and add them to the Alliance infrastructure. We will support researchers by a 24/7 help desk, which provides advice and often analysis; curation, storage, and display of worm-specific datasets; provision of customized analysis tools; and a community forum. For new data, we will specify software requirements for development at the Alliance.


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: 2026 ( Subtotal = $0 )
2026	2025	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	26	2/20/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2025 ( Subtotal = $1,440,192 )
2025	2025	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	26	9/22/2025	NON-COMPETING CONTINUATION	$1,440,192
														Subtotal = $1,440,192

Issue Date FY: 2024 ( Subtotal = $1,440,191 )
2024	2024	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	002	25	8/2/2024	NON-COMPETING CONTINUATION	$1,440,191
2024	2023	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	001	24	1/4/2024	COMPETING CONTINUATION	$194,262
2024	2022	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	23	1/4/2024	NON-COMPETING CONTINUATION	-$194,262
														Subtotal = $1,440,191

Issue Date FY: 2023 ( Subtotal = $1,469,582 )
2023	2023	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	24	8/24/2023	COMPETING CONTINUATION	$1,469,582
														Subtotal = $1,469,582

Issue Date FY: 2022 ( Subtotal = $1,763,499 )
2022	2022	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	23	7/12/2022	NON-COMPETING CONTINUATION	$1,763,499
														Subtotal = $1,763,499

Issue Date FY: 2021 ( Subtotal = $2,053,636 )
2021	2021	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	22	7/1/2021	NON-COMPETING CONTINUATION	$2,053,636
														Subtotal = $2,053,636

Issue Date FY: 2020 ( Subtotal = $2,200,324 )
2020	2020	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	21	7/31/2020	NON-COMPETING CONTINUATION	$2,200,324
														Subtotal = $2,200,324

Issue Date FY: 2019 ( Subtotal = $2,541,153 )
2019	2019	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	005	20	7/11/2019	NON-COMPETING CONTINUATION	$2,347,011
2019	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	003	19	2/4/2019	COMPETING CONTINUATION	$61,377
2019	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	002	19	2/1/2019	COMPETING CONTINUATION	-$30,688
2019	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	004	19	3/8/2019	COMPETING CONTINUATION	$0
2019	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	19	11/8/2018	COMPETING CONTINUATION	$0
2019	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	001	19	11/28/2018	COMPETING CONTINUATION	$163,453
														Subtotal = $2,541,153

Issue Date FY: 2018 ( Subtotal = $4,938,075 )
2018	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	000	19	9/5/2018	COMPETING CONTINUATION	$2,493,700
2018	2018	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Human Genome Research	001	19	9/11/2018	SUPPLEMENT FOR EXPANSION	$2,444,375
														Subtotal = $4,938,075

Grand Total All Awards = $17,846,652

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WormBase: a core data resource for C. elegans and other nematodes

Award Number: U24HG002223

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

PERIOD OF PERFORMANCE START DATE: 07/20/2000

PERIOD OF PERFORMANCE END DATE: 06/30/2028

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