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The EcoCyc Model Organism Database for Escherichia coli

Award Number: R01GM077678
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/15/1992
PERIOD OF PERFORMANCE END DATE: 09/29/2023

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The EcoCyc Model Organism Database for Escherichia coli - Project Summary SRI International and a group of collaborators propose to further develop the Escherichia coli EcoCyc database (DB). EcoCyc is and will continue to be freely and openly available, and is accessible to scien- tists through the Internet, as downloadable data ﬁles, and as a downloadable software application. Scientists from multiple disciplines make wide use of EcoCyc; it has been cited 3,428 times, and from 2015–2017, an average of 99,800 users per year visited the EcoCyc website. It serves as a gen- eral reference source on E. coli for experimental biologists, and is particularly useful for the analysis of functional-genomics experiments. The DB serves computational biologists who are undertaking global studies of E. coli; metabolic engineers who are developing new methods for chemicals production, in- cluding biofuels; and researchers and bioinformaticists who are using EcoCyc as the gold-standard dataset to develop new computational methods, including the prediction of operons, promoters, and protein functional linkages. Educators also use the DB. We will update EcoCyc in an ongoing fashion to reﬂect new information about the genes, metabolic pathways, and regulatory interactions of these important model organisms. Information will be inte- grated from the biomedical literature and from large-scale experiments, such as data on gene essential- ity, on nutrients supporting growth, and on protein interactions. We will continue a comprehensive and ongoing effort to reﬁne steady-state metabolic network models of these organisms by validating model predictions against many conditions of growth and non-growth for wildtype and knock-out strains. The resulting models will have applications in anti-microbial drug discovery and metabolic engineer- ing, and the model development process will lead to many improvements in the EcoCyc DB. We will launch a new effort to curate the genes and proteins of E. coli strains other than the strain served by EcoCyc. Thousands of E. coli strains have been sequenced; yet in many cases, their genome annotations are of low quality. We will project curated gene annotations from EcoCyc and from other E. coli strains to orthologs of those genes in the BioCyc DBs for hundreds of other E. coli strains, thus signiﬁcantly improving the annotation quality of other E. coli strains, in a cost-effective fashion. The project will also expand the Pathway Tools software used to query and analyze EcoCyc, such as adding a tool for projecting newly curated gene and protein annotations to orthologs in other E. coli strains.


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 = $0 )
2024	2022	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	000	31	2/25/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $0 )
2023	2022	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	000	31	9/22/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $1,162,075 )
2022	2022	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	000	31	6/27/2022	NON-COMPETING CONTINUATION	$1,162,075
														Subtotal = $1,162,075

Issue Date FY: 2021 ( Subtotal = $1,161,946 )
2021	2021	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	000	30	7/12/2021	NON-COMPETING CONTINUATION	$1,161,946
														Subtotal = $1,161,946

Issue Date FY: 2020 ( Subtotal = $1,161,946 )
2020	2020	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	001	29	7/1/2020	NON-COMPETING CONTINUATION	$1,161,946
2020	2019	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	000	28	6/18/2020	COMPETING CONTINUATION	$0
														Subtotal = $1,161,946

Issue Date FY: 2019 ( Subtotal = $1,160,384 )
2019	2019	SRI INTERNATIONAL	333 RAVENSWOOD AVE	MENLO PARK	CA	94025	SAN MATEO	USA	Biomedical Research and Research Training	000	28	7/4/2019	COMPETING CONTINUATION	$1,160,384
														Subtotal = $1,160,384

Grand Total All Awards = $4,646,351

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The EcoCyc Model Organism Database for Escherichia coli

Award Number: R01GM077678

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/15/1992

PERIOD OF PERFORMANCE END DATE: 09/29/2023

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