Computing with biochemical reactions is increasingly important in studying genomes, assessing toxicity, and developing therapeutics. There are several important information sources, but their data are rudimentary and often inaccurate. Incorporation of biochemical information into databases is extremely slow compared to that of sequence and structural information, and will lag further as large-scale surveys of gene expression and other reactions accelerate over the next few years. Mechanisms for review exist, but are manual, paper-dependent, and can be delayed for a year or more. As curators and coordinators of biochemical information sources, the applicants share a number of problems in the collection and review of information. Moreover, they are mutually dependent for the means to do so: compound information is critical in checking reaction data, reaction information is needed to spot errors in compound information, and the automatic verification algorithms for either are closely related and need both. The applicants, therefore, propose to build a curatorial exchange for the deposit and review of biochemical information by the scientific community. The applicants' goal is to demonstrate a system that will encourage the mandating of deposit while ensuring that the information is of the highest quality. The role of the exchange is to receive deposits, check and classify their biochemical information automatically, forward them to panels of human reviewers for vetting, and publish the information by release to the participating data sources--all over the World-Wide Web. It will track the origin and status of deposits and reviews, serve computations for the relevant pattern matching and simulation, and maintain an archival copy of data. The databases remain independent, and separately provide additional information. Algorithm development and testing depends on an adequate information infrastructure, so the applicants will complete a basic data set of compounds and reactions. They will use this experience to develop a more comprehensive domain model that better captures modern biochemistry, and implement it for deposit and review. Since the basic data and algorithms will be valuable to the community at large, they plan to serve these to the World-Wide Web. the exchange and its underlying data form the infrastructure necessary for sustainable, cost-effective development of biochemical informatics resources for biomedical research.
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| Levine, Andrew J; Singer, Elyse J; Shapshak, Paul (2009) The role of host genetics in the susceptibility for HIV-associated neurocognitive disorders. AIDS Behav 13:118-32 |
| Shapshak, Paul; Somboonwit, Charurut; Drumright, Lydia N et al. (2009) Molecular and contextual markers of hepatitis C virus and drug abuse. Mol Diagn Ther 13:153-79 |
| Minagar, Alireza; Commins, Deborah; Alexander, J Steven et al. (2008) NeuroAIDS: characteristics and diagnosis of the neurological complications of AIDS. Mol Diagn Ther 12:25-43 |
| Zarate, Selene; Pond, Sergei L Kosakovsky; Shapshak, Paul et al. (2007) Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol 81:6643-51 |
| Shapshak, Paul; Duncan, Robert; Nath, Avindra et al. (2006) Gene chromosomal organization and expression in cultured human neurons exposed to cocaine and HIV-1 proteins gp120 and tat: drug abuse and NeuroAIDS. Front Biosci 11:1774-93 |
| Chiappelli, Francesco; Shapshak, Paul; Younai, Fariba et al. (2006) Cellular immunology in HIV-1 positive African American women using alcohol and cocaine. Front Biosci 11:2434-41 |
| Kazic, Toni (2006) Putting semantics into the semantic web: how well can it capture biology? Pac Symp Biocomput :140-51 |
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| Sakharkar, Meena Kishore; Chow, Vincent Tak Kwong; Chaturvedi, Iti et al. (2004) A report on single exon genes (SEG) in eukaryotes. Front Biosci 9:3262-7 |
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