Dataset Information

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.

ABSTRACT: The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since then. Here, we present an updated version of ATLAS created from KEGG 2018 using an increased set of generalized reaction rules. Furthermore, we improved the accuracy of the enzymes that are predicted for catalyzing novel reactions. ATLAS now contains ?150?000 reactions, out of which 96% are novel. In this report, we present detailed statistics on the updated ATLAS and highlight the improvements with regard to the previous version. Most importantly, 107 reactions predicted in the original ATLAS are now known to KEGG, which validates the predictive power of our approach. The updated ATLAS is available at https://lcsb-databases.epfl.ch/atlas.

SUBMITTER: Hafner J

PROVIDER: S-EPMC7309321 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.

Hafner Jasmin J MohammadiPeyhani Homa H Sveshnikova Anastasia A Scheidegger Alan A Hatzimanikatis Vassily V

ACS synthetic biology 20200602 6

The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since then. Here, we present an updated version of ATLAS created from KEGG 2018 using an increased set of generalized reaction rules. Furthermore, we improved the accuracy of the enzymes tha ...[more]

PMID: 32421310

Similar Datasets

Project description:BackgroundReliable and updated maps of helminth (worm) infection distributions are essential to target control strategies to those populations in greatest need. Although many surveys have been conducted in endemic countries, the data are rarely available in a form that is accessible to policy makers and the managers of public health programmes. This is especially true in sub-Saharan Africa, where empirical data are seldom in the public domain. In an attempt to address the paucity of geographical information on helminth risk, this article describes the development of an updated global atlas of human helminth infection, showing the example of East Africa.MethodsEmpirical, cross-sectional estimates of infection prevalence conducted since 1980 were identified using electronic and manual search strategies of published and unpublished sources. A number of inclusion criteria were imposed for identified information, which was extracted into a standardized database. Details of survey population, diagnostic methods, sample size and numbers infected with schistosomes and soil-transmitted helminths were recorded. A unique identifier linked each record to an electronic copy of the source document, in portable document format. An attempt was made to identify the geographical location of each record using standardized geolocation procedures and the assembled data were incorporated into a geographical information system.ResultsAt the time of writing, over 2,748 prevalence surveys were identified through multiple search strategies. Of these, 2,612 were able to be geolocated and mapped. More than half (58%) of included surveys were from grey literature or unpublished sources, underlining the importance of reviewing in-country sources. 66% of all surveys were conducted since 2000. Comprehensive, countrywide data are available for Burundi, Rwanda and Uganda. In contrast, information for Kenya and Tanzania is typically clustered in specific regions of the country, with few records from areas with very low population density and/or environmental conditions which are unfavourable for helminth transmission. Information is presented on the prevalence and geographical distribution for the major helminth species.ConclusionFor all five countries, the information assembled in the current atlas provides the most reliable, up-to-date and comprehensive source of data on the distribution of common helminth infections to guide the rational implementation of control efforts.

Dataset Information

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.

Publications

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets