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. 2015 Jul 24:2015:bav068.
doi: 10.1093/database/bav068. Print 2015.

Human metabolic atlas: an online resource for human metabolism

Natapol Pornputtapong  1 , Intawat Nookaew  2 , Jens Nielsen  1
Affiliations

Human metabolic atlas: an online resource for human metabolism

Natapol Pornputtapong et al. Database (Oxford). .

Abstract

Human tissue-specific genome-scale metabolic models (GEMs) provide comprehensive understanding of human metabolism, which is of great value to the biomedical research community. To make this kind of data easily accessible to the public, we have designed and deployed the human metabolic atlas (HMA) website (http://www.metabolicatlas.org). This online resource provides comprehensive information about human metabolism, including the results of metabolic network analyses. We hope that it can also serve as an information exchange interface for human metabolism knowledge within the research community. The HMA consists of three major components: Repository, Hreed (Human REaction Entities Database) and Atlas. Repository is a collection of GEMs for specific human cell types and human-related microorganisms in SBML (System Biology Markup Language) format. The current release consists of several types of GEMs: a generic human GEM, 82 GEMs for normal cell types, 16 GEMs for different cancer cell types, 2 curated GEMs and 5 GEMs for human gut bacteria. Hreed contains detailed information about biochemical reactions. A web interface for Hreed facilitates an access to the Hreed reaction data, which can be easily retrieved by using specific keywords or names of related genes, proteins, compounds and cross-references. Atlas web interface can be used for visualization of the GEMs collection overlaid on KEGG metabolic pathway maps with a zoom/pan user interface. The HMA is a unique tool for studying human metabolism, ranging in scope from an individual cell, to a specific organ, to the overall human body. This resource is freely available under a Creative Commons Attribution-NonCommercial 4.0 International License.

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Figures

Figure 1.
Figure 1.
Web-based data query system. Users provide keywords into the filter input box. For complex keywords, ‘|’ and ‘+’ can be used to combine keyword with ‘or’ and ‘and’ operator, respectively.
Figure 2.
Figure 2.
Summary of Atlas map viewer functions. (A) The main view of Atlas with control panel comprises a pathway input box for selecting specific sub metabolic map to be opened. The pathway input box provides an autocompleting search by pathway names. Atlas starts with a global metabolic pathway map by default. (B) Sub metabolic map with data overlaid and bar plot representing the number of genes that are present in this pathway map for each cell type can be opened by the control panel, clicking on pathway name in every map and clicking on pathway id in the information window. (C) The information window represents information of reactions from the KEGG database and provides link to external databases for further information.
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