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Quantitative Biology

Quant. Biol.    2018, Vol. 6 Issue (1) : 30-39     https://doi.org/10.1007/s40484-017-0108-3
REVIEW |
Metabolic pathway databases and model repositories
Abraham A. Labena1,2, Yi-Zhou Gao1, Chuan Dong3, Hong-li Hua3, Feng-Biao Guo3()
1. School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
2. College of Computational and Natural Sciences, Dilla University, Dilla P.O.box.?419, Ethiopia
3. School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Abstract

Background: The number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly. These resources are diverse in the type of information/data, the analytical tools, and objectives. Here we present a review of the most popular metabolic pathway databases and model repositories, focusing on their scope, content including reactions, enzymes, compounds, and genes, and applicability. The review aims to help researchers choose a suitable database or model repository according to the information and data required, by providing an insight look of each pathway resource.

Results: Four pathways databases and three model repositories were selected on the basis of popularity and diversity. Our review showed that the pathway resources vary in many aspects, such as their scope, content, access to data and the tools. In addition, inconsistencies have been observed in nomenclature and representation of database entities. The three model repositories reviewed do not offer a brief description of the models’ characteristics such as simulation conditions.

Conclusions: The inconsistencies among the databases in representing their contents may hamper the maximal use of the knowledge accumulated in these databases in particular and the area of systems biology at large. Therefore, it is strongly recommended that the database creators and the metabolic network models developers should follow international standards for the nomenclature of reactions and metabolites. Besides, computationally generated models that could be obtained from model repositories should be utilized with manual curations as they lack some important components that are necessary for full functionality of the models.

Keywords metabolic pathway      database      model repository     
Corresponding Authors: Feng-Biao Guo   
Online First Date: 14 September 2017    Issue Date: 08 March 2018
 Cite this article:   
Abraham A. Labena,Yi-Zhou Gao,Chuan Dong, et al. Metabolic pathway databases and model repositories[J]. Quant. Biol., 2018, 6(1): 30-39.
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http://journal.hep.com.cn/qb/EN/10.1007/s40484-017-0108-3
http://journal.hep.com.cn/qb/EN/Y2018/V6/I1/30
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Abraham A. Labena
Yi-Zhou Gao
Chuan Dong
Hong-li Hua
Feng-Biao Guo
Name Description Website
Arabidopsis Reactome Curated knowledge base of plant biological pathways http://www.arabidopsisreactome.org
AtIPD Arabidopsis thaliana isoprenoid pathway database http://www.atipd.ethz.ch
BiGG Knowledge base of genome-scale metabolic network models http://bigg.ucsd.edu
BioCyc A collection of pathway/genome databases (PGDBs) and software tools for understanding their data http://biocyc.org
BioModels Online reference repository for quantitative, dynamic models of biological network models https://www.ebi.ac.uk/biomodels-main
BioPath Database on biochemical pathways https://www.mn-am.com/databases/biopath
BioSilico A web-based database system that facilitates the search and analysis of metabolic pathways http://biosilico.kaist.ac.kr
BRENDA Comprehensive enzyme information system http://www.brenda-enzymes.info
BsubCyc Database of the bacterium? Bacillus subtilis and is based on the updated? B. subtilis 168 genome sequence and annotation https://bsubcyc.org
CATHACyc Metabolic pathway database of Catharanthus roseus http://www.cathacyc.org
ECMDB Escherichia coli metabolome database http://ecmdb.ca
EcoCyc Encyclopedia of E.coli genes and metabolism https://ecocyc.org
EcoCyc Scientific database for the bacterium? E. coli K-12 MG1655 https://ecocyc.org
ENZYME A repository of information relative to the nomenclature of enzymes http://enzyme.expasy.org
ExPASy Biochemical pathway maps http://web.expasy.org/pathways
FlyReactome A curated knowledgebase of Drosophila melanogaster pathways http://fly.reactome.org
HMDB The human metabolome database http://www.hmdb.ca
HPD An integrated human pathway database http://discern.uits.iu.edu:8340/HPD
HUMANCyc An encyclopedic reference on human metabolic pathways https://humancyc.org
KaPPA-View4 Kazusa Plant Pathway Viewer http://kpv2.kazusa.or.jp/kpv4
KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp
LAMP Library of Apicomplexan metabolic pathways http://www.llamp.net
LIPID MAPS LIPID metabolites and pathways strategy http://www.lipidmaps.org/resources/resources.html
MaizeGDB Metabolic pathways in maize http://maizecyc.maizegdb.org
Malaria Malaria parasite metabolic pathways http://mpmp.huji.ac.il
MedicCyc A biochemical pathway database for Medicago truncatula http://mediccyc.noble.org
MetaCyc Knowledge of experimentally validated metabolic pathways https://metacyc.org
MetaNetX/MetanetX.?org Repository and webserver for genome-scale metabolic network models http://www.metanetx.org/
MetNetDB Contains information on networks of metabolic and regulatory and interactions in Arabidopsis http://metnetweb.gdcb.iastate.edu/MetNet_db.htm
MMMDB Mouse multiple tissue metabolome database http://mmdb.iab.keio.ac.jp
Model SEED Web-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic pathway models http://modelseed.org
MouseCyc Manually curated database of both known and predicted metabolic pathways for the laboratory mouse http://mousecyc.jax.org
PathCase Pathways database system http://nashua.cwru.edu/PathwaysWeb
PC2 Pathway Commons 2 (integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model) http://www.pathwaycommons.org/pc2
PMN Plant metabolic network http://www.plantcyc.org
Reactome A free, open-source, curated and peer-reviewed pathway database http://www.reactome.org
RGB Rat resource center http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways2
SABIO-RK Biochemical reaction kinetics database http://sabio.villa-bosch.de
SSER Species specific essential reactions database http://cefg.cn/sser/index.html.
UniPathWay Metabolic pathways database http://www.grenoble.prabi.fr/obiwarehouse/unipathway
YEASTNET A?consensus reconstruction of yeast metabolism http://www.comp-sys-bio.org/yeastnet
YMDB Yeast metabolome database http://www.ymdb.ca
Tab.1  List of available metabolic pathway resources
Database/content Reactions Compounds Pathways Proteins Version
KEGG 10307 17787 474838 6836 80.2
MetaCyc 15162 13585 2884 17090 20.5
Reactome 78927 88597 22072 120935 59
PMN 74013 2509 13117 279301 11.0
Tab.2  Contents of the databases
Name Tools Function
Reactome Pathway browser • A tool for visualizing and interacting with Reactome biological pathways
Analyze data • Merges pathway identifier mapping, over-representation, and expression analysis tools ?into a single tabbed data analysis portal with integrated visualization and summary ?features, which can accept a gene, protein or small molecule list, or an expression ?dataset
Species comparison • Allows users to compare pathways between human and any of the other species inferred ?from Reactome by orthology
Reactome FI network • Cytoscape plugin designed to find network patterns related to cancer and other types of ?diseases
MetaCyc Pathway tools • Development of organism-specific databases
• Metabolic reconstruction and modeling
• Scientific visualization, web publishing
• Visual analysis of gene expression and metabolomics datasets
• Computational inferences
• Comparative genome and pathway analyses
• Analysis of biological networks
PMN E2P2 • Enzyme function annotation software. Predicts metabolic enzymes in a sequenced ?genome
SAVI • Pathway validation software. Processes predicted metabolic pathways using pathway ?metadata such as taxonomic distribution and key reactions and makes decisions about ?which pathways to keep, remove, or subject to manual validation
KEGG PlantClusterFinder • A pipeline to predict metabolic gene clusters from plant genomes
KegHier • Java application for browsing BRITE hierarchy files
KegArray • Java application for microarray data analysis
KegDraw • Java application for drawing compound and glycan structures
Tab.3  Comparison of the databases based on additional functions
Name Tools Function
BiGG Escher map and model validation tool It is a web-based tool for building, viewing and sharing visualizations of biological pathways
BioModels Path2Models (automatic generation of GSM) It automatically generates metabolic models from biochemical pathway maps
MetaNetX Flux balance analysis (FBA), flux variability analysis (FVA), group of coupled reactions (GCR), reaction knock-out (RKO), peptide/gene knock-out (PKO), gap-filling (GAP), predict direction (DIR) A web-based resource for accessing, analysing and manipulating genome-scale metabolic networks. It also provides interactive comaprison of two or more models and interates data from various public resources
Tab.4  Comparison of tools in model repositories
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