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Quantitative Biology

Quant. Biol.
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   
 Cite this article:   
Abraham A. Labena,Yi-Zhou Gao,Chuan Dong, et al. Metabolic pathway databases and model repositories[J]. Quant. Biol., 14 September 2017. [Epub ahead of print] doi: 10.1007/s40484-017-0108-3.
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http://journal.hep.com.cn/qb/EN/10.1007/s40484-017-0108-3
http://journal.hep.com.cn/qb/EN/Y/V/I/0
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Abraham A. Labena
Yi-Zhou Gao
Chuan Dong
Hong-li Hua
Feng-Biao Guo
NameDescriptionWebsite
Arabidopsis ReactomeCurated knowledge base of plant biological pathwayshttp://www.arabidopsisreactome.org
AtIPDArabidopsis thaliana isoprenoid pathway databasehttp://www.atipd.ethz.ch
BiGGKnowledge base of genome-scale metabolic network modelshttp://bigg.ucsd.edu
BioCycA collection of pathway/genome databases (PGDBs) and software tools for understanding their datahttp://biocyc.org
BioModelsOnline reference repository for quantitative, dynamic models of biological network modelshttps://www.ebi.ac.uk/biomodels-main
BioPathDatabase on biochemical pathwayshttps://www.mn-am.com/databases/biopath
BioSilicoA web-based database system that facilitates the search and analysis of metabolic pathwayshttp://biosilico.kaist.ac.kr
BRENDAComprehensive enzyme information systemhttp://www.brenda-enzymes.info
BsubCycDatabase of the bacterium? Bacillus subtilis and is based on the updated? B. subtilis 168 genome sequence and annotationhttps://bsubcyc.org
CATHACycMetabolic pathway database of Catharanthus roseushttp://www.cathacyc.org
ECMDBEscherichia coli metabolome databasehttp://ecmdb.ca
EcoCycEncyclopedia of E.coligenes and metabolismhttps://ecocyc.org
EcoCycScientific database for the bacterium? E. coli K-12 MG1655https://ecocyc.org
ENZYMEA repository of information relative to the nomenclature of enzymeshttp://enzyme.expasy.org
ExPASyBiochemical pathway mapshttp://web.expasy.org/pathways
FlyReactomeA curated knowledgebase of Drosophila melanogaster pathwayshttp://fly.reactome.org
HMDBThe human metabolome databasehttp://www.hmdb.ca
HPDAn integrated human pathway databasehttp://discern.uits.iu.edu:8340/HPD
HUMANCycAn encyclopedic reference on human metabolic pathwayshttps://humancyc.org
KaPPA-View4Kazusa Plant Pathway Viewerhttp://kpv2.kazusa.or.jp/kpv4
KEGGKyoto Encyclopedia of Genes and Genomeshttp://www.kegg.jp
LAMPLibrary of Apicomplexan metabolic pathwayshttp://www.llamp.net
LIPID MAPSLIPID metabolites and pathways strategyhttp://www.lipidmaps.org/resources/resources.html
MaizeGDBMetabolic pathways in maizehttp://maizecyc.maizegdb.org
MalariaMalaria parasite metabolic pathwayshttp://mpmp.huji.ac.il
MedicCycA biochemical pathway database for Medicago truncatulahttp://mediccyc.noble.org
MetaCycKnowledge of experimentally validated metabolic pathwayshttps://metacyc.org
MetaNetX/MetanetX.?orgRepository and webserver for genome-scale metabolic network modelshttp://www.metanetx.org/
MetNetDBContains information on networks of metabolic and regulatory and interactions in Arabidopsishttp://metnetweb.gdcb.iastate.edu/MetNet_db.htm
MMMDBMouse multiple tissue metabolome databasehttp://mmdb.iab.keio.ac.jp
Model SEEDWeb-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic pathway modelshttp://modelseed.org
MouseCycManually curated database of both known and predicted metabolic pathways for the laboratory mousehttp://mousecyc.jax.org
PathCasePathways database systemhttp://nashua.cwru.edu/PathwaysWeb
PC2Pathway 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
PMNPlant metabolic networkhttp://www.plantcyc.org
ReactomeA free, open-source, curated and peer-reviewed pathway databasehttp://www.reactome.org
RGBRat resource centerhttp://rgd.mcw.edu/wg/home/pathway2/molecular-pathways2
SABIO-RKBiochemical reaction kinetics databasehttp://sabio.villa-bosch.de
SSERSpecies specific essential reactions databasehttp://cefg.cn/sser/index.html.
UniPathWayMetabolic pathways databasehttp://www.grenoble.prabi.fr/obiwarehouse/unipathway
YEASTNETA?consensus reconstruction of yeast metabolismhttp://www.comp-sys-bio.org/yeastnet
YMDBYeast metabolome databasehttp://www.ymdb.ca
Tab.1  List of available metabolic pathway resources
Database/contentReactionsCompoundsPathwaysProteinsVersion
KEGG1030717787474838683680.2
MetaCyc151621358528841709020.5
Reactome78927885972207212093559
PMN7401325091311727930111.0
Tab.2  Contents of the databases
NameToolsFunction
ReactomePathway 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
MetaCycPathway 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
PMNE2P2• 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
KEGGPlantClusterFinder• 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
NameToolsFunction
BiGGEscher map and model validation toolIt is a web-based tool for building, viewing and sharing visualizations of biological pathways
BioModelsPath2Models (automatic generation of GSM)It automatically generates metabolic models from biochemical pathway maps
MetaNetXFlux 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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