| 1 |
Biopath - Database on Biochemical Pathwayshttp://www.molecular-networks.com/databases/biopath |
| Contains biological transformation and regulations derived from the Roche Applied Science "biochemical pathways" wall chart. |
| | Schreiber F. High quality visualization of biochemical pathways in BioPath. In Silico Biol. 2002;2(2):59-73. PubMed PMID: 12066841. |
| 2002 | 100 |
|
| 2 |
CPA - Comparative Pathway Analyzerhttp://cpa.cebitec.uni-bielefeld.de |
| Investigates reaction content of a set of organisms. |
| | Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W433-7. Epub 2008 Jun 6. PubMed PMID: 18539612; PubMed Central PMCID: PMC2447754. |
| 2008 | 100 |
|
| 3 |
FMM - From Metabolite to Metabolitehttp://FMM.mbc.nctu.edu.tw |
| Reconstruct the pathway from one metabolite to another, comparison of the pathway among species. |
| | Chou CH, Chang WC, Chiu CM, Huang CC, Huang HD. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W129-34. Epub 2009 Apr 28. PubMed PMID: 19401437; PubMed Central PMCID: PMC2703958. |
| 2009 | 100 |
|
| 4 |
JWS - Java Web Simulationhttp://jjj.biochem.sun.ac.za |
| Repository of kinetic models describing biological systems which can be interactively run and interrogated over the internet. |
| | Snoep JL, Olivier BG. Java Web Simulation (JWS); a web based database of kinetic models. Mol Biol Rep. 2002;29(1-2):259-63. PubMed PMID: 12241068. |
| 2002 | 100 |
|
| 5 |
KEGG - Kyoto Encyclopedia of Genes and Genomeshttp://www.genome.jp/kegg |
| Database of metabolic pathways from different organisms, also provides reference pathways that describe a general pathway which is then projected onto a genome based on the presence of pathway enzymes in that genome. |
| | Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.PubMed PMID: 9847135; PubMed Central PMCID: PMC148090. |
| 1999 | 100 |
|
| 6 |
MedicCychttp://www.noble.org/mediccyc |
| Pathway database for Medicago truncatula. |
| | Urbanczyk-Wochniak E, Sumner LW. MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 2007 Jun 1;23(11):1418-23. Epub 2007 Mar 7. PubMed PMID: 17344243. |
| 2007 | 100 |
|
| 7 |
MetaCorehttp://www.genego.com/metacore.php |
| Database of molecular cellular pathways, and is designed to integrate data from different levels of cellular function. |
| | Ekins S, Nikolsky Y, Bugrim A, Kirillov E, Nikolskaya T. Pathway mapping tools for analysis of high content data. Methods Mol Biol. 2007;356:319-50. Review. PubMed PMID: 16988414. |
| 2007 | 100 |
License required to access the resource.
License required to access the resource. |
| 8 |
MetaCrophttp://pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=269:111:802960176267400 |
| Hand-curated information of major metabolic pathways in crops. |
| | Grafahrend-Belau E, Weise S, KoschFCtzki D, Scholz U, Junker BH, Schreiber F. MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 2008 Jan;36(Database issue):D954-8. Epub 2007 Oct 11. PubMed PMID: 17933764; PubMed Central PMCID: PMC2238923. |
| 2007 | 100 |
|
| 9 |
METAPATHhttp://scopes.biologie.hu-berlin.de/index.php?m=path |
| Calculation of minimal synthesis pathway. |
| | Handorf T, EbenhF6h O. MetaPath Online: a web server implementation of the network expansion algorithm. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W613-8. Epub 2007 May 5. PubMed PMID: 17483511; PubMed Central PMCID:PMC1933239. |
| 2007 | 100 |
|
| 10 |
MetExplorehttp://metexplore.toulouse.inra.fr/metexploreJoomla/index.php |
| A web resource that offers the possibility to link the metabolites identified in untargetted metabolomics experiments within the context of genome scale reconstructed metabolic network. |
| | Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. Epub 2010 May 5. PubMed PMID: 20444866; PubMed Central PMCID: PMC2896158. |
| 2010 | 100 |
|
| 11 |
MiMI - Michigan Molecular Interactionshttp://mimi.ncibi.org/MimiWeb/main-page.jsp |
| Contains pathway diagrams from KEGG and Reactome. |
| | Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720. |
| 2006 | 100 |
|
| 12 |
NCBI BioSystemshttp://www.ncbi.nlm.nih.gov/biosystems |
| Connects biosystem records with the associated literature, molecular and chemical data. |
| | Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol. 2009;10(8):R84. Epub 2009 Aug 14. PubMed PMID: 19682380; PubMed Central PMCID:PMC2745765. |
| 2009 | 100 |
|
| 13 |
PANTHER - Protein ANalysis Through Evolutionary Relationshipshttp://www.pantherdb.org |
| Gene expression data analysis, comparison of gene lists. |
| | Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. The PANTHERdatabase of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8. PubMed PMID: 15608197; PubMed Central PMCID: PMC540032. |
| 2005 | 100 |
|
| 14 |
PathLocdbhttp://pathloc.cbi.pku.edu.cn |
| Search and comparison of the metabolic pathway by their subcellular localization and organisms. Discover the regulatory mechanisms of these pathways. |
| | Zhao M, Qu H. PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. BMC Genomics. 2010 Dec 2;11 Suppl 4:S13. PubMed PMID: 21143796; PubMed Central PMCID: PMC3005916. |
| 2010 | 100 |
|
| 15 |
PathPred - Pathway Prediction serverhttp://www.genome.jp/tools/pathpred |
| Enzyme catalyzed metabolic pathway prediction server. |
| | Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M.PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W138-43. Epub 2010 Apr 30. PubMed PMID:20435670; PubMed Central PMCID: PMC2896155. |
| 2010 | 100 |
|
| 16 |
Pathway Commonshttp://www.pathwaycommons.org/pc/ |
| Provides researchers with convenient access to the collection of publicly available pathways from many different organisms. |
| | Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. Epub 2010 Nov 10. PubMed PMID: 21071392; PubMed Central PMCID: PMC3013659. |
| 2010 | 100 |
|
| 17 |
PlantCychttp://www.plantcyc.org |
| Contains pathways, genes, catalytic enzymes and compounds from many different plant species. |
| | Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY. Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol. 2010 Aug;153(4):1479-91. Epub 2010 Jun 3. PubMed PMID: 20522724; PubMed Central PMCID:PMC2923894. |
| 2010 | 100 |
|
| 18 |
Protein Loungehttp://www.proteinlounge.com |
| Contains curated pathways for many different organisms. |
| | Not available | 100 |
|
| 19 |
ResNethttp://www.ariadnegenomics.com/products/databases/ariadne-resnet |
| Pathway database completely extracted from PubMed using MedScan and natural language processing tools. |
| | Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics. 2004 Mar 22;20(5):604-11. Epub 2004 Jan 22. PubMed PMID:15033866. |
| 2004 | 100 |
|
| 20 |
RiceCyc - Rice metabolic pathwayshttp://www.gramene.org/pathway/ricecyc.html |
| Information on metabolic pathways in rice. |
| | Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D717-23. PubMed PMID: 16381966; PubMed Central PMCID: PMC1347516. |
| 2007 | 100 |
|
| 21 |
SoyBase - USDA-ARS Soybean Genetics and Genome Databasehttp://soybase.ncgr.org |
| Information about molecules and enzymes involved in soybean metabolic pathway. |
| | Grant D, Nelson RT, Cannon SB, Shoemaker RC. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6. Epub 2009 Dec 14. PubMed PMID: 20008513; PubMed Central PMCID:PMC2808871. |
| 2009 | 100 |
|
| 22 |
TRRD - Transcription Regulatory Regions Databasehttp://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd |
| Information on the structural and functional organization of transcription regulatory regions in the eukaryotic genes. |
| | Kel' AE, Kolchanov NA, Kel' OV, Romashchenko AG, Anan'ko EA, Ignat'eva EV, Merkulova TI, Podkolodnaia OA, Stepanenko IL, Kochetov AV, Kolpakov FA,Podkolodnyi NL, Naumochkin AA. [TRRD: a database of transcription regulatory regions in eukaryotic genes]. Mol Biol (Mosk). 1997 Jul-Aug;31(4):626-36.Russian. PubMed PMID: 9340490. |
| 1997 | 100 |
|
| 23 |
VisANThttp://visant.bu.edu |
| Visual analysis tool for biological networks, predict the function of a network module. |
| | Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5:17. PubMed PMID: 15028117; PubMed Central PMCID: PMC368431. |
| 2004 | 100 |
|
| 24 |
WikiPathwayshttp://wikipathways.org |
| Open, public space for pathway editing. |
| | Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C.WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184.PubMed PMID: 18651794; PubMed Central PMCID: PMC2475545. |
| 2008 | 100 |
|
