UniPathway: a Resource for the Exploration and Annotation of Metabolic Pathways

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Nov 22

PMID 22102589

Citations 59

Authors

Anne Morgat

Eric Coissac

Elisabeth Coudert

Kristian B Axelsen

Guillaume Keller

Amos Bairoch

Alan Bridge

Lydie Bougueleret

Ioannis Xenarios

Alain Viari

Affiliations

Soon will be listed here.

Abstract

UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc, as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled vocabulary for pathway annotation. We introduce here the basic concepts underlying the UniPathway resource, with the aim of allowing users to fully exploit the information provided by UniPathway.

Citing Articles

A severe asthma phenotype of excessive airway Haemophilus influenzae relative abundance associated with sputum neutrophilia.

Versi A, Azim A, Ivan F, I Abdel-Aziz M, Bates S, Riley J Clin Transl Med. 2024; 14(9):e70007.

PMID: 39187935 PMC: 11347389. DOI: 10.1002/ctm2.70007.

Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes.

Palacios N, Wilkinson J, Bjornevik K, Schwarzschild M, McIver L, Ascherio A Ann Neurol. 2023; 94(3):486-501.

PMID: 37314861 PMC: 10538421. DOI: 10.1002/ana.26719.

MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis.

Lopez-Ibanez J, Pazos F, Chagoyen M Nucleic Acids Res. 2023; 51(W1):W305-W309.

PMID: 37178003 PMC: 10320153. DOI: 10.1093/nar/gkad405.

DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases.

Bajic V, Salhi A, Lakota K, Radovanovic A, Razali R, Zivkovic L PLoS One. 2022; 17(7):e0271737.

PMID: 35877764 PMC: 9312389. DOI: 10.1371/journal.pone.0271737.

ContactPFP: Protein function prediction using predicted contact information.

Kagaya Y, Flannery S, Jain A, Kihara D Front Bioinform. 2022; 2.

PMID: 35875419 PMC: 9302406. DOI: 10.3389/fbinf.2022.896295.

References

Overbeek R, Begley T, Butler R, Choudhuri J, Chuang H, Cohoon M . The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33(17):5691-702. PMC: 1251668. DOI: 10.1093/nar/gki866. View

Kosuge T, Hoshino T . Lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus. FEMS Microbiol Lett. 1998; 169(2):361-7. DOI: 10.1111/j.1574-6968.1998.tb13341.x. View

Dairi T, Kuzuyama T, Nishiyama M, Fujii I . Convergent strategies in biosynthesis. Nat Prod Rep. 2011; 28(6):1054-86. DOI: 10.1039/c0np00047g. View

Finn R, Mistry J, Tate J, Coggill P, Heger A, Pollington J . The Pfam protein families database. Nucleic Acids Res. 2009; 38(Database issue):D211-22. PMC: 2808889. DOI: 10.1093/nar/gkp985. View

Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro: the integrative protein signature database. Nucleic Acids Res. 2008; 37(Database issue):D211-5. PMC: 2686546. DOI: 10.1093/nar/gkn785. View

Sayers E, Barrett T, Benson D, Bryant S, Canese K, Chetvernin V . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2008; 37(Database issue):D5-15. PMC: 2686545. DOI: 10.1093/nar/gkn741. View

Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M . KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2009; 38(Database issue):D355-60. PMC: 2808910. DOI: 10.1093/nar/gkp896. View

. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2009; 38(Database issue):D331-5. PMC: 2808930. DOI: 10.1093/nar/gkp1018. View

Sigrist C, Cerutti L, de Castro E, Langendijk-Genevaux P, Bulliard V, Bairoch A . PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 2009; 38(Database issue):D161-6. PMC: 2808866. DOI: 10.1093/nar/gkp885. View

10.

. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 2010; 39(Database issue):D214-9. PMC: 3013648. DOI: 10.1093/nar/gkq1020. View

11.

Hudson A, Gilvarg C, Leustek T . Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase. J Bacteriol. 2008; 190(9):3256-63. PMC: 2347407. DOI: 10.1128/JB.01381-07. View

12.

Caspi R, Altman T, Dale J, Dreher K, Fulcher C, Gilham F . The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2009; 38(Database issue):D473-9. PMC: 2808959. DOI: 10.1093/nar/gkp875. View

13.

Green M, Karp P . The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res. 2006; 34(13):3687-97. PMC: 1540720. DOI: 10.1093/nar/gkl438. View

14.

de Matos P, Alcantara R, Dekker A, Ennis M, Hastings J, Haug K . Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 2009; 38(Database issue):D249-54. PMC: 2808869. DOI: 10.1093/nar/gkp886. View

15.

Lima T, Auchincloss A, Coudert E, Keller G, Michoud K, Rivoire C . HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res. 2008; 37(Database issue):D471-8. PMC: 2686602. DOI: 10.1093/nar/gkn661. View

16.

Webb K, White T . UML as a cell and biochemistry modeling language. Biosystems. 2005; 80(3):283-302. DOI: 10.1016/j.biosystems.2004.12.003. View

17.

Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C . Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 2004; 33(Database issue):D297-302. PMC: 539993. DOI: 10.1093/nar/gki039. View

18.

Karp P, Riley M, Paley S . EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 1996; 24(1):32-9. PMC: 145574. DOI: 10.1093/nar/24.1.32. View

19.

Henry C, DeJongh M, Best A, Frybarger P, Linsay B, Stevens R . High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010; 28(9):977-82. DOI: 10.1038/nbt.1672. View

20.

Claudel-Renard C, Chevalet C, Faraut T, Kahn D . Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res. 2003; 31(22):6633-9. PMC: 275543. DOI: 10.1093/nar/gkg847. View