Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.

Literature DB >> 33156326

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.

Sébastien Moretti¹, Van Du T Tran¹, Florence Mehl¹, Mark Ibberson¹, Marco Pagni¹.

Abstract

MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).

Entities: CellLine Chemical Disease Gene Species

Year: 2021 PMID： 33156326 PMCID： PMC7778905 DOI： 10.1093/nar/gkaa992

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

44 in total

1. Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks.

Authors: A Kiparissides; V Hatzimanikatis
Journal: Metab Eng Date: 2016-11-12 Impact factor: 9.783

2. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Authors: Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N Mendoza; Anne Richelle; Almut Heinken; Hulda S Haraldsdóttir; Jacek Wachowiak; Sarah M Keating; Vanja Vlasov; Stefania Magnusdóttir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu H J Chan; Maike K Aurich; Catherine M Clancy; Jennifer Modamio; John T Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C El Assal; Luis V Valcarcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M Le; Ding Ma; Yuekai Sun; Lin Wang; James T Yurkovich; Miguel A P Oliveira; Phan T Vuong; Lemmer P El Assal; Inna Kuperstein; Andrei Zinovyev; H Scott Hinton; William A Bryant; Francisco J Aragón Artacho; Francisco J Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A Saunders; Costas D Maranas; Nathan E Lewis; Thomas Sauter; Bernhard Ø Palsson; Ines Thiele; Ronan M T Fleming
Journal: Nat Protoc Date: 2019-03 Impact factor: 13.491

3. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.

Authors: Akhil Kumar; Patrick F Suthers; Costas D Maranas
Journal: BMC Bioinformatics Date: 2012-01-10 Impact factor: 3.169

4. ChEBI in 2016: Improved services and an expanding collection of metabolites.

Authors: Janna Hastings; Gareth Owen; Adriano Dekker; Marcus Ennis; Namrata Kale; Venkatesh Muthukrishnan; Steve Turner; Neil Swainston; Pedro Mendes; Christoph Steinbeck
Journal: Nucleic Acids Res Date: 2015-10-13 Impact factor: 16.971

5. Updates in Rhea - an expert curated resource of biochemical reactions.

Authors: Anne Morgat; Thierry Lombardot; Kristian B Axelsen; Lucila Aimo; Anne Niknejad; Nevila Hyka-Nouspikel; Elisabeth Coudert; Monica Pozzato; Marco Pagni; Sébastien Moretti; Steven Rosanoff; Joseph Onwubiko; Lydie Bougueleret; Ioannis Xenarios; Nicole Redaschi; Alan Bridge
Journal: Nucleic Acids Res Date: 2016-10-26 Impact factor: 16.971

6. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

Authors: Alyaa M Abdel-Haleem; Hooman Hefzi; Katsuhiko Mineta; Xin Gao; Takashi Gojobori; Bernhard O Palsson; Nathan E Lewis; Neema Jamshidi
Journal: PLoS Comput Biol Date: 2018-01-04 Impact factor: 4.475

Review 7. Current status and applications of genome-scale metabolic models.

Authors: Changdai Gu; Gi Bae Kim; Won Jun Kim; Hyun Uk Kim; Sang Yup Lee
Journal: Genome Biol Date: 2019-06-13 Impact factor: 13.583

8. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

Authors: Mathias Ganter; Thomas Bernard; Sébastien Moretti; Joerg Stelling; Marco Pagni
Journal: Bioinformatics Date: 2013-01-28 Impact factor: 6.937

9. The MetaCyc database of metabolic pathways and enzymes.

Authors: Ron Caspi; Richard Billington; Carol A Fulcher; Ingrid M Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Peter E Midford; Quang Ong; Wai Kit Ong; Suzanne Paley; Pallavi Subhraveti; Peter D Karp
Journal: Nucleic Acids Res Date: 2018-01-04 Impact factor: 16.971

Review 10. Advances in metabolic modeling of oleaginous microalgae.

Authors: Juan D Tibocha-Bonilla; Cristal Zuñiga; Rubén D Godoy-Silva; Karsten Zengler
Journal: Biotechnol Biofuels Date: 2018-09-05 Impact factor: 6.040

16 in total

1. eQuilibrator 3.0: a database solution for thermodynamic constant estimation.

Authors: Moritz E Beber; Mattia G Gollub; Dana Mozaffari; Kevin M Shebek; Avi I Flamholz; Ron Milo; Elad Noor
Journal: Nucleic Acids Res Date: 2022-01-07 Impact factor: 16.971

2. Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002.

Authors: Supreeta Vijayakumar; Claudio Angione
Journal: STAR Protoc Date: 2021-09-29

3. SALARECON connects the Atlantic salmon genome to growth and feed efficiency.

Authors: Maksim Zakhartsev; Filip Rotnes; Marie Gulla; Ove Øyås; Jesse C J van Dam; Maria Suarez-Diez; Fabian Grammes; Róbert Anton Hafþórsson; Wout van Helvoirt; Jasper J Koehorst; Peter J Schaap; Yang Jin; Liv Torunn Mydland; Arne B Gjuvsland; Simen R Sandve; Vitor A P Martins Dos Santos; Jon Olav Vik
Journal: PLoS Comput Biol Date: 2022-06-10 Impact factor: 4.779

4. Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB.

Authors: Marc Feuermann; Emmanuel Boutet; Anne Morgat; Kristian B Axelsen; Parit Bansal; Jerven Bolleman; Edouard de Castro; Elisabeth Coudert; Elisabeth Gasteiger; Sébastien Géhant; Damien Lieberherr; Thierry Lombardot; Teresa B Neto; Ivo Pedruzzi; Sylvain Poux; Monica Pozzato; Nicole Redaschi; Alan Bridge
Journal: Metabolites Date: 2021-01-12

5. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies.

Authors: Alina Renz; Lina Widerspick; Andreas Dräger
Journal: Metabolites Date: 2021-04-09

6. Enhancing Microbiome Research through Genome-Scale Metabolic Modeling.

Authors: Nana Y D Ankrah; David B Bernstein; Matthew Biggs; Maureen Carey; Melinda Engevik; Beatriz García-Jiménez; Meiyappan Lakshmanan; Alan R Pacheco; Snorre Sulheim; Gregory L Medlock
Journal: mSystems Date: 2021-12-14 Impact factor: 6.496

7. Rhea, the reaction knowledgebase in 2022.

Authors: Parit Bansal; Anne Morgat; Kristian B Axelsen; Venkatesh Muthukrishnan; Elisabeth Coudert; Lucila Aimo; Nevila Hyka-Nouspikel; Elisabeth Gasteiger; Arnaud Kerhornou; Teresa Batista Neto; Monica Pozzato; Marie-Claude Blatter; Alex Ignatchenko; Nicole Redaschi; Alan Bridge
Journal: Nucleic Acids Res Date: 2022-01-07 Impact factor: 16.971

8. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism.

Authors: Alina Renz; Laura J Dunphy; Dawson D Payne; Taylor Lewis; Andreas Dräger; Jason A Papin
Journal: NPJ Syst Biol Appl Date: 2021-10-08

9. GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.

Authors: Marzia Di Filippo; Chiara Damiani; Dario Pescini
Journal: PLoS Comput Biol Date: 2021-11-08 Impact factor: 4.475

Review 10. Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus.

Authors: Alina Renz; Andreas Dräger
Journal: NPJ Syst Biol Appl Date: 2021-06-29