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Updates in Rhea—a manually curated resource of biochemical reactions

Anne Morgat, Kristian B. Axelsen, Thierry Lombardot, Rafael Alcántara, Lucila Aimo, Mohamed Zerara, Anne Niknejad, Eugeni Belda, Nevila Hyka-Nouspikel, Elisabeth Coudert, Nicole Redaschi, Lydie Bougueleret (+3 others)
2014 Nucleic Acids Research  
Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest)  ...  Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual  ...  exchanges and expert curation of the ChEBI entries essential for Rhea.  ... 
doi:10.1093/nar/gku961 pmid:25332395 pmcid:PMC4384025 fatcat:rg4drak3onguteit2c7wovb7wy

Rhea—a manually curated resource of biochemical reactions

Rafael Alcántara, Kristian B. Axelsen, Anne Morgat, Eugeni Belda, Elisabeth Coudert, Alan Bridge, Hong Cao, Paula de Matos, Marcus Ennis, Steve Turner, Gareth Owen, Lydie Bougueleret (+2 others)
2011 Nucleic Acids Research  
Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions.  ...  Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference.  ...  ACKNOWLEDGEMENTS The authors thank Amos Bairoch, Kirill Degtyarenko, Henning Hermjakob and Eric Coissac for their help and encouragement in the early stages of this project, and Andrea Auchincloss and  ... 
doi:10.1093/nar/gkr1126 pmid:22135291 pmcid:PMC3245052 fatcat:7fuig2gnurhttn2mi3cwfxrjbq

An updated metabolic view of the Bacillus subtilis 168 genome

E. Belda, A. Sekowska, F. Le Fevre, A. Morgat, D. Mornico, C. Ouzounis, D. Vallenet, C. Medigue, A. Danchin
2013 Microbiology  
Curation of chemical compounds and reactions in ChEBI and RHEA resources.  ...  RHEA is a European resource of expert-curated biochemical reactions that are defined based on chemical compounds from the ChEBI, and that are stoichiometrically balanced for mass and charge at pH 7.3 (  ... 
doi:10.1099/mic.0.064691-0 pmid:23429746 fatcat:7z5ugwvw4jb77l2fmbqp62x2ue

Enzyme annotation in UniProtKB using Rhea [article]

Anne Morgat, Thierry Lombardot, Elisabeth Coudert, Kristian Axelsen, Teresa B. Neto, Sebastien Gehant, Parit Bansal, Jerven Bolleman, Elisabeth Gasteiger, Edouard de Castro, Delphine Baratin, Monica Pozzato (+5 others)
2019 bioRxiv   pre-print
Motivation: To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants  ...  Results: We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB.  ...  Team of EMBL-EBI for their work in maintaining and developing ChEBI.  ... 
doi:10.1101/709899 fatcat:on6h54ejxnc4tdttnk4qrvfqwe

Enzyme annotation in UniProtKB using Rhea

2019 Bioinformatics  
To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants  ...  We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB.  ...  Team of EMBL-EBI for their work in maintaining and developing ChEBI.  ... 
doi:10.1093/bioinformatics/btz817 pmid:31688925 pmcid:PMC7162351 fatcat:p4xejuaqhnaqvfbqmrbp22wsde

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan Bridge, Anne Morgat, Marco Pagni
2015 Nucleic Acids Research  
MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular  ...  MNXref and MetaNetX are regularly updated and freely available.  ...  ACKNOWLEDGEMENTS Computation and maintenance of the MetaNetX.org server are provided by the Vital-IT center for high-performance computing of the SIB Swiss Institute of Bioinformatics (http://www.vital-it.ch  ... 
doi:10.1093/nar/gkv1117 pmid:26527720 pmcid:PMC4702813 fatcat:ccrzjdpzbjaoneo6bzhodes4ii

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

David Vallenet, Eugeni Belda, Alexandra Calteau, Stéphane Cruveiller, Stefan Engelen, Aurélie Lajus, François Le Fèvre, Cyrille Longin, Damien Mornico, David Roche, Zoé Rouy, Gregory Salvignol (+4 others)
2012 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would like to thank all MaGe users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ...  They also thank the entire system network team of Genoscope for its essential contribution to the efficiency of the platform, and Antoine Danchin for his careful editing of the manuscript.  ...  Curation includes the update of the Product and EC number annotation fields and also the manual validation of the corresponding reactions in MetaCyc (1.17.1.1-RXN) and RhEA (RHEA: 19653 and RHEA: 19657  ... 
doi:10.1093/nar/gks1194 pmid:23193269 pmcid:PMC3531135 fatcat:inrau5amu5btxjbw2ykwehkfny

Reconciliation of metabolites and biochemical reactions for metabolic networks

T. Bernard, A. Bridge, A. Morgat, S. Moretti, I. Xenarios, M. Pagni
2012 Briefings in Bioinformatics  
By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network  ...  The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic  ...  All computations were performed at the Vital-IT Center for high-performance computing of the Swiss Institute of Bioinformatics (http://www.vital-it.ch).  ... 
doi:10.1093/bib/bbs058 pmid:23172809 pmcid:PMC3896926 fatcat:ztz6xxdddnc5xkcnfcjy7bxsai

Complex Portal 2022: new curation frontiers

Birgit H M Meldal, Livia Perfetto, Colin Combe, Tiago Lubiana, João Vitor Ferreira Cavalcante, Hema Bye-A-Jee, Andra Waagmeester, Noemi del-Toro, Anjali Shrivastava, Elisabeth Barrera, Edith Wong, Bernhard Mlecnik (+7 others)
2021 Nucleic Acids Research  
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms.  ...  with manually curated Complex Portal content through a new bot.  ...  would like to acknowledge Andrew Su for providing virtual workspace and staff for collaboration, Sabah Ul-Hasan for proofreading and improving the manuscript and Eliot Ragueneau for advising on aspects of  ... 
doi:10.1093/nar/gkab991 pmid:34718729 pmcid:PMC8689886 fatcat:klvf2ls6eveivdlytrjs6ycyvu

UniPathway: a resource for the exploration and annotation of metabolic pathways

Anne Morgat, Eric Coissac, Elisabeth Coudert, Kristian B. Axelsen, Guillaume Keller, Amos Bairoch, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, Alain Viari
2011 Nucleic Acids Research  
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.  ...  early stages of this project.  ... 
doi:10.1093/nar/gkr1023 pmid:22102589 pmcid:PMC3245108 fatcat:jc6lq5ovzvg7zjide6a4qnuk3y

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee (+122 others)
2020 Nucleic Acids Research  
In this article, we describe significant updates that we have made over the last two years to the resource.  ...  We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal.  ...  Rhea knowledgebase of biochemical reactions (13) .  ... 
doi:10.1093/nar/gkaa1100 pmid:33237286 pmcid:PMC7778908 fatcat:6rwvp6l5uzb3li4lygf2gny6qq

The InterPro protein families database: the classification resource after 15 years

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew (+24 others)
2014 Nucleic Acids Research  
InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource.  ...  The InterPro database (http://www.ebi.ac.uk/ interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and  ...  Several sources are used for the reaction sets, including InterPro annotations and GO terms, and curated associations of GO functions to reactions in the RhEA database (26) .  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

The Gene Ontology resource: enriching a GOld mine

Gene Ontology Consortium
2020 Nucleic Acids Research  
In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific  ...  To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure  ...  ACKNOWLEDGEMENTS We want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/ page/acknowledgments-contributors), and all the authors  ... 
doi:10.1093/nar/gkaa1113 pmid:33290552 pmcid:PMC7779012 fatcat:socxl3x5svamfoc2sobzyvjjoy

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Samuel M D Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P Faria, Janaka N Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E Beber, Aaron A Best, Matthew DeJongh (+10 others)
2020 Nucleic Acids Research  
molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical 'Rosetta Stone' to facilitate comparison and  ...  Isomer and Cis/Trans: reaction present but utilizing different isomer or cis/trans metabolite; Subreaction/Lump: reaction present but is a merge or split version of a ModelSEED reaction; Charge: reaction  ...  As such, a number of unconventional compounds and reactions, such as those that were manually created for individual published models, or incompletely curated reactions in some BioCyc databases, are included  ... 
doi:10.1093/nar/gkaa1143 pmid:33179751 fatcat:xj6g5txnzbhkzfyaswirgrke5y

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Samuel M D Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P Faria, Janaka N Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E Beber, Aaron A Best, Matthew DeJongh (+10 others)
2020 Nucleic Acids Research  
molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical 'Rosetta Stone' to facilitate comparison and  ...  For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes.  ...  As such, a number of unconventional compounds and reactions, such as those that were manually created for individual published models, or incompletely curated reactions in some BioCyc databases, are included  ... 
doi:10.1093/nar/gkaa746 pmid:32986834 fatcat:73mt7mv7frfjvgbsj55vwqyjaq
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