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Updates in Rhea – an expert curated resource of biochemical reactions

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 (+4 others)
2016 Nucleic Acids Research  
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks  ...  Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research.  ...  We would also like to thank the Cheminformatics and Metabolism Team at the European Bioinformatics Institute for their invaluable work in maintaining and developing ChEBI.  ... 
doi:10.1093/nar/gkw990 pmid:27789701 pmcid:PMC5210663 fatcat:26f75w5d6zdpbh4kzsom6la2ka

Updates in Rhea – an expert curated resource of biochemical reactions

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 (+4 others)
2016 Nucleic Acids Research  
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks  ...  Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research.  ...  We would also like to thank the Cheminformatics and Metabolism Team at the European Bioinformatics Institute for their invaluable work in maintaining and developing ChEBI.  ... 
doi:10.1093/nar/gkw1299 pmid:27980062 pmcid:PMC5397180 fatcat:jzdvhp7ldrdunmqr4ezr4z5jw4

Updates in Rhea: SPARQLing biochemical reaction data

Thierry Lombardot, Anne Morgat, Kristian B Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alex Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan Bridge
2018 Nucleic Acids Research  
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction  ...  Here we describe recent developments in Rhea, focusing on a new resource description framework representation of Rhea reaction data and an SPARQL endpoint (https://sparql.rhea-db.org/sparql) that provides  ...  We would also like to thank the Cheminformatics and Metabolism Team of EMBL-EBI for their work in maintaining and developing ChEBI and Andrea Cristofori of the Web Production team of EMBL-EBI for invaluable  ... 
doi:10.1093/nar/gky876 pmid:30272209 pmcid:PMC6324061 fatcat:sgbcc47ct5bkloc74x6kfm7vsm

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)  ...  Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research.  ...  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.  ...  This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic  ...  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

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

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

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

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

The SwissLipids knowledgebase for lipid biology

Lucila Aimo, Robin Liechti, Nevila Hyka-Nouspikel, Anne Niknejad, Anne Gleizes, Lou Götz, Dmitry Kuznetsov, Fabrice P.A. David, F. Gisou van der Goot, Howard Riezman, Lydie Bougueleret, Ioannis Xenarios (+1 others)
2015 Bioinformatics  
SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures.  ...  We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge. Availability: SwissLipids is freely available at http://www.swisslipids.org/.  ...  We would also like to thank Marcus Ennis, Janna Hastings, Gareth Owen and Steve Turner of the Cheminformatics and Metabolism Team at the European Bioinformatics Institute for expert curation of ChEBI entries  ... 
doi:10.1093/bioinformatics/btv285 pmid:25943471 pmcid:PMC4547616 fatcat:dr5osi34wfe5fkdji6t5jbqbuu

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

2015 Nucleic Acids Research  
Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources.  ...  In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, EN-ZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap  ...  Acknowledgements to Additional SIB Members (non-coauthors) The authors would like to explicitly thank the following SIB members not mentioned in the co-author list above:  ... 
doi:10.1093/nar/gkv1310 pmid:26615188 pmcid:PMC4702916 fatcat:oxgje3pvj5hv5mqgjcvm4w2xiy

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.  ...  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  ...  early stages of this project.  ... 
doi:10.1093/nar/gkr1023 pmid:22102589 pmcid:PMC3245108 fatcat:jc6lq5ovzvg7zjide6a4qnuk3y

The Gene Ontology resource: enriching a GOld mine

Gene Ontology Consortium
2020 Nucleic Acids Research  
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  ...  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  ...  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 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  ...  As an additional beneficial outcome, 35 new GO terms were created as part of this work, 74 new reactions were curated into RhEA (with the curation of additional chemical entities in the ChEBI database  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme
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