Rhea
Names
More detailed information about this field from each metasource.
Rhea
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
rhea
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
Names
More detailed information about this field from each metasource.
Rhea
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
rhea
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
Names
More detailed information about this field from each metasource.
Rhea
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
rhea
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.
Description
More detailed information about this field from each metasource.
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Expert-curated biochemical reactions
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Rhea is a freely available and comprehensive resource of expert-curated biochemical reactions. It has been designed to provide a non-redundant set of chemical transformations for applications such as the functional annotation of enzymes, pathway inference and metabolic network reconstruction. There are three types of reaction participants (reactants and products): Small molecules, Rhea polymers, Generic compounds. All three types of reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both mass and charge balance of the reactions. We have populated the database with the reactions found in the enzyme classification (i.e. in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included.
metasource: re3data.orgversion: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest developed by the Swiss-Prot group at SIB Swiss Institute of Bioinformatics. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
Webpage:
http://www.rhea-db.orgWebpage
More detailed information about this field from each metasource.
http://www.rhea-db.org
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://www.ebi.ac.uk/rhea/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
https://www.rhea-db.org/
metasource: re3data.orgversion: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
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Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
CC
metasource: re3data.orgversion: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
CC-BY-NC-4.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
URL: https://creativecommons.org/licenses/by/4.0/
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
Publications:
(6)
Publications
More detailed information about this field from each metasource.
Rhea--a manually curated resource of biochemical reactions
PMID: 22135291
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Enzyme annotation in UniProtKB using Rhea
PMID: 31688925
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Updates in Rhea: SPARQLing biochemical reaction data
PMID: 30272209
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
Updates in Rhea--a manually curated resource of biochemical reactions
PMID: 25332395
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Updates in Rhea - an expert curated resource of biochemical reactions
PMID: 27789701
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gku961
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Rhea--a manually curated resource of biochemical reactions
PMID: 22135291
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Enzyme annotation in UniProtKB using Rhea
PMID: 31688925
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Updates in Rhea: SPARQLing biochemical reaction data
PMID: 30272209
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
Updates in Rhea--a manually curated resource of biochemical reactions
PMID: 25332395
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Updates in Rhea - an expert curated resource of biochemical reactions
PMID: 27789701
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gku961
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Rhea--a manually curated resource of biochemical reactions
PubMed citations: 34.
34 articles citing: Rhea--a manually curated resource of biochemical reactions
Similarity based enzymatic retrosynthesis. PMID:35685792
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues. PMID:35240125
Biocatalysed synthesis planning using data-driven learning. PMID:35181654
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. PMID:31870296
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. PMID:30192979
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
A Method for Finding Metabolic Pathways Using Atomic Group Tracking. PMID:28068354
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
Mapping the patent landscape of synthetic biology for fine chemical production pathways. PMID:27489206
Reaction Decoder Tool (RDT): extracting features from chemical reactions. PMID:27153692
Characterising Complex Enzyme Reaction Data. PMID:26840640
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. PMID:25520953
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Integrated network analysis and effective tools in plant systems biology. PMID:25408696
UniProt: a hub for protein information. PMID:25348405
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
Profiling the orphan enzymes. PMID:24906382
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. PMID:24708835
The Reactome pathway knowledgebase. PMID:24243840
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. PMID:23895341
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. PMID:23580552
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
Molecular tools for chemical biotechnology. PMID:23528237
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. PMID:23193269
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
The EBI enzyme portal. PMID:23175605
Reconciliation of metabolites and biochemical reactions for metabolic networks. PMID:23172809
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PMID:22693442
A chemical specialty semantic network for the Unified Medical Language System. PMID:22577759 -
Enzyme annotation in UniProtKB using Rhea
PubMed citations: 32.
32 articles citing: Enzyme annotation in UniProtKB using Rhea
Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Berberine in the Treatment of Ischaemic Stroke. PMID:35815278
Metabolite-Based Mutualistic Interaction between Two Novel Clostridial Species from Pit Mud Enhances Butyrate and Caproate Production. PMID:35695571
Similarity based enzymatic retrosynthesis. PMID:35685792
Identification of functionally important miRNA targeted genes associated with child obesity trait in genome-wide association studies. PMID:35546387
Thompson loop: opportunities for antitubercular drug design by targeting the weak spot in demethylmenaquinone methyltransferase protein. PMID:35520325
Comparative proteomics identify HSP90A, STIP1 and TAGLN-2 in serum extracellular vesicles as potential circulating biomarkers for human adenomyosis. PMID:35495589
Icariin: A Potential Molecule for Treatment of Knee Osteoarthritis. PMID:35479319
Action Mechanism Underlying Improvement Effect of Fuzi Lizhong Decoction on Nonalcoholic Fatty Liver Disease: A Study Based on Network Pharmacology and Molecular Docking. PMID:35096103
Rhea, the reaction knowledgebase in 2022. PMID:34755880
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. PMID:34606614
The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control. PMID:34549894
Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster. PMID:34544379
Efficient machine learning model for predicting drug-target interactions with case study for Covid-19. PMID:34271420
In-Pero: Exploiting Deep Learning Embeddings of Protein Sequences to Predict the Localisation of Peroxisomal Proteins. PMID:34203866
A Novel GH Family 20 β-N-acetylhexosaminidase With Both Chitosanase and Chitinase Activity From Aspergillus oryzae. PMID:34095233
Interpreting the lipidome: bioinformatic approaches to embrace the complexity. PMID:34091802
Clustering FunFams using sequence embeddings improves EC purity. PMID:33978744
Network Pharmacology Analysis of ZiShenWan for Diabetic Nephropathy and Experimental Verification of Its Anti-Inflammatory Mechanism. PMID:33883881
A Vernalization Response in a Winter Safflower (Carthamus tinctorius) Involves the Upregulation of Homologs of FT, FUL, and MAF. PMID:33859660
Lack of Molecular Mimicry between Nonhuman Primates and Infectious Pathogens: The Possible Genetic Bases. PMID:33748822
Evaluation of female Aedes aegypti proteome via LC-ESI-MS/MS using two protein extraction methods. PMID:33717682
An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli. PMID:33619446
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Study on Network Pharmacological Analysis and Preliminary Validation to Understand the Mechanisms of Plantaginis Semen in Treatment of Gouty Nephropathy. PMID:33312224
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
Bioinformatics Analysis Revealed Novel 3'UTR Variants Associated with Intellectual Disability. PMID:32858868
Current Knowledge on the Function of α-Methyl Acyl-CoA Racemase in Human Diseases. PMID:32760737
Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis. PMID:32732995
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Synthesis, In Vitro Evaluation and Molecular Docking of the 5-Acetyl-2-aryl-6-hydroxybenzo[b]furans against Multiple Targets Linked to Type 2 Diabetes. PMID:32156083
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905 -
Updates in Rhea: SPARQLing biochemical reaction data
PubMed citations: 28.
28 articles citing: Updates in Rhea: SPARQLing biochemical reaction data
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP. PMID:35688826
The Immunometabolic Atlas: A tool for design and interpretation of metabolomics studies in immunology. PMID:35550647
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. PMID:35546409
PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search. PMID:35404943
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Development of RIKEN Plant Metabolome MetaDatabase. PMID:34918130
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
The reactome pathway knowledgebase 2022. PMID:34788843
Rhea, the reaction knowledgebase in 2022. PMID:34755880
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
Complex Portal 2022: new curation frontiers. PMID:34718729
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. PMID:34587449
In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. PMID:34570957
Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. PMID:34314492
Graph transformation for enzymatic mechanisms. PMID:34252947
Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. PMID:34222327
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence. PMID:34056560
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
Simulating the enzymes of ganglioside biosynthesis with Glycologue. PMID:33828618
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
The reactome pathway knowledgebase. PMID:31691815
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883 -
Updates in Rhea--a manually curated resource of biochemical reactions
PubMed citations: 23.
23 articles citing: Updates in Rhea--a manually curated resource of biochemical reactions
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. PMID:34587449
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
Intracrine Regulation of Estrogen and Other Sex Steroid Levels in Endometrium and Non-gynecological Tissues; Pathology, Physiology, and Drug Discovery. PMID:30283331
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. PMID:29914475
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge. PMID:28158609
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis. PMID:27924274
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
A stable genetic polymorphism underpinning microbial syntrophy. PMID:27258948
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. PMID:27131375
SensiPath: computer-aided design of sensing-enabling metabolic pathways. PMID:27106061
MBROLE 2.0-functional enrichment of chemical compounds. PMID:27084944
The UniProtKB guide to the human proteome. PMID:26896845
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
The SwissLipids knowledgebase for lipid biology. PMID:25943471
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. PMID:25855807 -
Updates in Rhea - an expert curated resource of biochemical reactions
PubMed citations: 20.
20 articles citing: Updates in Rhea - an expert curated resource of biochemical reactions
Design and application of a knowledge network for automatic prioritization of drug mechanisms. PMID:35561182
Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins. PMID:35049101
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. PMID:32313937
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. PMID:31662430
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. PMID:31071110
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
RetroRules: a database of reaction rules for engineering biology. PMID:30321422
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PMID:29791443
The Reactome Pathway Knowledgebase. PMID:29145629
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis. PMID:28952528
Tags:
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
biocuration
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
chemical entity
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
chemical formula
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
curated information
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
reaction data
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
transport
metasource: Fairsharing.org
version: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
bioinformatics
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
chemical reactions
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
enzymes - analysis
metasource: re3data.org
version: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
enzymes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
chemistry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:12.319463
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
biocuration
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
chemical entity
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
chemical formula
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
curated information
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
enzymatic reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
reaction data
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
transport
metasource: Fairsharing.orgversion: FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: April 16, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metabolic pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
bioinformatics
metasource: re3data.orgversion: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
chemical reactions
metasource: re3data.orgversion: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
enzymes - analysis
metasource: re3data.orgversion: re3data.org: Rhea; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3332H last accessed: 2022-11-04
enzymes
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
chemistry
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:12.319463
biocuration chemical entity chemical formula enzymatic reaction reaction data small molecule transport metabolic and signaling pathways metabolic and signaling pathways bioinformatics chemical reactions enzymes - analysis enzyme chemistry molecular interactions, pathways and networks
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