Tag: enzymatic reaction

The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By su ...

The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any struct ...

The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biolo ...

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-ca ...

SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines. SED-ML encodes in a computer-readable exchange format ...

The MIASE Guidelines, initiated by the BioModels.net effort, are a community effort to identify the Minimal Information About a Simulation Experiment, necessary to enable the reproducible simulation experiments. Consequently, the MIASE Guidelines lis ...

IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification ...

PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provid ...

Structure Function Linkage Database (SFLD) is a database of enzymes classified by linking sequences to chemical function. A hierachical systems is used to classify enzymes by family or superfamily other category levels include functional domain, subg ...

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes o ...

The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and mo ...

M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA: 'Detailed mechanism' entries are mor ...

Systems Biology Results markup language (SBRML) specifies models composed of molecular species, and their interactions (including reactions). The markup language is intended to specify results from operations carried out on models Ñ SBRML. This resou ...

The "Enzyme Mechanism Ontology " describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.

The BioModels Ontology is an OWL Representation of the models in the BioModels repository. This resource has not been updated recently within BioPortal, and no official homepage can be found, therefore we have marked its status as Uncertain. Please g ...

MDL reaction Format is used to describe the kinetics of chemical reactions and the chemical structure of the reactants and products.

EnzymeML is a free and open standard XML-based interchange format for data on enzyme-catalyzed reactions. The purpose of EnzymeML is to store and exchange enzyme kinetics data between instruments, software tools, and databases. EnzymeML will allow sc ...

XGMML (eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. XGMML uses tags to describe nodes and edges of a graph. The purpose of XGMML is to make possible the exchange of graphs betw ...