Tag: pathway model

Found 44 sources
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Reactome - a curated knowledgebase of biological pathways

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.

Comparative Toxicogenomics Database

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

Systems Biology Markup Language

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 ...

Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...


WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

Minimal Information Required In the Annotation of Models

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 ...

Systems Biology Graphical Notation

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 ...

Biological Pathway eXchange

BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange bet ...

Pharmacogenomics Knowledge Base

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...


MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

Pathway Commons

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

Systems Biology Ontology

The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles ( ...

Small Molecule Pathway Database

The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

Minimum Information About a Simulation Experiment

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 ...

Interologous Interaction Database

I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs).

The Network Data Exchange (NDEx)

NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytosc ...

Maize Genetics and Genomics Database

MaizeGDB is the maize research community's central repository for genetics and genomics information.


The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

Sol Genomics Network

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughou ...

Integrated Pathway Analysis and Visualization System

iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate, filter, browse, search, analyze, visualize ...


HumanCyc is a bioinformatics database that describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional ...

Pathway Ontology

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 ...

KEGG Mark-up Language

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 ...

PRofils pour l'Identification Automatique du Metabolisme

In English, PRIAM stands for enzyme-specific profiles for metabolic pathway prediction. PRIAM is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.

Extracellular RNA Atlas

The exRNA Atlas is the data and metadata repository of the Extracellular RNA Communication Consortium (ERCC), an NIH Common Fund initiative to learn more about exRNAs in a variety of different contexts. The exRNA Atlas includes small RNA sequencing a ...

BioModels Ontology

OWL Representation of the models in the BioModels repository.

MetaCrop 2.0

The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. ...


The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

Enzyme Portal

The Enzyme Portal is for those interested in the biology of enzymes and proteins with enzymatic activity. It integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds. It contai ...

Enzyme Mechanism Ontology

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.


A database for systems biology of DNA dynamics during the cell life.

Melanoma Molecular Map Project

A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.

Agronomic Linked Data

The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RD ...

Signal Transduction Classification Database

The signal molecules and pathways are classified and illustrated by graphs in this database.

Therapeutically Relevant Multiple Pathways Database

The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands ...

Cell Signaling Technology Pathway Database

A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.

Signaling Pathways Project

The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcript ...

reactive oxygen species-mediated signaling pathway database

ROSPath was developed for the purpose of aiding the research of ROS-mediated signaling pathways including growth factor-, stress- and cytokine-induced signaling that are main research interests of the Division of Molecular Life Sciences and Center fo ...

Graphical Pathway Markup Language

Markup Language for graphical representations of biological pathways.

Human Interaction Network Ontology

The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has incorporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed following the OBO Foundry principle ...


YeastCyc is a Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae S288c. In addition to genomic information, the database contains metabolic pathway, reaction, enzyme, and compound information, which has been manually curated from ...

MDL reaction Format

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

eXtensible Graph Markup and Modeling Language

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 ...

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