Tag: pathway model

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

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.

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 ...

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 ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

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 ...

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 ...

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 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 ...

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 ...

InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...

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, ...

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 ...

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 ...

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

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.

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 ( ...

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

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

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 ...

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 ...

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 ...

The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

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 ...

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 ...

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 ...

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.

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.

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 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 ...

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 ...

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

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

miRwayDB provides information on experimentally validated microRNA-pathway associations for pathophysiological conditions. Information includes disease condition, associated microRNAs, experimental sample types, regulation pattern (up/down), and path ...

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 ...

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 ...

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

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.

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 ...

Markup Language for graphical representations of biological pathways.

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

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 ...

PRIMESDB is a systems biology platform that is being developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES is investigating ...