Tag: network model

Found 45 sources
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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 ...


NeuroML is a model description language developed in XML (extensible Markup Language) that was created to facilitate data archiving, data and model exchange, database creation, and model publication in the neurosciences. One of the goals of the Neuro ...


BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

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 ...

BiGG Models

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

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.

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 ...

VirHostNet 2.0

VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.

SIGnaling Network Open Resource

The SIGnaling Network Open Resource. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are comp ...


ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. A ModelDB entry contains a model's source code, concise description, and a citation of the article that published it. Models can be code ...


VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions. vir ...

Arabidopsis Information Portal

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

Termini-Oriented Protein Function INferred Database

The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing sta ...

Protein Interaction Network Analysis platform

Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...


MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. Meta ...


SignaLink is an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. it allows browsing of signaling pathways, cross-talks and multi-pathway proteins; selection of transcriptional, post- ...

YEASTNET: A consensus reconstruction of yeast metabolism

This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from ...


The PyNN API aims to support modelling at a high-level of abstraction (populations of neurons, layers, columns and the connections between them) while still allowing access to the details of individual neurons and synapses when required. PyNN provide ...

Signaling Pathway Integrated Knowledge Engine

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...


GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...

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 ...

BioModels Ontology

OWL Representation of the models in the BioModels repository.

Bacterial Protein Interaction Database

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

GeneNet Engine

GeneNet Engine is an exploratory tool to aid hypothesis and biomarker development at a systems-level for genotype-phenotype relationships. Expressed phenotypes may arise due to interactions between multiple genes in a system and effects from the surr ...

Interaction Network Ontology

The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interact ...


DyNet is a Cytoscape application that provides a range of functionalities for the visualization, realtime synchronization, and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the mos ...

Brainstem Connectome

Database of all known neuronal connections of the rat brainstem. Connections are directed, weighted and bilateral. It is built using the neuroVIISAS platform. The Brainstem Connectome is a highly structured neuroontology composed of datasets from ove ...

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.

Pathway and Annotated-list Gene-signature Electronic Repository

Pathway and Annotated-list Gene-signature Electronic Repository (PAGER) is an repository for pathways, annotated-lists, and gene signatures (PAGs) related to human network biology.


DISNOR is a resource that uses a comprehensive collection of disease associated genes, as annotated in DisGeNET, to interrogate SIGNOR (https://signor.uniroma2.it) in order to assemble disease-specific logic networks linking disease associated genes ...

Genome-wide Integrated Analysis of gene Networks in Tissues 2.0

GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional ...


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

Automatic molecular interaction predictions

InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interac ...

Animal Trait Correlation Database

A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene express ...

Domain Interaction Graph Guided ExploreR

DIGGER is an essential resource for studying the mechanistic consequences of alternative splicing such as isoform-specific interaction and consequence of exon skipping. The database integrates information of domain-domain and protein-protein interact ...


Translocatome is a database that collects and characterises manually curated and predicted translocating proteins from human cells. The prediction is made by a gradient boosting based machine learning algorithm (XGBoost), using highly curated positiv ...


OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

ModelSEED Biochemistry Database

For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. The ModelSEED biochemistry database is the foundation of the biochemical data underlyi ...

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 ...

Compartmentalized Protein-Protein Interaction

The compartmentalized protein-protein interaction database (ComPPI), provides qualitative information on the interactions, proteins and their localizations integrated from multiple databases for protein-protein interaction network analysis.

MDL reaction Format

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


DBpedia is a crowd-sourced community effort to extract structured content from the information created in various Wikimedia projects. This structured information resembles an open knowledge graph (OKG).

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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