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Systems Biology Databases

Name Description Publications Comments
BioFNet BioFNet is a biological functional network database for analysis and synthesis of biological systems PUBMED
BioModels Database BioModels Database serves as a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. PUBMED PDF
BioSystems The NCBI BioSystems Database provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. PUBMED PDF
ESCAPE Embryonic Stem Cells Atlas of Pluripotency Evidence ESCAPE integrates data based on mouse and human embryonic stem cells from diverse high-throughput studies including: gene expression microarrays, RNA-seq, ChIP-chip/seq, genome-wide inhibitory RNA (RNAi) screens, immunoprecipitation followed by mass spectrometry (IP-MS) proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and identify known and novel regulatory interactions across various regulatory layers, as well as predict the effects of combinatorial knockdowns. PUBMED PDF
Genome Proteome Search engine (GPSe) GPSe is formulated using the Google search feature to fetch data from different biological data sources. The spectrum of biological databases GPSE processes include Genome, Proteome, Transcriptome, Metabolome, Interactome, Structural databases and also major Genome Browsers like Ensembl, UCSC, NCBI Entrez. In addition data sources and web server useful for systems biology and model building are also processed. The aim is to bring in a single common interface for biological data mining.
InnateDB InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. PUBMED PDF
IPAD IPAD is the Integrated Pathway Analysis Database for Systematic Enrichment Analysis, defining inter-association between pathway, disease, drug and organ specificity. PUBMED PDF
JWS Online Cellular Systems Modelling JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models. PUBMED PDF
JWS Online is an important component of the research initiative "The Silicon Cell".
KBase The Department of Energy (DOE) Systems Biology Knowledgebase provides an open, extensible framework for secure sharing of data, tools, and scientific conclusions in predictive and systems biology. As a community resource, KBase provides a computational framework and tools for integrating and analyzing large, diverse datasets generated by the scientific community to advance predictive understanding, manipulation, and design of biological processes. The purpose of KBase is to enable users to integrate a wide spectrum of genomics and systems biology data, models, and information for microbes, microbial communities, and plants. Broschure, Facebook link, Twitter link
MEMOSys The Metabolic Models System Database is a bioinformatic platform for Genome-scale metabolic models. PUBMED PDF
PANTHER (Protein ANalysis THrough Evolutionary Relationships) The PANTHER Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. The database includes genes from over 80 genomes, pathways, and ontologies. PUBMED PDF
PhosphoPep 2.0 PhospoPep supports systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms. Currently there is data from the fly ( Drosophila melanogaster), human ( Homo sapiens), worm ( Caenorhabditis elegans), and yeast ( Saccharomyces cerevisiae). PUBMED PDF
The experimental data was collected and analyzed by the Aebersold group at the Swiss Federal Institute of Technology (ETH) in collaboration with the Functional Genomics Center (FGCZ) in Zurich, Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA.
Plant Systems Biology Modelling (PlaSMo) In PlaSMo plant mathematical models useful to the UK plant systems biology community are stored. The portal disseminates the models, and example of their output, and provides an interface to enable researchers to share reviews, annotations and enhancements of models.
PlateletWeb PlateletWeb provides a novel systems biology workbench for the analysis of platelet signaling in the functional context of integrated networks. The database was established combining data from recent platelet proteome and transcriptome (SAGE) studies with information on protein-protein interactions and kinase-substrate relationships extracted from bioinformatical databases as well as published literature. PUBMED PDF
SABIO-RK Biochemical Reaction Kinetics Database SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. PUBMED
SysMO-DB SysMO-DB is a project that is creating a web-based platform, and tooling, for finding, sharing and exchanging Data, Models and Processes in Systems Biology. It was designed to support the SysMO Consortium (Systems Biology for Micro-Organisms), but the principles and methods employed are equally applicable to other multi-site Systems Biology projects.
Systems Biology and Medicine Database (SBM DB) SBM DB is comprehensive database of gene expression profiles, which enable to compare the transcriptome of various tissues, organs and experiments.
There are 3 types of databases:
  • Reference database for gene expression analysis (RefExA)
  • HUVEC database for vascular endothelial research (HUVEC DB)
  • Protein expression database using immunohistochemistory (IHC DB)
All gene expression data in this database is produced by Laboratory for Systems Biology and Medicine (LSBM) and the collaborators.
Systems Biology Ontology (SBO) The SBO is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use.
SYSTOMONAS genome Database SYSTOMONAS (SYSTems biology of pseudOMONAS) provides an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology. In the database experimental metabolome, proteome and transcriptome data, as well as gene-regulatory networks are stored. In addition, several tools for the analysis of stored data and for the visualization of the corresponding results are provided. PUBMED PDF
The Systems Biology Researcher Database (SysBiolDB) SysBiolDB intends to provide a joint exchange and information platform for all systems biology researchers worldwide (collaborations, funding opportunities, jobs, student positions). SysBiolDB is part of the EUSYSBIO project which is funded by the 6th Research Framework Programme (FP6) of the European Union.

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