Content | |
---|---|
Description | A repository for storing, exchanging and retrieving computational models of biological interest. |
Data types captured | computational models |
Organisms | all |
Contact | |
Research center | EMBL-EBI, BI, Caltech |
Primary citation | PMID 20587024 |
Release date | 2005 |
Access | |
Standards | MIRIAM |
Data format | SBML, BioPAX, SciLab, Octave, XPP, VCML, RDF/XML |
Website | EBI main instance, Caltech mirror |
Download URL | EBI FTP |
Web service URL | SOAP |
Tools | |
Web | Model display, multiple browsing strategies, advanced search, bulk download, model of the month |
Miscellaneous | |
License | CC0 Public Domain Dedication |
Version | 28 (September 2014) |
Curation policy | yes (manual) |
Bookmarkable entities | yes |
BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. [1] [2] [3] All the models in the curated section of BioModels Database have been described in peer-reviewed scientific literature.
The models stored in BioModels' curated branch are compliant with MIRIAM, the standard of model curation and annotation. The models have been simulated by curators to check that when run in simulations, they provide the same results as described in the publication. Model components are annotated, so the users can conveniently identify each model element and retrieve further information from other resources.
Modellers can submit the models in SBML and CellML. Models can subsequently be downloaded in SBML, VCML Archived 2006-12-09 at the Wayback Machine , XPP, SciLab, Octave, BioPAX and RDF/XML. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java applet, in which some networks were presented by following Systems Biology Graphical Notation. And a human readable summary of each model is available in PDF.
BioModels is composed of several branches. The curated branch hosts models that are well curated and annotated. The non-curated-branch provides models that are still not curated, are non-curatable (spatial models, steady-state models etc.), or too huge to be curated. Non-curated models can be later moved into the curated branch. The repository also hosts models which were automatically generated from pathways databases.
All the models are freely available under the Creative Commons CC0 Public Domain Dedication, and can be easily accessed via the website or Web Services. [4] One can also download archives of all the models from the EBI FTP server.
BioModels announced its 31st release on June 26, 2017. [5] It now publicly provides 144,710 models. This corresponds to 1,640 models published in the literature and 143,070 models automatically generated from pathway resources.
Deposition of models in BioModels is advocated by many scientific journals, included Molecular Systems Biology, all the journals of the Public Library of Science, all the journals of BioMed Central and all the journals published by the Royal Society of Chemistry.
BioModels is developed by the BioModels.net Team at the EMBL-EBI, UK, the Le Novère lab at the Babraham Institute, UK, and the SBML Team in Caltech, USA. [6]
BioModels Development has benefited from the funds of the European Molecular Biology Laboratory, the Biotechnology and Biological Sciences Research Council, the Innovative Medicines Initiative, the Seventh Framework Programme (FP7), the National Institute of General Medical Sciences, the DARPA, and the National Center for Research Resources.
BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is an electronic resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a web-based user interface that allows a convenient and sophisticated access to the data.
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today.
Reactome is a free online database of biological pathways. It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format.
The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling.
MIRIAM is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities.
The minimum information about a simulation experiment (MIASE) is a list of the common set of information a modeller needs to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models.
Bernhard Örn Pálsson is the Galletti Professor of Bioengineering and an adjunct professor of Medicine at the University of California, San Diego.
SABIO-RK is a web-accessible database storing information about biochemical reactions and their kinetic properties.
LibSBML is an open-source software library that provides an application programming interface (API) for the SBML format. The libSBML library can be embedded in a software application or used in a web servlet as part of the application or servlet's implementation of support for reading, writing, and manipulating SBML documents and data streams. The core of libSBML is written in ISO standard C++; the library provides API for many programming languages via interfaces generated with the help of SWIG.
The MIRIAM Registry, a by-product of the MIRIAM Guidelines, is a database of namespaces and associated information that is used in the creation of uniform resource identifiers. It contains the set of community-approved namespaces for databases and resources serving, primarily, the biological sciences domain. These shared namespaces, when combined with 'data collection' identifiers, can be used to create globally unique identifiers for knowledge held in data repositories. For more information on the use of URIs to annotate models, see the specification of SBML Level 2 Version 2.
JSBML is an open-source Java (API) for the SBML format. Its API strives to attain a strong similarity to the Java binding of the corresponding library libSBML, but is entirely implemented in Java and therefore platform independent. JSBML provides an elaborated abstract type hierarchy, whose data types implement or extend many interfaces and abstract classes from the standard Java library. In this way, JSBML integrates smoothly into existing Java projects, and provides methods to read, write, evaluate, and manipulate the content of SBML documents.
Identifiers.org is a project providing stable and perennial identifiers for data records used in the Life Sciences. The identifiers are provided in the form of Uniform Resource Identifiers (URIs). Identifiers.org is also a resolving system, that relies on collections listed in the MIRIAM Registry to provide direct access to different instances of the identified records.
The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. KiSAO is part of the BioModels.net project and of the COMBINE initiative.
The Simulation Experiment Description Markup Language (SED-ML) is a representation format, based on XML, for the encoding and exchange of simulation descriptions on computational models of biological systems. It is a free and open community development project.
Terminology for the Description of Dynamics (TEDDY) aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
Nicolas Le Novère is a British and French biologist. His research focuses on modeling signaling pathways and developing tools to share mathematical models.
Mirit I. Aladjem is an Israeli-American biologist researching cellular signaling pathways that regulate DNA synthesis. She is a senior investigator in the National Cancer Institute's developmental therapeutics branch and head of the DNA replication group.
Herbert M. Sauro is a Welsh biochemist who works in the field of metabolic control analysis and systems biology.