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BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

Nucleic acids research | Jan 1, 2006

BioModels Database (, part of the international initiative, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

Pubmed ID: 16381960 RIS Download

Mesh terms: Biochemical Phenomena | Cell Physiological Phenomena | Databases, Factual | Genes | Internet | Kinetics | Models, Biological | User-Computer Interface | Vocabulary, Controlled

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A system for identifying content objects in the digital environment. DOI names are assigned to any entity for use on digital networks. They are used to provide current information, including where they (or information about them) can be found on the Internet. Information about a digital object may change over time, including where to find it, but its DOI name will not change. The DOI System provides a framework for persistent identification, managing intellectual content, managing metadata, linking customers with content suppliers, facilitating electronic commerce, and enabling automated management of media. DOI names can be used for any form of management of any data, whether commercial or non-commercial. The DOI System is an ISO International Standard. Using DOI names as identifiers makes managing intellectual property in a networked environment much easier and more convenient, and allows the construction of automated services and transactions.


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For computational modeling to become more widely used in biological research, researchers must be able to exchange and share their results. The development and broad acceptance of common model representation formats such as SBML is a crucial step in that direction, allowing researchers to exchange and build upon each other''s work with greater ease and accuracy. The project is another step: an international effort to: 1. define agreed-upon standards for model curation 2. define agreed-upon vocabularies for annotating models with connections to biological data resources 3. provide a free, centralized, publicly-accessible database of annotated, computational models in SBML and other structured formats To facilitate assembling useful collections of quantitative models of biological phenomena, it is crucial to establish standards for the vocabularies used in model annotations as well as criteria for minimum quality levels of those models. The project aims to bring together a community of interested researchers to address these issues. We are working towards defining these standards through white papers and process definitions. All of the products of our efforts are open and freely available through this site.


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