The Next Step After Standard Formats
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 BioModels.net project is another step: an international effort to:
- define agreed-upon standards for model curation
- define agreed-upon vocabularies for annotating models with connections to biological data resources
- provide a free, centralized, publicly-accessible database of annotated, computational models in SBML and other structured formats
Helping to Define Community Standards
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 BioModels.net 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.
Standards and Processes Developed Hand-in-Hand with a New Database
The database component of BioModels.net is especially designed for working with annotated computational models: each model is carefully reviewed and augmented by human annotators on the BioModels.net team to add metadata linking the model elements to other biological databases and resources. The BioModels Database at the EBI system goes far beyond other collections of models by being a true database, featuring browsing, cross-referencing, searching, and facilities for visualization, exporting models in different formats, and remote API access.
The projects we are currently coordinating are:
- BioModels Database
- MIRIAM and the associated set of qualifiers and MIRIAM Registry