Minimum information requested in the annotation of biochemical models (MIRIAM)

By N. Novère, A. Finney, Michael Hucka, U. Bhalla, F. Campagne, Julio Collado-Vides, E. Crampin, Matt D. B. Halstead, E. Klipp, Pedro Mendes and 6 more. Nature Biotechnology, 2005

648 citations recorded by the source corpus.

Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The lack of a standard description format, lack of stringent reviewing and authors' carelessness are the main causes for incomplete model descriptions. With today's increased interest in detailed biochemical models, it is necessary to define a minimum quality standard for the encoding of those models. We propose a set of rules for curating quantitative models of biological systems. These rules define procedures for encoding and annotating models represented in machine-readable form. We believe their application will enable users to (i) have confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fa895abd129eb7b1867121bbc5ce7d3d26b95b71

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In Molecular Biology

Citations in the corpus

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum (2013, methodology): “All model components were extensively annotated to adhere to the MIRIAM standard for biological models [41].”
MIFlowCyt: The Minimum Information about a Flow Cytometry Experiment (2008, background): “The importance of minimal data reporting standards is illustrated by both community-driven standards such as MIAME (13), MIRIAM (14), MISFISHIE (15), and the CON-SORT checklist (16), and cross-community efforts including MIBBI (5), FuGE (6), and OBI (7).”
Controlled vocabularies and semantics in systems biology (2011, neutral): “The CellML initiative also plans to incorporate support for SBO by providing annotation of components with ‘MIRIAM’ URIs”
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008, methodology): “SBML also provides the necessary standardized means ('Minimum Information Requested in the Annotation of biochemical Models' or MIRIA”
Chaste: An Open Source C++ Library for Computational Physiology and Biology (2013, methodology): “Minimum information standards have been suggested for models (MIRIAM [5]) and simulations (MIASE [6]), defining vital requirements underpinning reuse and reproducibility.”
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems (2005, methodology): “To be accepted in BioModels Database, a model must be compliant with MIRIAM, the Minimal Information Requested in the Annotation of Models (10).”
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, methodology): “In the curated branch , models are compliant with the MIRIAM (Minimum Information Required in the Annotation of Models) reporting guidelines [49].”
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project (2008, background): “Similarly, minimum information guidelines for reporting proteomics experiments and describing systems biology models are gaining broader support in their respective database communitie”
BioModels—15 years of sharing computational models in life science (2019, methodology): “To maximise the impact and reusability of the models, the MIRIAM guidelines were proposed (11) and the models are annotated following them in BioModels.”