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

Abstract

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.During the genomic era we have witnessed a vast increase in availability of large amounts of quantitative data. This is motivating a shift in the focus of molecular and cellular research from qualitative descriptions of biochemical interactions towards the quantification of such interactions and their dynamics. One of the tenets of systems biology is the use of quantitative models (see Box 1 for definitions) as a mechanism for capturing precise hypotheses and making predictions 1,2 . Many specialized models exist that attempt to explain aspects of the cellular machinery. However, as has happened with other types of biological information, such as sequences, macromolecular structures or Box 1 GlossarySome terms are used in a very specific way throughout the article. We provide here a precise definition of each one.Quantitative biochemical model. A formal model of a biological system, based on the mathematical description of its molecular and cellular components, and the interactions between those components.Encoded model. A mathematical model written in a formal machine-readable language, such that it can be systematically parsed and employed by simulation and analysis software without further human translation. MIRIAM-compliant model. A model that passes all the tests and fulfills all the conditions listed in MIRIAM.Reference description. A unique document that describes, or references the description of the model, the structure of the model, the numerical values necessary to instantiate a simulation from the model, or to perform a mathematical analysis of the model, and the results one expects from such a simulation or analysis.Curation process. The process by which the compliance of an encoded model with MIRIAM is achieved and/or verified. The curation process may encompass some or all of the following tasks: encoding of the model, verification of the reference correspondence and annotation of the model.Reference correspondence. The fact that the...

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“…Such a structured format should facilitate the generation of models compliant with the MIRIAM guidelines for model curation (Le Novère et al, 2005).…”

A physiome standards-based model publication paradigm

“…ebi.ac.uk/compneur-srv/miase/). The MIASE project is a community effort along the same lines as the MIRIAM specification (Le Novère et al 2005), with the goal of defining recommendations for the minimum information required in order for simulation experiments to be exactly duplicated. In our framework, a simulation experiment can be described by a collection of graphs defined using the CellML graphing metadata.…”

“…The MIRIAM standard (Le Novère et al 2005) defines a set of criteria that need to be met in order for a model description to be deemed MIRIAM compliant. Valid models encoded and described using the framework above, we believe, meet all the requirements of a MIRIAM-compliant reference correspondence.…”

“…(ii) Resource annotation At a minimum, all resources in the model description should be annotated to satisfy the annotation requirements of the minimum information requested in the annotation of biochemical model (MIRIAM) specification (Le Novère et al 2005; e.g. author attribution, modification history, etc., as described in Lloyd et al (2008)).…”

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“…The importance of using community-developed standards to represent models in systems biology is well established [12]. As such, reconstructions are generated in Systems Biology Markup Language (SBML) [13] and are semantically annotated according to the MIRIAM standard [14]. They can be formatted in such a way that they can be loaded into the COBRA Toolbox [15], allowing constraint based analyses to be performed on the model, using techniques such as Flux Balance Analysis (FBA) [16].…”