26:(Minimum Information Required In The Annotation of Models) 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.
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144:'External resource annotation' defines the manner in which annotations should be constructed. Those annotations contain references to entities in databases, classifications, ontologies, etc. One of the purposes of annotation is to allow unambiguous identification of the various model components.
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So far, annotation is mainly a manual work, so to ensure their longevity the usage of perennial URIs is necessary. It was recognised that the generation of valid and unique URIs for annotation required the creation of a catalogue of shared namespaces for use by the community. This function is
182:. The Registry also provides a variety of supporting auxiliary features to enable automated procedures based upon these URIs. The ability to generate resolvable identifiers is provided through the use of the resolving layer,
79:'Reference correspondence' deals with the basic reference information needed to make use of the model, detailing on a gross level the format of the model file, and its instantiability for simulation purposes.
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The original article used the verb "requested", but this has evolved through community use into "required", and is in line with other
Minimum Information (MI) standards available through the MIBBI portal
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Qualifiers (optional) should be used to refine the link between the model components and the referenced information, for example "has_a", "is_version_of" and "is_homolog_to".
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When instantiated, the model must be capable of reproducing representative results as given in the reference description, within an epsilon (algorithms, round-up errors).
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The model must be instantiable; necessary quantitative parameters, such as initial conditions, should be provided if they are needed for a simulation.
261:; Finney, Andrew; Hucka, Michael; Bhalla, Upinder S; Campagne, Fabien; Collado-Vides, Julio; Crampin, Edmund J; Halstead, Matt; et al. (2005).
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The model should be linked to a precise statement about its terms of use and distribution, regardless of whether it is 'free to use' or not.
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The date and time of model creation and last modification should be specified. A model history is useful but not required.
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The model must be associated with a reference description or publication detailing its origin, even if it is a composite.
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119:'Attribution annotation' deals with the attribution information that must be embedded within the model file.
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The encoded model structure must reflect the (biological) process(es) detailed in the reference description.
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is a registered project of the MIBBI (minimum information for biological and biomedical investigations).
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The model must include a citation of the reference description identifying the authors of the model.
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The collection-specific identifier should be analysed within the framework of the data collection.
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The idea of "a set of good practices" including "some obligatory metadata" was first proposed by
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The annotation must unambiguously relate a piece of knowledge to a model constituent.
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The model file must be encoded in a public, standardized, machine-readable format (
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More information about the existing qualifiers is available from BioModels.net.
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The model must include the name and contact details of the model creators.
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The model file must be valid with respect to its encoding schema.
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Minimum
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The referenced information should be described using a triplet
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