MIRIAM

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MIRIAM, Minimal Information Requested In the Annotation of biochemical Models, is an effort to standardize the annotation and curation process of quantitative models of biological systems.

The goal of the project, initiated by the BioModels.net effort, is to produce a set of guidelines suitable for use with any structured format for computational models, in order to allow different groups to collaborate on annotating and curating computational models in biology.

Contents

[edit] Standard

A first part specifies that a model must be encoded in a public standardized machine-readable format, clearly related to a single reference description, and must reflect the biological processes listed in the reference description. All quantitative attributes have to be defined, including initial conditions, and the model must be able to reproduce reasonably well the results given in the reference description. A second part of the standard deals with the annotation of the model. A model has to provide the citation of the reference description, lists its creators, and be attached to some terms of distribution. Finally, each component of a model must be annotated to allow its unambiguous identification. This annotation is based on a set of standard Unique Resource Identifiers that describe a specific piece of knowledge. In order to resolve this annotation, the community has to agree on a set of valid URIs and possesses ways of automating their treatment.

[edit] Uniform Resource Identifiers

An important part of the standard consists in the controlled annotation of model components, based on Uniform Resource Identifiers. For more information on the use of those URIs to annotate models, see the specification of SBML Level 2 Version 2. In order to enable interoperability of this annotation, the community has to agree on a set of recognised data resources. MIRIAM database (using MySQL) is an online resource created to catalogue the data resources, their URIs and the corresponding physical URLs, whether these are controlled vocabularies or databases.

Each entry contains a diverse set of details about the resource: official name and synonyms, root URIs (URL and URN forms), patterns of identifiers, documentation, etc. Each data resource can be associated with several physical locations. For instance:

Note that the URIs can be take either a URL form (www.uniprot.org/) or a URN form (urn:lsid:uniprot.org). A URI is NOT a "real" website, but a unique string. For instance the URI representing the enzyme classification is www.ec-code.org/.

[edit] Resources

A freely available web site is been developed, using an Apache Tomcat server to provide an interface for the database. Users are able to perform queries such as retrieving valid physical locations (URLs) corresponding to a given URI (whether a generic data-type or a precise piece of knowledge), retrieving all the information stored about a data-type (such as its name, its synonyms, links to some documentation, etc.) and immediately get the results in a dynamic way, using AJAX.

Moreover, a programmatic access through Web Services (based on Apache Axis and SOAP messages) is available. This API permits not only to resolved model annotations, but also to generate the correct URIs based on resource name and accession numbers.

MIRIAM database and Web Services are developed at the European Bioinformatics Institute in the Computational Neurobiology Group.

[edit] References

  1. Le Novère, N. et al (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology 23:1509-1515. PMID 16333295
  2. Le Novère, N. et al (2006) Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34:D689-D691. PMID 16381960

[edit] See also

[edit] External links

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