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. 2007 Dec 13;1:58.
doi: 10.1186/1752-0509-1-58.

MIRIAM Resources: Tools to Generate and Resolve Robust Cross-References in Systems Biology

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Free PMC article

MIRIAM Resources: Tools to Generate and Resolve Robust Cross-References in Systems Biology

Camille Laibe et al. BMC Syst Biol. .
Free PMC article

Abstract

Background: The Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) is a set of guidelines for the annotation and curation processes of computational models, in order to facilitate their exchange and reuse. An important part of the standard consists in the controlled annotation of model components, based on Uniform Resource Identifiers. In order to enable interoperability of this annotation, the community has to agree on a set of standard URIs, corresponding to recognised data types. MIRIAM Resources are being developed to support the use of those URIs.

Results: MIRIAM Resources are a set of on-line services created to catalogue data types, their URIs and the corresponding physical URLs (or resources), whether data types are controlled vocabularies or primary data resources. MIRIAM Resources are composed of several components: MIRIAM Database stores the information, MIRIAM Web Services allows to programmatically access the database, MIRIAM Library provides an access to the Web Services and MIRIAM Web Application is a way to access the data (human browsing) and also to edit or add entries.

Conclusions: The project MIRIAM Resources allows an easy access to MIRIAM URIs and the associated information and is therefore crucial to foster a general use of MIRIAM annotations in computational models of biological processes.

Figures

Figure 1
Figure 1
MIRIAM Database browser. Users can browse the content of MIRIAM Database and view the details of current entries, as well as propose new entries.
Figure 2
Figure 2
Structure of MIRIAM Resources. Diagram representing the different components of MIRIAM Resources and their relationships.
Figure 3
Figure 3
Detail of an entry of MIRIAM Database. The example represents the entry of Enzyme Nomenclature. Note the three alternative resources giving access to the same data types.

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References

    1. Hucka M, Bolouri H, Finney A, Sauro H, Doyle J, H K, Arkin A, Bornstein B, Bray D, Cuellar A, Dronov S, Ginkel M, Gor V, Goryanin I, Hedley W, Hodgman T, Hunter P, Juty N, Kasberger J, Kremling A, Kummer U, Le Novère N, Loew L, Lucio D, Mendes P, Mjolsness E, Nakayama Y, Nelson M, Nielsen P, Sakurada T, Schaff J, Shapiro B, Shimizu T, Spence H, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics. 2003;19:524–531. doi: 10.1093/bioinformatics/btg015. - DOI - PubMed
    1. Lloyd C, Halstead M, Nielsen P. CellML: its future, present and past. Progress in Biophysics & Molecular Biology. 2004;85:433–450. doi: 10.1016/j.pbiomolbio.2004.01.004. - DOI - PubMed
    1. Luciano J. PAX of mind for pathway researchers. Drug Discovevry Today. 2005;10:937–42. doi: 10.1016/S1359-6446(05)03501-4. - DOI - PubMed
    1. Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro BE, Snoep JL, Spence HD, Wanner BL. Minimum Information Requested in the Annotation of biochemical Models (MIRIAM) Nature Biotechnology. 2005;23:1509–1515. doi: 10.1038/nbt1156. - DOI - PubMed
    1. Le Novère N. 4th Workshop on Computation of Biochemical Pathways and Genetic Networks. Berlin: Logos; 2005. BioModels.net, tools and resources to support Computational Systems Biology; pp. 69–74.

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