standards > reporting guideline > DOI:10.25504/FAIRsharing.ap169a


ready Minimal Information Required In the Annotation of Models

Abbreviation: MIRIAM


Recommended
General Information
The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any structured format for computational models.


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How to cite this record FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: Aug. 7, 2018, 1:08 p.m.; Last accessed: Nov 20 2018 3:17 p.m.


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Record updated: July 17, 2018, 10:17 p.m. by The FAIRsharing Team.

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Publications

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

Nicolas Le Novère, Andrew Finney, Michael Hucka, Upinder S Bhalla, Fabien Campagne, Julio Collado-Vides, Edmund J Crampin, Matt Halstead, Edda Klipp, Pedro Mendes, Poul Nielsen, Herbert Sauro, Bruce Shapiro, Jacky L Snoep, Hugh D Spence, Barry L Wanner
Nat. Biotechnol. 2005

View Paper (PubMed) View Publication

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.

Juty N,Le Novere N,Laibe C
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.

Laibe C,Le Novere N
BMC Syst Biol 2007

View Paper (PubMed) View Publication


Implementing Databases (5)
Identifiers.org Registry
The core of the Registry is a catalogue of data collections (corresponding to e.g. controlled vocabularies, databases), their URIs and the corresponding physical URLs (or resources). These resources are monitored daily to ensure data accessibility and the validity of the resolution mechanism.

A repository of mathematical models of biological and biomedical systems
BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.

YEASTNET: A consensus reconstruction of yeast metabolism
This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.

JWS Online
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.

BiGG Models
BiGG is a freely compendium of published genome-scale metabolic networks, combined into a single database. NCBI genome annotations are used to map genes, and metabolites are linked to many external databases such as KEGG, PubChem as well as others..


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Grant Number(s)

  • BB/E005748/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • JPA 1729 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)