Minimal Information Required In the Annotation of Models
In the following recommendations:
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: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 21 2020 5:28 a.m.
Record updated: July 17, 2018, 10:17 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.ap169a' by 'The FAIRsharing Team' at 22:17, 17 Jul 2018 (approved): 'miriam_url' has been modified: Before: None After:
No XSD schemas defined
Conditions of UseApplies to: Data use
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
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.
Juty N,Le Novere N,Laibe C
Nucleic Acids Res 2011
No guidelines defined
Models and Formats
No identifier schema standards defined
No metrics standards defined
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.
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 is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated 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..
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
Engineering and Physical Sciences Research Council (EPSRC), UK (Government body)
COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)
ELIXIR-Hub, UK (Government body)
BB/E005748/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
JPA 1729 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)