Minimum information requested in the annotation of biochemical models (MIRIAM).
Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The lack of a standard description format, lack of stringent reviewing and authors' carelessness are the main causes for incomplete model descriptions. With today's increased interest in detailed biochemical models, it is necessary to define a minimum quality standard for the encoding of those models. We propose a set of rules for curating quantitative models of biological systems. These rules define procedures for encoding and annotating models represented in machine-readable form. We believe their application will enable users to (i) have confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models.
Le Novère
Nicolas
N
European Bioinformatics Institute, Hinxton, CB10 1SD, UK. lenov@ebi.ac.uk
Finney
Andrew
A
Hucka
Michael
M
Bhalla
Upinder S
US
Campagne
Fabien
F
Collado-Vides
Julio
J
Crampin
Edmund J
EJ
Halstead
Matt
M
Klipp
Edda
E
Mendes
Pedro
P
Nielsen
Poul
P
Sauro
Herbert
H
Shapiro
Bruce
B
Snoep
Jacky L
JL
Spence
Hugh D
HD
Wanner
Barry L
BL
D001671:Biochemistry / Q000379:methods* / Q000592:standards; D002468:Cell Physiological Phenomena; D016208:Databases, Factual; D004282:Documentation / Q000379:methods* / Q000592:standards*; D017408:Guidelines as Topic; D033181:Information Dissemination / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods* / Q000592:standards; D008954:Models, Biological; D009626:Terminology as Topic