Abstract
Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SB...Continue Reading
References
Mar 4, 2003·Bioinformatics·M HuckaUNKNOWN SBML Forum
May 15, 2004·Progress in Biophysics and Molecular Biology·Catherine M LloydPoul F Nielsen
Jun 18, 2004·Bioinformatics·Tom OinnPeter Li
Dec 8, 2005·Nature Biotechnology·Nicolas Le NovèreBarry L Wanner
Dec 31, 2005·Nucleic Acids Research·Nicolas Le NovèreMichael Hucka
Nov 23, 2006·BMC Neuroscience·Nicolas Le Novère
Aug 2, 2007·Molecular Systems Biology·Laurence CalzoneBela Novak
Dec 15, 2007·BMC Systems Biology·Camille Laibe, Nicolas Le Novère
May 9, 2009·PLoS Computational Biology·Christian I HongAttila Csikász-Nagy
Citations
Sep 26, 2013·Bioinformatics·Thomas CokelaerJulio Saez-Rodriguez
Oct 1, 2013·Bioinformatics·Kai-Cheng Hsu, Feng-Sheng Wang
Nov 23, 2006·BMC Neuroscience·Ivan ArisiVittorio Rosato
Jul 1, 2010·BMC Systems Biology·Chen LiCamille Laibe
May 3, 2011·Annual Review of Biomedical Engineering·Thomas S DeisboeckVittorio Cristini
Feb 26, 2013·Briefings in Bioinformatics·Chen LiDietrich Rebholz-Schuhmann
Jul 31, 2013·Briefings in Bioinformatics·Hiroyuki KurataTakenori Takata
Aug 21, 2012·Cellular and Molecular Life Sciences : CMLS·Miguel Ángel Medina
Aug 5, 2011·Amino Acids·Armando Reyes-PalomaresMiguel Angel Medina
May 15, 2012·Expert Opinion on Drug Metabolism & Toxicology·Nina Jeliazkova
Sep 4, 2014·BMC Systems Biology·Sarala M WimalaratneCamille Laibe
Mar 10, 2016·Biophysical Journal·Mark A WalkerRaimond L Winslow
Jun 4, 2011·Proteins·Sneha Bairy, Chung F Wong
Nov 13, 2015·Bioinformatics·Goksel MisirliAnil Wipat
Oct 27, 2011·Molecular Systems Biology·Mélanie CourtotNicolas Le Novère
Dec 20, 2013·CPT: Pharmacometrics & Systems Pharmacology·P ViciniA Rostami-Hodjegan
Aug 1, 2015·CPT: Pharmacometrics & Systems Pharmacology·N JutyV Chelliah
Nov 22, 2014·Nucleic Acids Research·Vijayalakshmi ChelliahCamille Laibe
Jan 30, 2015·Database : the Journal of Biological Databases and Curation·Saikat Chowdhury, Ram Rup Sarkar
Jun 23, 2016·Microbial Cell Factories·Nusrat JahanHiroyuki Kurata
Nov 7, 2017·Nucleic Acids Research·Mihai GlontHenning Hermjakob
Oct 22, 2014·Integrative Biology : Quantitative Biosciences From Nano to Macro·Douglas B Kell, Etheresia Pretorius
Jan 27, 2016·Ecology and Evolution·Alice Roy-BolducMohamed Hijri
Mar 17, 2011·PloS One·Yi-An ChenKenji Mizuguchi
Nov 29, 2012·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Zhihui WangThomas S Deisboeck
Jul 1, 2020·Journal of Integrative Bioinformatics·Falk SchreiberDagmar Waltemath
Aug 8, 2015·Briefings in Bioinformatics·David J Duffy
Nov 29, 2015·Briefings in Bioinformatics·Thomas PfauThomas Sauter
Jun 3, 2021·Metabolites·Thomas PfauThomas Sauter
Feb 18, 2011·Science Signaling·Julio Saez-RodriguezGustavo Stolovitzky