MIRIAM (Minimum Information Required In The Annotation of Models) is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities.
18-525: The idea of "a set of good practices" including "some obligatory metadata" was first proposed by Nicolas Le Novère in October 2004 as part of a discussion to develop a common database of models in systems biology (which led to the creation of BioModels Database ). These initial ideas were further refined at a meeting in Heidelberg, during ICSB 2004, with representatives from many other interested groups. MIRIAM
36-463: A catalogue of shared namespaces for use by the community. This function is provided by the MIRIAM Registry . The Registry also provides a variety of supporting auxiliary features to enable automated procedures based upon these URIs. The ability to generate resolvable identifiers is provided through the use of the resolving layer, Identifiers.org . Nicolas Le Nov%C3%A8re Nicolas Le Novère
54-414: A comprehensive set of symbols with precise semantics, together with detailed syntactic rules regarding the construction and interpretation of maps. Using these three notations, a life scientist can represent in an unambiguous way networks of interactions (for example biochemical interactions). These notations make use of an idea and symbols similar to that used by electrical and other engineers and known as
72-493: A network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. The SBGN Entity Relationship (ER) language allows to see all the relationships in which a given entity participates, regardless of the temporal aspects. Relationships can be seen as rules describing the influences of entities nodes on other relationships. The SBGN Activity Flow (AF) language depicts
90-518: A research group at the European Bioinformatics Institute (EMBL-EBI) . The group studied the signaling pathways underlying synaptic plasticity , in particular the allosteric calcium sensors. In parallel, his group coordinated the development of a consistent set of standards in systems biology, including the graphical notation SBGN , the guidelines MIRIAM and MIASE , the languages SED-ML and PharmML, and ontologies such as
108-655: Is a British and French biologist. His research focuses on modeling signaling pathways and developing tools to share mathematical models . Le Novère obtained his Baccalauréat at the Prytanée National Militaire . He received a MSc (1993) in Biology and Biochemistry from the École Normale Supérieure , a BSc in Cellular Biology and Physiology (1991), and a PhD in Molecular and Cellular Pharmacology (1998) from
126-490: Is a registered project of the MIBBI (minimum information for biological and biomedical investigations). The MIRIAM Guidelines are composed of three parts, reference correspondence , attribution annotation , and external resource annotation , each of which deals with a different aspect of information that should be included within a model. 'Reference correspondence' deals with the basic reference information needed to make use of
144-569: Is a standard graphical representation intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst communities of biochemists, biologists, and theoreticians. The system was created over several years by a community of biochemists , modelers and computer scientists . SBGN is made up of three orthogonal languages for representing different views of biological systems: Process Descriptions , Entity Relationships and Activity Flows . Each language defines
162-566: The International Society for Computational Biology , he served on its board of directors from 2017 to 2018. In September 2018, Le Novère was sentenced for 8 month (suspended for 2 years) when he admitted downloading indecent images of a child and possession of an extreme pornographic image. Subsequently, he was dismissed from the Babraham Institute where he was working. SBGN The Systems Biology Graphical Notation (SBGN)
180-572: The Pierre and Marie Curie University . From 1999 to 2001, he was a Postdoctoral Fellow at the University of Cambridge (UK). The first part of Le Novère's career, in the laboratory of Jean-Pierre Changeux at the Pasteur Institute , was focused on studying Nicotinic acetylcholine receptors in the brain. He reconstructed their phylogeny, predicted and modeled their structure. He also investigated
198-669: The Systems Biology Ontology . He also created BioModels Database and the Identifiers.org URIs. Le Novère moved his group to the Babraham Institute from 2012 to 2018. He was associate editor of the journals BMC Systems Biology and npj Systems Biology and Applications until September 2018. He has been section head for the section Systems and Network Biology of the Faculty of 1000 from 2017 to 2018. Senior member of
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#1732895207522216-521: The block diagram . The simplicity of SBGN syntax and semantics makes SBGN maps suitable for use at the high school level. Some software support for SBGN is already available, mostly for the Process Description language. SBGN visualizations can be exchanged with the XML-based file format SBGN-ML. The SBGN Process Description (PD) language shows the temporal courses of biochemical interactions in
234-541: The flow of information between biochemical entities in a network. It omits information about the state transitions of entities and is particularly convenient for representing the effects of perturbations, whether genetic or environmental in nature. Work on defining a set of symbols to describe interactions and relationships of molecules was pioneered by Kurt Kohn at the National Cancer Institute with his Molecular Interaction Maps (MIM). The development of SBGN
252-427: The model, detailing on a gross level the format of the model file, and its instantiability for simulation purposes. 'Attribution annotation' deals with the attribution information that must be embedded within the model file. 'External resource annotation' defines the manner in which annotations should be constructed. Those annotations contain references to entities in databases, classifications, ontologies, etc. One of
270-400: The purposes of annotation is to allow unambiguous identification of the various model components. More information about the existing qualifiers is available from BioModels.net. So far, annotation is mainly a manual work, so to ensure their longevity the usage of perennial URIs is necessary. It was recognised that the generation of valid and unique URIs for annotation required the creation of
288-429: The role of the alpha6 subunit in the dopaminergic neurons of the mesencephalon. During his post-doctoral fellowship in the group of Dennis Bray at the University of Cambridge , he modeled the molecular networks underlying bacterial chemotaxis . Le Novère then became involved in the development standards to share mathematical models such as SBML , of which he would later become editor. In 2003, Le Novère built
306-700: Was initiated by Hiroaki Kitano , supported by a funding from the Japanese New Energy and Industrial Technology Development Organization . The meeting that initiated development of the Systems Biology Graphical Notation took place on February 11–12, 2006, at the National Institute of Advanced Industrial Science and Technology (AIST), in Tokyo, Japan. The first specification of SBGN Process Description language – then called Process Diagrams –
324-529: Was released on August 23, 2008 (Level 1 Version 1). Corrections of the document were released on September 1, 2009 (Level 1 Version 1.1), October 3, 2010 (Level 1 Version 1.2) and February 14, 2011 (Level 1 Version 1.3). The first specification of SBGN Entity relationship language was released on September 1, 2009 (Level 1 Version 1). Corrections of the document were released on October 6, 2010 (Level 1 Version 1.1) and April 14, 2011 (Level 1 Version 1.2). The first specification of SBGN Activity Flow language
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