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1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes Nature Precedings
Nick Juty; Camille Laibe; Nicolas Le Novere.
(1) An overview of the MIRIAM identifier scheme is presented, together with a description of the supporting tools and resources which allow its use as a robust cross-referencing framework.
(2) An overview of existing identifier schemes within the life sciences is presented, describing the status of each scheme, the prerequisites that a user must meet to use them, and their limitations.
Tipo: Presentation Palavras-chave: Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6154/version/1
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BioModels Database: curation and annotation Nature Precedings
Michael Schubert; Ishan Ajmera; Vijayalakshmi Chelliah; Lukas Endler; Nicolas Rodriguez; Camille Laibe; Nicolas Le Novère.
The BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published, peer-reviewed quantitative models of biological processes.

In this poster we provide an overview of its capabilities, as well as the curation and annotation process with two use cases concerning blood coagulation and glucose homeostasis.
Tipo: Poster Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6361/version/1
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BioModels Database: Next generation model repository Nature Precedings
Camille Laibe; Michael Hoehl.
Public announce that the software system running BioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) will evolve from open source to a community developed project.
Tipo: Presentation Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5127/version/1
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Curation and annotation for BioModels Database, a resource of published quantitative kinetic models Nature Precedings
Chelliah Vijayalakshmi; Lukas Endler; Camille Laibe; Chen Li; Nicolas Le Novère.
BioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) is a free resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and export of models in various other commonly used formats.

To offer scientists reliable information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its mathematical relations....
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3124/version/1
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Identifiers.org and MIRIAM Registry: perennial identifiers for crossreferencing purposes Nature Precedings
Camille Laibe.
The MIRIAM Registry provides unique, perennial and location independent identifiers for data used in the biomedical domain. At its core is a shared catalogue of data collections, for each of which a unique namespace is created, and extensive metadata recorded. This namespace allows the generation of Uniform Resource Identifiers (URIs) to uniquely identify any record in a collection. We present here the new Identifiers.org service which is built upon the information stored in the Registry and which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs). The flexibility of the identification scheme and resolving system allows its use in many different fields, where unambiguous and perennial identification of data entities...
Tipo: Presentation Palavras-chave: Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6479/version/1
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Identifiers.org/MIRIAM Registry annotation and cross-referencing framework Nature Precedings
Nick Juty; Camille Laibe; Nicolas Le Novere.
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We describe the existing MIRIAM URI identifiers, and the newly minted resolvable, parallel forms of these identifiers which use Identifiers.org URLs.
Tipo: Poster Palavras-chave: Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6396/version/1
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Kinetic Simulation Algorithm Ontology Nature Precedings
Anna Zhukova; Dagmar Waltemath; Nick Juty; Camille Laibe; Nicolas Le Novère.
To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in...
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6330/version/1
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Management and provision of computational models Nature Precedings
Camille Laibe.
Quantitative models of biological systems provide an understanding of chemical and biological phenomena based on their underlying mechanisms. Moreover, they can be used for example, to predict the behaviour of a system under given conditions or direct future experiments. This has made quantitative models the perfect tools to answer a variety of questions in the biological sciences and has lead to a steady growth of the number of published models.

To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. BioModels Database(http://www.ebi.ac.uk/biomodels/) has been developed to exactly fulfil those needs....
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012 URL: http://precedings.nature.com/documents/7013/version/1
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MIRIAM Resources: a robust annotation and cross referencing framework Nature Precedings
Camille Laibe; Nick Juty; Nicolas Le Novère.
_Background_
More than ever, the era of data integration has highlighted the key requirement to reference specific data in an unambiguous and perennial way, in order to enable community-level sharing, development, exchange and reuse of information. In the field of Systems Biology, which is concerned with creating quantitative models of biological processes, these requirements have directly led to the creation of the Minimal Information Required In the Annotation of Models (MIRIAM, "http://biomodels.net/miriam/":http://biomodels.net/miriam/). MIRIAM provides a specific set of guidelines that can be implemented within any structured modelling format.

_Objectives_
To...
Tipo: Poster Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5128/version/1
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MIRIAM Resources: next steps Nature Precedings
Camille Laibe.
This presentation gives a short introduction of MIRIAM Resources ("http://www.ebi.ac.uk/miriam/":http://www.ebi.ac.uk/miriam/), a robust annotation and cross referencing framework, based on URNs.

The presentation also explains some potential issues with the current system and presents a possible solution.

Finally, the presentation introduces some forthcoming and suggested updates and extensions to the current infrastructure.
Tipo: Presentation Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5130/version/1
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SBML Level 3 Package Proposal: Annotation Nature Precedings
Dagmar Waltemath; Neil Swainston; Allyson L. Lister; Frank Bergmann; Ron Henkel; Stefan Hoops; Michael Hucka; Nick Juty; Sarah Keating; Christian Knuepfer; Falko Krause; Camille Laibe; Wolfram Liebermeister; Catherine Lloyd; Goksel Misirli; Marvin Schulz; Morgan Taschuk; Nicolas Le Novère.
The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.

With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.

SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5610/version/1
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The System Biology Format Converter Nature Precedings
Gaël Jalowicki; Nicolas Rodriguez; Martina Kutmon; Jean-Baptiste Pettit; Lu Li; Arnaud Henry; Kedar Nath Natarajan; Camille Laibe; Chris T. Evelo; Nicolas Le Novère.
The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules.SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We will also allow to...
Tipo: Poster Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6363/version/1
Registros recuperados: 12
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