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| Registros recuperados: 210 | |
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| Delphine Dauga. |
| The curation process is significantly slowed down by missing information in the articles analyzed (for example, the identity of the clones used to generate ISH probes, the precise sequences tested in reporter assays, etc..). To help authors ensure in the future that necessary information is present in their article, we defined the Article Minimum Information Standard (AMIS) guidelines. This standard describes for each experiment the mandatory information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, _Nature Biotechnology_). This standard was deduced from the ANISEED curation pipeline (Tassy, Dauga, Daian, Sobral et al.... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5054/version/1 |
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| John Wilbanks. |
| Openness at the layer of cultural works and data is the key to the data infrastructure we need to accelerate science. This article lays out three key elements of data infrastructure - collaboration, classification, and openness - which draw us inevitably towards the long-claimed, but rarely-achieved, goal of the scientific method: to make claims that are reproducible under similar circumstances by someone other than the claimant, to be reproducible. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6032/version/1 |
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| Gudmundur A. Thorisson; Mikael Linden; Anthony J. Brookes; Myles Byrne; Juha Muilu; Tommi Nyronen. |
| Motivation for the IRISC workshop came from the observation that identity and digital identification are increasingly important factors in modern scientific research, especially with the now near-ubiquitous use of the Internet as a global medium for dissemination and debate of scientific knowledge and data, and as a platform for scientific collaborations and large-scale e-science activities.

The 1 1/2 day IRISC2011 workshop sought to explore a series of interrelated topics under two main themes: i) unambiguously identifying authors/creators & attributing their scholarly works, and ii) individual identification and access management in the context of identity federations. Specific aims of the workshop... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6609/version/1 |
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| Yukio Maruyama; Yoshifumi Kawamura; Takao Isogai; Nobuo Nomura; Naoki Goshima. |
| HGPD ("http://www.HGPD.jp/":http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression data. HGPD was launched in November 2008 and, since then, 33,275 human Gateway entry clones have been constructed from ORFs of full-length cDNAs, thus representing the largest collection in the world. Sequence information and protein expression of Gateway entry clones can also be retrieved from HGPD. The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database ("http://flj.hinv.jp/v01/cgi/index.cgi":http://flj.hinv.jp/v01/cgi/index.cgi), which was constructed as human cDNA sequence analysis database focusing on mRNA... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5070/version/1 |
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| Nick Juty. |
| The Systems Biology Ontology (SBO) is composed of hierarchically arranged sets of controlled vocabularies that are commonly used in mathematical modelling, providing an additional layer of semantic information. We present recent developments in SBO, including the ontology's OBO Foundry status, its relationship to SBGN, and detail some of the restructuring work that has been undertaken. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5121/version/1 |
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| 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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| Michael Hucka; Frank Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; Darren J. Wilkinson. |
| This is the specification for _Release 1 Candidate_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.

SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.

 More information about SBML and this specification is available online at "http://sbml.org/Documents/Specifications/... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4123/version/1 |
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| Susanna-Assunta Sansone. |
| Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends in both the regulatory arena and commercial science.

Proliferation of standards is a positive sign of stakeholders’ engagement, but how much do we know about these standards? Which ones are mature and stable enough to use or recommend? Which tools and databases implement which standard? Etc...

The BioSharing catalogue (www.biosharing.org) aims... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6151/version/1 |
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| Michael Hucka. |
| SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.

The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional "packages" that add topic-specific features to the Core to support more specialized models and application areas. In this presentation, I provide a very brief overview of SBML Level 3 activity areas. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5011/version/2 |
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| Registros recuperados: 210 | |
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