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Registros recuperados: 210
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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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*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol* Nature Precedings
Thomas Perls; Nir Barzilai.
The "Archon Genomics X PRIZE Validation Protocol":http://precedings.nature.com/documents/5731/version/1 has been posted in part to solicit comments from the scientific community. Here, we suggest 100 subjects age >=105 years as the source of DNAs for the competition.

Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5756/version/1
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1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy Nature Precedings
Mihail Bota; Larry Swanson.
The goal of this workshop was to agree on a general strategy for developing a systematic, useful, and scientifically appropriate framework for neuroanatomical nomenclature. The workshop focused on general principles that will serve as a basis for future decisions on implementation strategies. The report discusses the problems arising from the use of different parcellation schemes and use of different terminologies and highlights the need of a universal vocabulary for describing the structural organization of the nervous system. Workshop participants encourage the creation of an International Coordinating Committee for Neuroanatomical Nomenclature and propose short- and long-term goals for such a committee.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008 URL: http://precedings.nature.com/documents/1780/version/1
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1st INCF Workshop on NeuroImaging Database Integration Nature Precedings
Lars Forsberg; Per Roland.
The goal of this meeting was to map existing neuroimaging databases, particularly databases containing primary data, and to identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases. The report provides an overview of existing neuroimaging databases that were discussed during the workshop and examines the feasibility of database federations. The report includes several recommendations for future developments.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008 URL: http://precedings.nature.com/documents/1781/version/1
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1st INCF Workshop on Sustainability of Neuroscience Databases Nature Precedings
Jack Van Horn; Jaap van Pelt.
The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008 URL: http://precedings.nature.com/documents/1983/version/1
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A community of biocurators Nature Precedings
Pascale Gaudet.
Biocuration is a difficult mission: biological data is highly heterogeneous, and there are few areas where guidelines for data preservation and exchange exist. This has hampered the speed, quantity and diversity of data possible to capture. Hence, a major challenge for the biocuration community is to explore innovative ways to capture, represent and display information. It is also essential to increase the involvement of researchers, publishers and funding agencies in this process. I will discuss the work of the International Society for Biocuration to build a community of biocurators to achieve these goals.
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5134/version/1
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A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0 Nature Precedings
Michael T. Cooling.
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources. 

We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic...
Tipo: Poster Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6391/version/1
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A Unified Approach for Representing Structurally-Complex Models in SBML Level 3 Nature Precedings
Robert Muetzelfeldt.
The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.

The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/4372/version/1
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ACBD: Database for Ascidian Chemical Genomics Nature Precedings
Yuichiro Hira; Jun Terai; Mitsuru Nakamura; Etsu Tashiro; Masaya Imoto; Kotaro Oka; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems,using small molecules such as a specific activator or inhibitor of protein, a hormone-likeinducer, or a neurotransmitter etc. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database).

First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster Palavras-chave: Developmental Biology; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5087/version/2
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Agenda of the “BioSharing workshop - Unifying Bio-Resources Descriptors” Nature Precedings
Susanna-Assunta Sansone; Philippe Rocca-Serra; Pascale Gaudet; Dawn Field.
Organized by members of the BioSharing initiative (www.biosharing.org) and the International Society for Biocuration (ISB, www.biocurator.org), this workshop brought together developers, curators, journal editors and researchers to discuss the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications.

The focus on the workshop was a strawman uniform system for describing these bio-resources (www.biodbcore.org), in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement (www.biosharing.org/standards).

Location: ISMB/ECCB,...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6148/version/1
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Agenda of the "BioSharing workshop - Bringing catalogues of bio-resource and standards together" Nature Precedings
Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Pascale Gaudet.
This workshop has brought together representatives of groups developing catalogues of bio-resources and its aims were twofold:

1. Ensure that BioSharing (www.biosharing.org), a catalogue of minimal information checklists, terminologies and exchange formats (hereafter called standards) and policies, complements and links to existing catalogues of tools and databases, and also to publications and related material;

2. Outline the technical implementations of the bioDBcore checklist (www.biodbcore.org), the proposed uniform system for describing the catalogues of tools and databases, in particular, how to ensure (bi-directional) linking to the BioSharing catalogue....
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6145/version/1
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AMIS, The Article Minimum Information Standard Nature Precedings
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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Annotating Whole Genome Sequencing in COSMIC (The Catalogue of Somatic Mutations in Cancer) Nature Precedings
C Y Kok; S A Forbes; N Bindal; S Bamford; C G Cole; M Jia; D Breare; R Shepherd; A Menzies; K Leung; J Teague; M R Stratton; P A Futreal.
"COSMIC, the Catalogue Of Somatic Mutations In Cancer":http://www.sanger.ac.uk/cosmic is designed to store and display somatic mutation information relating to human cancers, combining detailed information on publications, samples and mutation types. The information is curated both from the primary literature and the laboratories at the Cancer Genome Project, Sanger Institute, UK, and then semi-automatically entered into the COSMIC database. The v47 release (May 2010) contained the curation of 9202 papers describing 116,977 mutations across 466,851 samples. In order to provide consistent annotation of the data, COSMIC has developed a classification system for cancer histology and tissue ontology, and adapted HGVS mutation nomenclature...
Tipo: Poster Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5106/version/1
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Annotation of SBML Models Through Rule-Based Semantic Integration Nature Precedings
Allyson L. Lister; Phillip Lord; Matthew Pocock; Anil Wipat.
*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009 URL: http://precedings.nature.com/documents/3286/version/1
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Archon Genomics X PRIZE Validation Protocol Nature Precedings
Larry Kedes; Granger Sutton; Edison Liu; Victor Jongeneel.
This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5731/version/1
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BBSRC Data Sharing Policy Nature Precedings
Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to getting the best value for the funds we invest and believes that making research data more readily available will reinforce open scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6015/version/1
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Best practices for building interoperable systems for translational research Nature Precedings
Warren Kibbe.
Research databases, clinical systems, and lab systems all have different standards, formats and drivers for data capture, operation, analysis and integration. For interdisciplinary nutritional researchers, however, there is a dependence on all of these areas and technologies. While building and integrating these systems can be difficult, using agile practices including short iterations, testing and continuous integration methods, and close engagement with all stakeholders to create useful systems for translational research. Interoperability also requires good data standards, including the use of structured data dictionaries and existing data standards such as HL7, UMLS, LOINC, ICD, and OBO foundry ontologies.
Tipo: Presentation Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5197/version/1
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bioDBcore: overview of the checklist and steps towards implementation Nature Precedings
Pascale Gaudet (Pascale.Gaudet@isb-sib.ch); Philippe Rocca-Serra (proccaserra@googlemail.com).
Members of the International Society for Biocuration (ISB, biocurator.org) and the BioSharing (biosharing.org) initiative work together to develop and implement BioDBcore (biodbcore.org), a community-defined, uniform system for describing the core attributes of biological databases, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. The BioSharing catalogue offers this “one-stop shop” for those seeking information about the standards and data sharing policies.

This presentation illustrates the rational for BioDBcore(P Gaudet) and the progresses for its implementation (P Rocca-Serra),...
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6167/version/1
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Biological resource catalog: NIF and NeuroLex Nature Precedings
Anita E. Bandrowski.
In the digital age one can find data and teaching materials on the web, however data and materials of a high quality are not always ranked very high on commercial search engines that look at the number of other sites that link to a page rather than the quality of the information. Additionally, many such materials are maintained within databases that are inaccessible to search technology. To solve these problems, the Neuroscience Information Framework (NIF: http://www.neuinfo.org) was created to aid the neuroscience community to discover useful digital resources, such as academic databases, and it has also developed a large digital catalog of resources that are related to neuroscience.
NIF has developed a “resource...
Tipo: Presentation Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6238/version/1
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BioMed Central - open data guidance for authors Nature Precedings
Naomi Attar.
All research articles published by BioMed Central are open access. In keeping with the spirit of open access publishing, we aim to maximize the availability of data associated with these articles.
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6234/version/1
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