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| Registros recuperados: 210 | |
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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| 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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| Registros recuperados: 210 | |
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