Consulta: subjectFacets:"Data Standards"
Registros recuperados: 210
Data/hora: 05/06/2024 18:22:55

AMIS, The Article Minimum Information Standard
Provedor de dados: 17
Autores: 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

CASIMIR &amp;#x26; ENFIN
Provedor de dados: 17
Autores: John Hancock.
I review the development of draft database registries in the CASIMIR and ENFIN projects and the development of the CASIMIR Database Description Framework.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6158/version/1

Openness as Infrastructure
Provedor de dados: 17
Autores: 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

FieldML
Provedor de dados: 17
Autores: Poul M. F. Nielsen; Christopher Bradley; Randall Britten; Richard Christie; Peter Hunter; Caton Little; Andrew Miller.
FieldML is an open format for storing and exchanging models containing field information. It is able to represent a wide variety of field value types, including scalar, vector, tensor, logical, and strings. Fields are defined over domains explicitly in terms of functions. Domains may be nested to form embedding hierarchies.
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6386/version/1

Identity in research infrastructure and scientific communication: Report from the 1st IRISC workshop, Helsinki Sep 12-13, 2011
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The 1 1/2 day IRISC2011 workshop sought to explore a series of interrelated topics under two main themes: i) unambiguously identifying authors/creators &amp;#x26; 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

The Latest Information and Perspective of Human Gene and Protein Database (HGPD) as Human Proteome Study
Provedor de dados: 17
Autores: Yukio Maruyama; Yoshifumi Kawamura; Takao Isogai; Nobuo Nomura; Naoki Goshima.
HGPD (&amp;#x22;http://www.HGPD.jp/&amp;#x22;: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 (&amp;#x22;http://flj.hinv.jp/v01/cgi/index.cgi&amp;#x22;: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 &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5070/version/1

Systems Biology Ontology: Update
Provedor de dados: 17
Autores: 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&amp;#x27;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

SED-ML Script Language
Provedor de dados: 17
Autores: Frank Bergmann.
The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6105/version/1

Metabolic Network Representation in SBGN PD: EC and Identity Gate
Provedor de dados: 17
Autores: Alexander Mazein.
This presentations describes proposed changes in SBGN PD that would allow this language to be better adopted for representing metabolic network.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4974/version/1

Querying Drosophila In-Situ Expression Data using SPARQL and D2RQ
Provedor de dados: 17
Autores: Chris Mungall.
I describe a SPARQL endpoint for a database containing annotated images of gene expression in fruitfly embryogenesis. The images depict the actual expression of genes at a microscopic level using a technique called insitu hybridisation. The results were recorded in a relational database, and the images were annotated using the fly anatomy ontology.
Tipo: Marker Paper / Data Plan
Palavras-chave: Developmental Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5522/version/1

MIRIAM Resources: a robust annotation and cross referencing framework
Provedor de dados: 17
Autores: Camille Laibe; Nick Juty; Nicolas Le Nov&amp;#xe8;re.
_Background_&amp;#xd;&amp;#xa;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, &amp;#x22;http://biomodels.net/miriam/&amp;#x22;:http://biomodels.net/miriam/). MIRIAM provides a specific set of guidelines that can be implemented within any structured modelling format.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Objectives_&amp;#xd;&amp;#xa;To...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5128/version/1

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa; More information about SBML and this specification is available online at &amp;#x22;http://sbml.org/Documents/Specifications/...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4123/version/1

Overview of BioSharing
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Proliferation of standards is a positive sign of stakeholders&amp;#x2019; 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...&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

Progress report: SBML  Level 3 package FBA
Provedor de dados: 17
Autores: Brett G. Olivier; Frank T. Bergmann.
The SBML Level 3 &amp;#x22;FBA&amp;#x22; package is a proposal for an extension to the current Level 3 Core specification that allows for the description and annotation of constraint based models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This allows one to e.g. store information related to flux balance analysis in SBML Level 3 models.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5033/version/1

Hierarchical Model Composition updates
Provedor de dados: 17
Autores: Lucian Smith.
A summary of the status of the hierarchical model composition package for SBML Level 3, and of its current implementation.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6402/version/1

1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;(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

F1000 and data publishing
Provedor de dados: 17
Autores: Rebecca Lawrence.
Utility of the BioSharing standards and the BioDBCore registry in F1000 journal publishing.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6172/version/1

SBML Level 3 Brief Update
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional &amp;#x22;packages&amp;#x22; 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

Foregut microbiome in development of esophageal adenocarcinoma
Provedor de dados: 17
Autores: Liying Yang; William  E. Oberdorf; Erika Gerz; Tamasha  Parsons; Pinak  Shah; Sukhleen Bedi; Carlos W. Nossa; Stuart  M. Brown; Yu Chen; Mengling Liu; Michael Poles; Fritz Francois; Morris Traube; Navjeet  Singh; Todd Z. DeSantis; Gary L. Andersen; Monika  Bihan; Les Foster; Aaron  Tenney; Daniel  Brami; Mathangi  Thiagarajan; Indresh K. Singh; Manolito   Torralba; Shibu  Yooseph; Yu-Hui  Rogers; Eoin L. Brodie; Karen E. Nelson; Zhiheng Pei.
Esophageal adenocarcinoma (EA), the type of cancer linked to heartburn due to gastroesophageal reflux diseases (GERD), has increased six fold in the past 30 years.  This cannot currently be explained by the usual environmental or by host genetic factors. EA is the end result of a sequence of GERD-related diseases, preceded by reflux esophagitis (RE) and Barrett&amp;#x2019;s esophagus (BE). Preliminary studies by Pei and colleagues at NYU on elderly male veterans identified two types of microbiotas in the esophagus. Patients who carry the type II microbiota are &amp;#x3e;15 fold likely to have esophagitis and BE than those harboring the type I microbiota. In a small scale study, we also found that 3 of 3 cases of EA harbored the type II biota. The findings...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5026/version/1

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis  of Alzheimer&amp;#x2019;s Disease and Cancers
Provedor de dados: 17
Autores: I. C. Baianu; M Charles; V. I. Prisecaru.
The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer&amp;#x27;s disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer&amp;#x27;s disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7111/version/2

Current State of JUMMP
Provedor de dados: 17
Autores: Martin Gr&amp;#xe4;&amp;#xdf;lin.
In computational biology there is a strong need to exchange quantitative models of biological processes in a standardized way. For storing and retrieving peer-reviewed models the BioModels Database has been available for several years. But at the moment there is no tool available to bring a model from development in the lab directly to the peer-reviewed online resource.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The JUMMP (JUst a Model Management Platform) project aims at providing a generic model management platform for any standardized model file. Through a well-elaborated security layer models can be developed and shared privately and later on be made available to the curation process and the broader community. Each change to a model is recorded in a version...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6371/version/1

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5272/version/1

SBRML Interoperability
Provedor de dados: 17
Autores: Frank T. Bergmann.
This presentation summarizes an initial meeting of SED-ML and SBRML editors in order to facilitate reuse and sharing of components of each language.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6329/version/1

COMBINE - What it is, what it could be
Provedor de dados: 17
Autores: Nicolas Le Novere.
The &amp;#x27;COmputational Modeling in BIology&amp;#x27; NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6332/version/1

Ontology-&amp;#xad;based Tools to Enhance the Curation Workflow
Provedor de dados: 17
Autores: Trish Whetzel.
In order to effectively search, retrieve, and analyze data oftentimes it is curated and tagged with ontology terms.  However, the amount of effort to curate the existing set of data resources is beyond the limits of purely manual curation.  We present three ontology-based tools developed by the National Center for Biomedical Ontology to enhance the curation workflow: Ontology Widgets, Notes, and the Annotator.  The Ontology Widgets provide a mechanism to use ontologies in Web-based forms without the need to locally parse and store the ontology.  The widgets provide a variety of functionality including term autocompletion and ontology visualization.  The Ontology Widgets are implemented for all BioPortal ontologies, including those from the OBO Foundry and...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5213/version/1

Publishing Interactive Articles: Integrating Journals And Biological Databases
Provedor de dados: 17
Autores: Karen Yook; Arun  Rangarajan; Hans-Michael Muller; Paul Sternberg; Tracey DePellegrin-Connelly; Tim Schedl; Mike Cherry; William  Gelbart; Juancarlos Chan; Stephen  Haenel; Lolly  Otis; Sharon Faelten; Marek S. Skrzypek; Steven Marygold.
In collaboration with the journal GENETICS, we&amp;#x27;ve developed and launched a pipeline by which interactive full-text HTML/PDF journal articles are published with named entities linked to corresponding resource pages in &amp;#x22;WormBase&amp;#x22;:http://www.wormbase.org/ (WB). Our interactive articles allow a reader to click on over ten different data type objects (gene, protein, transgene, etc.) and be directed to the relevant webpage. This seamless connection from the article to summaries of data types promotes a deeper level of understanding for the na&amp;#xef;ve reader, and incisive evaluation for the sophisticated reader. Further, this collaboration allows us to identify and collect information before the publication of the article. The...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5146/version/1

The BRIF (Bioresource Research Impact Factor) as a tool for improving bioresource sharing in biomedical research
Provedor de dados: 17
Autores: Laurence Mabile; Raymond Dalgleish; Gudmundur  A. Thorisson; Myl&amp;#xe8;ne Desch&amp;#xea;nes; Robert Hewitt; Jane Carpenter; Elena Bravo; Pierre-Antoine Gourraud; Paul Hofman; Jennifer Harris; Maria Angeles Munoz-Fernandes; Anne Cambon-Thomsen.
The central aim of the BRIF (Bioresource Research Impact Factor) initiative is to construct a quantitative parameter to evaluate bioresources, modeled to some degree on the Journal Impact Factor (JIF), and to provide guidance and methodology for optimizing recognition of bioresources, their use and their sharing at international level. To implement this concept an international working group has been set up. Specific tasks have been assigned to several sub-groups: BRIF digital identifier schemes; BRIF parameters, measures and indicators; journal guidelines for resource citing and referencing; policies for bioresource access and sharing. These are discussed in the present manuscript.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Pharmacology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6568/version/1

SBFC - The Systems Biology Format Converter Framework
Provedor de dados: 17
Autores: Martina Kutmon; Nicolas Rodriguez.
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.  Recently a prototype has been developed with OSGi to achieve a more modular framework structure. 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...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6370/version/1

First Report of 1 Micron Spatial Resolution Chemical Imaging of a Zirconium Single Crystal by FT-NIR Microspectroscopy
Provedor de dados: 17
Autores: I. C. Baianu.
This is the first report of 1 micron resolution chemical images of a Zirconium single crystal by FT-NIR Microspectroscopy. The FT-NIR spectra were obtained with a PerkinElmer SpectrumONE NTS spectrometer. The chemical images were obtained with a PerkinElmer Autoimage model FT-NIR microscope equipped with a very high sensitivity In /GaAs detector capable of precise measurements at ~10 ng, that was coupled to the SpectrumONE NTS FT-NIR spectrometer.
Tipo: Manuscript
Palavras-chave: Chemistry; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6599/version/1

CellML: current status and future directions
Provedor de dados: 17
Autores: David Nickerson.
An overview of the current status of the CellML project and some ideas on where things are heading.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6417/version/1

neXtProt, a new knowledgebase  on human proteins
Provedor de dados: 17
Autores: Lydie Lane.
In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from ~20&amp;#x27;300 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, subcellular locations, etc). This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5104/version/1

libSBML Status update
Provedor de dados: 17
Autores: Sarah M. Keating.
Overview of current status of libSBML development.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6394/version/1

BRIF and Variant Databases
Provedor de dados: 17
Autores: Raymond Dalgleish.
Databases of sequence variation in human genes (LSDBs) are an important resource for biology and medicine. Currently, the measurement of importance is not as objective as it might be and the establishment of impact factors would be of benefit to those who curate LSDBs. Specific issues relating to such databases are discussed.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5586/version/1

Standards and infrastructure for managing experimental metadata
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra.
*See also &amp;#x22;related poster&amp;#x22;:http://precedings.nature.com/documents/3144/version/1*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Today&amp;#x2019;s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as &amp;#x2018;omics&amp;#x2019;). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Standards initiatives normally cater to particular domains. However, several synergistic...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3145/version/1

Towards a Modelling Ecosystem for Libraries of Modular, Reusable Components
Provedor de dados: 17
Autores: Michael T. Cooling.
CellML 1.1 [1] is an XML-based model exchange protocol with inherent support for modularity.&amp;#xd;&amp;#xa;To assist in answering complex biomedical research questions, we are developing libraries of modular model components that facilitate mathematical model construction. &amp;#xd;&amp;#xa;Stored in the online, publicly accessible CellML Repository [2], the libraries vary from genetic and associated regulatory components for Synthetic Biology [3] to quantifying the Systems Biology of cardiovascular wall mal-adaptation [4,5].&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Currently however, using the libraries is not as easy as it should be. Here I describe progress towards a modelling ecosystem to encompasses component search and retrieval,...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6392/version/1

A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0
Provedor de dados: 17
Autores: 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. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

Marker Paper: The Urethral Microbiome of Adolescent Males
Provedor de dados: 17
Autores: J. Dennis Fortenberry; David E. Nelson; Qunfeng Dong.
Project ID: 46317 &amp;#x2013; No publication moratorium.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The microflora of the anterior male urethra during adolescence is poorly described and no data address the range of &amp;#x201c;typical&amp;#x201d; urethral organisms during adolescence as functions of pubertal development or onset of various types of partnered sexual activity. This means that current understanding of the urethral microbiome in adolescent men rests entirely on limited data inferred from adults, and from epidemiologic and behavioral explanations. Marked ethnic group variation in adolescent sexual behaviors and disparity in conditions such as sexually transmitted infections (STI) justifies exploration of potential ethnic group differences in the...
Tipo: Marker Paper / Data Plan
Palavras-chave: Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5221/version/1

Gene Curation Software at the Rat Genome Database (RGD)
Provedor de dados: 17
Autores: Stanley J. F. Laulederkind; Mary  Shimoyama; Brad Taylor; Victoria  Petri; Timothy F. Lowry; G. Thomas Hayman; Shur-Jen Wang; Jennifer R. Smith; Rajni Nigam; Jeff De Pons; Weisong Liu; George Kowalski; Melinda R. Dwinell; Diane H. Munzenmaier; Howard J. Jacob.
At model organism databases data is curated for numerous biological categories using various ontologies and vocabularies.  The Rat Genome Database (RGD) uses four different ontologies to standardize annotation information for genes and their associations with disease, phenotypes, and pathways. For manual gene curation this is all done in a single user interface of a web-based annotation tool developed at RGD.  The same interface can be used for the curation of QTLs and strains. The development of the tool has been achieved through a collaboration of curators and software developers.  Features have been tailored to the needs of the curators to allow optimum efficiency of the data entry portion of the curation process.  Annotations using the Gene Ontology,...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5058/version/1

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments
Provedor de dados: 17
Autores: Toshinori Endo; Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Kohji Hotta; Yutaka Satou; Lixy Yamada; Michio Ogasawara; Hiroki Takahashi; Ayako Nakajima; Mia Nakachi; Mamoru Nomura; Junko Yaguchi; Alu Konno; Sasakura Yasunori; Akiyasu C. Yoshizawa; Hisaaki Taniguchi; Chisato Yamasaki; Miho Sera; Tadashi Imanishi; Kazuo Inaba.
CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata.  Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans.  Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data.  The CIPRO database is aimed at not only collecting published data, but also presenting unique information,...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5435/version/1

Update: MIRIAM Registry and SBO
Provedor de dados: 17
Autores: Nick Juty.
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We also describe current status and planned improvements to this system, as well as providing an update on the Systems Biology ontology since the last COMBINE meeting in Edinburgh (2010). &amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6405/version/1

SBML Team facilities &amp;#x26; software
Provedor de dados: 17
Autores: Frank T. Bergmann; Sarah M. Keating.
This presentation provides a brief overview of the new SBML online validator and the updates in the SBML Tool Matrix. This presentation ends with an update on the new version of the SBML Toolbox.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6401/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/2

Functional Curation: Potential Future Directions for SED-ML
Provedor de dados: 17
Autores: Jonathan Cooper; Gary Mirams.
&amp;#x22;Functional curation&amp;#x22;:http://dx.doi.org/10.1016/j.pbiomolbio.2011.06.003 of models is essentially about enabling a set of models to be tested for reproduction of a particular behaviour under some protocol. The idea is to examine which of the models are capable of replicating experimentally observed results, and evaluate their suitability for &amp;#xd;&amp;#xa;reuse in particular modelling studies. This requires a description of the protocol being performed on the models, and ideally a community agreed standard for these. Clearly SED-ML is the obvious candidate here, however, in its current form it has a few limitations that preclude this application.  This talk discusses the requirements posed by functional curation, and introduces our...
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6327/version/1

BRIF Workshop Minutes
Provedor de dados: 17
Autores: Laurence Mabile.
This document is a detailed summary of the presentations and discussions from the BRIF (Bioresource Impact Factor) workshop, held in Toulouse on 17-18 january 2011.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5879/version/1

SBML Level 3 Package Proposal: Flux
Provedor de dados: 17
Autores: Frank Bergmann; Brett G. Olivier.
This document describes  an easy to implement  package for storing information related &amp;#xd;&amp;#xa;to flux balance analysis of  SBML  Level  3 models  (the  FBA  package). In addition,  &amp;#xd;&amp;#xa;we  provide  an  example  of  how  this package  may be  implemented and  used as  a SBML&amp;#xd;&amp;#xa;Level 2 annotation.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4236/version/1

The Physiome languages: CellML and FieldML
Provedor de dados: 17
Autores: Peter J. Hunter.
Discussion of the markup languages being defined by the VPH/Physiome project for multiscale, multiphysics modeling.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4982/version/1

Integrating &amp;#xa0;text-&amp;#xad;mining&amp;#xa0;effort requires&amp;#x9;output standards
Provedor de dados: 17
Autores: Andra Waagmeester.
We recently released a plugin to Pathvisio to assist the curator with automatic integration of heterogeneous pathway knowledge. Pathway curation involves gathering this knowledge not only through discussions with peers, but also from biological databases and the scientific literature. Integrating this all into one pathway is challenging and to date still mainly a laborious manual process. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;More and more biological databases provide webservices (ie. REST or SOAP). The main objective of webservices is to provide an interface for other computer applications. Our plug-in uses these interfaces to gather binary relationships of a given pathway entity and present the relation in star shaped figures to the curator. The plug-in...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5850/version/1

Systems Biology on Bio-Linux
Provedor de dados: 17
Autores: Mesude Bicak.
This presentation introduces the Bio-Linux Operating System which is a popular Computational Biology workstation with 500+ bioinformatics software. It then provides an overview of popular modelling approaches in systems biology, covering top-down, bottom-up and hybrid modelling. Finally it highlights the challenges being faced by systems biology modellers, agent-based modellers in particular, regarding standardisation efforts.
Tipo: Presentation
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6348/version/1

SED-ML: Nested Simulation Proposal
Provedor de dados: 17
Autores: Frank T. Bergmann.
This document describes a second version of the proposal for nested simulation experiments for SED-ML (http://sed-ml.org). The proposal has been updated to include the feedback received in the meantime and has been enhanced by examples. A full implementation is available with libSedML (http://libsedml.sf.net) and the SED-ML Web Tools (http://sysbioapps.dyndns.org/SED-ML_Web_Tools/)
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/4257/version/2

Some thoughts about the future of SBML
Provedor de dados: 17
Autores: Nicolas Le Novere.
SBML was designed in 2000, merely 2 years after the first official specification of XML. 11 years afterward, the current structure of the language is largely unchanged. Since then, its user base evolved much, as did the whole field of modeling in biology. &amp;#xd;&amp;#xa;If one wants SBML to evolve in the next decade, it is time to start discussing the basics now. The presentation covers a series of fundamental issues such as SBML coverage, unity of the language, use of elements and attributes etc.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6387/version/1

Workshop report: 1st INCF Workshop on Large-scale Modeling of the Nervous System
Provedor de dados: 17
Autores: Mikael Djurfeldt; Anders Lansner.
The goal of this workshop was to survey current demands, ongoing activities, and plans relating to development of tools for scalable neural network simulation. Areas covered included software components for preprocessing/model setup, as well&amp;#xd;&amp;#xa;as for storage, analysis, and visualization of results. Participants discussed the need for coordinated action in the field with regard to model, method and tool development. The reports a description of the state-of-art in the field as well as recommendations for actions to facilitate infrastructure developments.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/262/version/1

bioDBcore: overview of the checklist and steps towards implementation
Provedor de dados: 17
Autores: 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 &amp;#x201c;one-stop shop&amp;#x201d; for those seeking information about the standards and data sharing policies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

Java support for SED-ML
Provedor de dados: 17
Autores: Richard R. Adams.
This presentation describes Java support for the SED-ML simulation experiment description language. Firstly, a Java API library for low-level manipulations of the SED-ML object model, and secondly a SED-ML editor, SED-ED, for visualizing and editing SED-ML workflows
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6334/version/1

Annotation of SBML Models Through Rule-Based Semantic Integration
Provedor de dados: 17
Autores: 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

The Neonatal Microbiome and Necrotizing Enterocolitis.
Provedor de dados: 17
Autores: Phillip I. Tarr; Barbara Warner; Erica Sodergren; William Shannon; Aaron Hamvas; Vincent Magrini; George Weinstock.
Necrotizing enterocolitis (NEC) is a devastating disorder that affects approximately 10% of premature infants. Its mortality remains high (15-30%), and its cause remains unknown. About 80% of cases occur within 35 days of birth among hospitalized newborns of low birth weight. Probiotics diminish the incidence and severity of NEC, and NEC does not occur antepartum. NEC affects a readily identifiable at-risk group, has a tightly defined interval before its onset, occurs in an organ system that is intimately associated with a microbial population in flux, has a plausible association with the intestinal microbiota, and cohorts at risk have rarely been studied in large numbers, or prospectively. This disorder, therefore, provides a unique opportunity to explore...
Tipo: Marker Paper / Data Plan
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5285/version/1

Chloroplast and Cell Imaging at Submicron Resolution by Two-Photon Excitation
Provedor de dados: 17
Autores: I C. Baianu.
Novel, two-photon NIR excitation fluorescence correlation microspectroscopy tests and preliminary results were presented in this article with submicron resolution for concentrated suspensions of functional cells and chloroplast membranes. Related developments of these technique involve applications of Fluorescence Cross-Correlation Spectroscopy (FCCS) detection to monitoring: &amp;#xd;&amp;#xa;DNA- telomerase interactions, DNA hybridization kinetics, ligand-receptor interactions, and HIV-HBV testing. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7116/version/1

Deciphering the genome structure and paleohistory of _Theobroma cacao_
Provedor de dados: 17
Autores: Xavier Argout; Jerome Salse; Jean Marc Aury; Gaetan Droc; Jerome Gouzy; Mathilde Allegre; Cristian Chaparro; Thierry Legavre; Mark Guiltinan; Siela Maximova; Michael Abrouk; Florent Murat; Olivier Fouet; Julie Poulain; Manuel Ruiz; Yolande Roguet; Maguy Rodier-Goud; Jose Fernandes Barbosa-Neto; Francois Sabot; Dave Kudrna; Jetty Siva S. Ammiraju; Stephan C. Schuster; John E. Carlson; Erika Sallet; Schiex T.; Anne Dievart; Melissa Kramer; Laura Gelley; Zi Sh; Aur&amp;#xe9;lie B&amp;#xe9;rard; Christopher Viot; Michel Boccara; Ange Marie Risterucci; Valentin Guignon; Xavier Sabau; Michael Axtell; Zhaorong Ma; Yufan Zhang; Spencer Brown; Mickael Bourge; Wolfgang Golser; Xiang Song; Didier Clement; Ronan Rivalan; Mathias Tahi; Joseph Moroh Akaza; Bertrand Pitollat; Karina Gramacho; Ang&amp;#xe9;lique D&amp;#x2019;Hont; Dominique Brunel; Diogenes Infante; Ismael Kebe; Pierre Costet; Rod Wing; W.  Richard McCombie; Emmanuel Guiderdoni; Francis Quetier; Olivier Panaud; Patrick Wincker; Stephanie Sidibe-Bocs; Claire Lanaud.
We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4908/version/1

Dynamic Structures in SBML
Provedor de dados: 17
Autores: Chris Myers.
This talk describes ideas on how to integrate dynamic structures in SBML.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6342/version/1

BioSharing: Standards, Policies and Communication in Bioscience
Provedor de dados: 17
Autores: Dawn Field; Susanna-Assunta Sansone; Philippe Rocca-Serra.
BioSharing works at the global level to build stable linkages between journals, funders, implementing data sharing policies, and well-constituted standardization efforts in the biosciences domain, to expedite the communication and the production of an integrated standards-based framework for the capture and sharing of high-throughput genomics and functional genomic bioscience data.
Tipo: Presentation
Palavras-chave: Biotechnology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6436/version/1

The BioGRID Interaction Database
Provedor de dados: 17
Autores: Michael S. Livstone; Bobby-Joe Breitkreutz; Chris Stark; Lorrie Boucher; Andrew Chatr-Aryamontri; Rose Oughtred; Julie Nixon; Teresa Reguly; Jennifer Rust; Andrew Winter; Kara Dolinski; Mike Tyers.
The goal of the Biological General Repository for Interaction Datasets (BioGRID) (http://www.thebiogrid.org) is to archive and freely disseminate collections of genetic and protein interactions from major model organisms. BioGRID currently houses over 335,000 interactions curated from high-throughput datasets and individual focused studies found in the primary literature, as derived from some 23,000 publications. Complete coverage of the entire literature for both the budding yeast _Saccharomyces cerevisiae_ and the fission yeast _Schizosaccharomyces pombe_ has been achieved, resulting in the curation of over 246,000 interactions, and efforts to expand curation across multiple species are underway. Through collaborations with the Gene Ontology (GO)...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5627/version/1

Agenda of the  &amp;#x22;BioSharing workshop -  Bringing catalogues of bio-resource and standards together&amp;#x22;
Provedor de dados: 17
Autores: 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:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

BioSharing Overview
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Dawn Field; Annapaola Santarsiero; Eamonn  Maguire; Philippe Rocca-Serra; Chris Taylor; Lee Harland; The BioSharing  Communities.
Download this poster providing an overview of the BioSharing effort.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5936/version/1

semanticSBML 2.0 - A Collection of Online Services for SBML Models
Provedor de dados: 17
Autores: Falko Krause; Timo Lubitz; Marvin Schulz; Edda Klipp.
semanticSBML 2.0 is a collection of online services for the processing of biochemical networks in the SBML (Systems Biology Markup Language) document format. It allows users to edit SBO (Systems Biology Ontology) and RDF based MIRIAM (Minimum Information Required in the Annotation of Models) annotations, check for semantic validity, compare and merge SBML documents, and to create submodels. Given an annotated SBML document similar SBML documents can be retrieved from the BioModels Database via a ranked similarity search. Further  features of semanticSBML 2.0 include  graph visualization of SBML documents, parameter balancing, creation of SBML documents using shorthand SBML, and an interface to the BioModels Database that allows the comparison of document...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5402/version/1

Tales From the Code Front:  Translating Modularity
Provedor de dados: 17
Autores: Lucian P. Smith.
In translating modular Antimony models to and from CellML, two differences appeared:  CellML&amp;#x27;s &amp;#x27;black box&amp;#x27; approach vs. Antimony&amp;#x27;s &amp;#x27;model composition&amp;#x27; approach, and CellML&amp;#x27;s math-based encoding vs. Antimony&amp;#x27;s object and rule-based encoding.  The latter turned out to have a much larger impact on the translation than anticipated.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5132/version/1

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain
Provedor de dados: 17
Autores: Michael Hawrylycz; Jyl Boline; Albert Burger; Tsutomu Hashikawa; G. Allan Johnson; Maryann Martone; Lydia Ng; Jonathan Nissanov; Luis Puelles; Seth Ruffins; Fons Verbeek; Ilya Zaslavsky.
The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/4000/version/1

OneStop:JWS Online&amp;#x27;s access point to SBML,SBGN and MIRIAM compliant annotation
Provedor de dados: 17
Autores: Franco B. Du Preez; Stuart Owen; Katherine Wolstencroft; Olga Krebs; Wolfgang M&amp;#xfc;ller; Carole Goble; Jacky L. Snoep.
We have developed an online model constructor and validator called OneStop, which is compliant with SBGN, SBML and MIRIAM standards. Key features of OneStop are: 1) a human readable input form (in addition to SBML upload and saving); 2) live visualization (SBGN graphics) of the reaction network during the construction phase; and 3) online access from any machine with a compatible browser. Sophisticated error feedback simplifies the debugging process during model construction significantly and guides the efforts of new users in a step by step fashion. OneStop is seamlessly integrated with the JWS Online model repository and simulator and also facilitates the importation of models from the BioModels database. In addition, OneStop is part of the SysMO-SEEK...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6349/version/1

Collaborative platforms for streamlining workflows in Open Science
Provedor de dados: 17
Autores: Konrad U. F&amp;#xf6;rstner; Gregor  Hagedorn; Claudia  Koltzenburg; M. Fabiana   Kubke; Daniel  Mietchen.
Despite the internet&amp;#x2019;s dynamic and collaborative nature, scientists continue to produce grant proposals, lab notebooks, data files, conclusions etc. that stay in static formats or are not published online and therefore not always easily accessible to the interested public. Because of limited adoption of tools that seamlessly integrate all aspects of a research project (conception, data generation, data evaluation, peer-reviewing and publishing of conclusions), much effort is later spent on reproducing or reformatting individual entities before they can be repurposed independently or as parts of articles.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We propose that workflows - performed both individually and collaboratively - could potentially become more...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6066/version/1

A community of biocurators
Provedor de dados: 17
Autores: 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

SBML Level 3 Package Proposal: Annotation
Provedor de dados: 17
Autores: 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 Nov&amp;#xe8;re.
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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

The &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) specification
Provedor de dados: 17
Autores: Pelin  Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette  Johnston; Guy Cochrane; Robert  Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine  A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn  Maguire; Barbara A. Meth&amp;#xe9;; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; J&amp;#xf6;rg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aym&amp;#xe9; Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Gl&amp;#xf6;ckner.
We present the Genomic Standards Consortium&amp;#x2019;s (GSC) &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5252/version/2

Towards a web-based simulation experiment description repository
Provedor de dados: 17
Autores: Michael Guravage; Roeland M. H. Merks.
Modellers are producing more and more complex models. Unless these models are sufficiently characterised and made available to the research community their reuse will be minimal, and reproducing simulation experiments incorporating them will prove problematic. Consensus on the content and form of experiment recipes that combine models and simulations will encourage model sharing and facilitate reuse.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A set of guidelines specifying the &amp;#x27;Minimum Information About a Simulation Experiment&amp;#x27;(MIASE)  proposes a common set of information necessary to reproduce simulation experiments that incorporate quantitative models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have instantiated these guidelines in a web-based...
Tipo: Poster
Palavras-chave: Plant Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6346/version/1

Determination of Soybean Oil, Protein and Amino Acid Residues in Soybean Seeds by High Resolution Nuclear Magnetic Resonance (NMRS) and Near Infrared (NIRS)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina Costescu; P R. Lozano; Valentin Prisecaru; Randall   L. Nelson.
A detailed account is presented of our high resolution nuclear magnetic resonance (HR-NMR) and near infrared (NIR) calibration models, methodologies and validation procedures, together with a large number of composition analyses for soybean seeds. NIR calibrations were developed based on both HR-NMR and analytical chemistry reference data for oil and twelve amino acid residues in mature soybeans and soybean embryos. This is our first report of HR-NMR determinations of amino acid profiles of proteins from whole soybean seeds, without protein extraction from the seed.  It was found that the best results for both oil and protein calibrations were obtained with a Partial Least Squares Regression (PLS-1) analysis of our extensive NIR spectral data, acquired...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7053/version/1

The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic Analysis
Provedor de dados: 17
Autores: Jacques  Ravel; Larry J. Forney.
The vaginal microbiota play an important protective role in maintaining the health of women. Disruption of the mutualistic relationship that exists between bacterial communities in the vagina and their hosts can lead to bacterial vaginosis (BV), a condition in which lactic acid producing bacteria are supplanted by a diverse array of strictly anaerobic bacteria. BV has been shown to be an independent risk factor for adverse outcomes including preterm delivery and low infant birth weight, acquisition of sexually transmitted infections and HIV, and development of pelvic inflammatory disease. National surveys indicate the prevalence of BV among U.S. women is 29.2%, and yet, despite considerable effort, the etiology of BV remains unknown. Moreover, there are no...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5062/version/1

Integrating Open Lab Notebooks with Online Databases
Provedor de dados: 17
Autores: Carl Boettiger.
My slides from a presentation and panel discussion on integrating open lab notebooks with online databases.  A video archive of the presentation is available here: http://vimeo.com/20100632
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6853/version/1

Updates to the SBML Level 3 Flux Balance Constraints (FBC) package
Provedor de dados: 17
Autores: Brett B. G. Olivier.
In this presentation I introduce the need for an SBML package and introduce recent updates to the proposal.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The Flux Balance Constraints package is a proposed SBML Level 3 extension that allows the definition of constraint based (a.k.a steady state, flux balance analysis, FBA) models.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6352/version/1

Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness
Provedor de dados: 17
Autores: Melanie Dulong de Rosnay.
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitates innovation and how this openness can be achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that prevent others...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2083/version/1

LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Nov&amp;#xe8;re; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Vill&amp;#xe9;ger.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4967/version/1

Comments and Suggestions for Improvement of the  Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Alexander Wait Zaranek; Tom Clegg; Ward  Vandewege; Joseph V. Thakuria.
This document is a comment on the X PRIZE validation protocol written by Kedes et al. (2011).  We propose several modifications which we think will improve the fairness and transparency of the contest while keeping the cost of the validation process under control.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5766/version/1

Identifiers.org/MIRIAM Registry annotation and cross-referencing framework
Provedor de dados: 17
Autores: 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

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere.
With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models.  The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/58/version/2

Standardising bioresource acknowledgement in papers
Provedor de dados: 17
Autores: Dr Robert Hewitt.
This presentation describes the speakers experience of gathering performance indicator data, for biobank assessment.  Problems encountered in collecting data on the number of publications resulting from supported studies are described.  These include difficulty in obtaining a complete record of all the resulting publications and also frequent misnaming of the biobank in the acknowledgment section of papers.  The presentation also includes a discussion of approaches to providing credit to all the contributors in the biobanking effort.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5607/version/1

SBGN-ED &amp;#x2013; working with the Systems Biology Graphical Notation
Provedor de dados: 17
Autores: Tobias Czauderna; Falk Schreiber.
The Systems Biology Graphical Notation - SBGN [1] provides a standard for the visual representation of biochemical and cellular processes. SBGN aims to improve information exchange and to support the collaborative creation of large maps based on individual modules. The language contains three views of biological processes covering different levels of detail:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(1) Process Description (PD): this sublanguage provides a detailed presentation of the temporal dependencies of biological  interactions in a network;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(2) Entity Relationship (ER): this sublanguage displays the relationships in which a given entity can participate in a network; and&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(3) Activity Flow...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6445/version/1

Ontology-driven International Maize Information System (IMIS) for Phenotypic and Genotypic Data Exchange
Provedor de dados: 17
Autores: Rosemary Shrestha; Hector Sanchez; Claudio Ayala; Peter Wenzl; Elizabeth Arnaud.
The Consultative Group on International Agricultural Research (CGIAR; http://www.cgiar.org/) centres have developed the International Crop Information System (ICIS; http://www.icis.cgiar.org) for the management and integration of global information on genetic resources, and germplasm improvement for any crop. The Maize breeding programs at CIMMYT (http://beta.cimmyt.org/) have different software tools to manage phenotypic, genotypic, and environmental information for their experiments generated worldwide. These tools have the capacity of collecting information in the field, wet lab, and store it into different relational databases. The IMIS (http://imis.cimmyt.org/confluence/display/IMIS/Crop+Finder) is an implementation of the ICIS, which is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5029/version/1

libSBML New conversion API
Provedor de dados: 17
Autores: Sarah M. Keating; Frank T. Bergmann.
Description of the new API for including converters within libSBML.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6395/version/1

SBGN Activity Flow Update
Provedor de dados: 17
Autores: Huaiyu Mi.
SBGN Activity Flow specification was released in September 2009.  In this talk, a brief review is provided on the specification, and a number of issues raised by the community are discussed.  Particular focus was on the issue of graphical representation of entity decoration of a biological activity.  A number of proposals from the community are discussed in detail.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5680/version/1

Information and Data Sharing Policy, Genomic Science Program, DOE
Provedor de dados: 17
Autores: Susan Gregurick.
The Office of Biological and Environmental Research (OBER) will require that all publishable information resulting from GTL funded research must conform to community recognized standard formats when they exist, be clearly attributable, and be deposited within a community recognized public database(s) appropriate for the research conducted. Furthermore, all experimental data obtained as a result of GTL funded research must be kept in an archive maintained by the Principal Investigator (PI) for the duration of the funded project. Any publications resulting from the use of shared experimental data must accurately acknowledge the original source or provider of the attributable data. The publication of information resulting from GTL funded research must be...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5973/version/1

ACBD: Database for Ascidian Chemical Genomics
Provedor de dados: 17
Autores: 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 &amp;#x22;chemical genomics&amp;#x22;. 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).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Provedor de dados: 17
Autores: Michael Hucka; Frank T. Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; James C. Schaff; Lucian P. Smith; Darren J. Wilkinson.
This is the final specification for _Release 1_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;More information about SBML and this specification is available online at...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4959/version/1

InterPro Curation: Integrating Predictive Protein Signatures Into Biological Hierarchies
Provedor de dados: 17
Autores: Sarah Burge.
InterPro is an integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. As InterPro curators, we are responsible for assimilating information from our member databases and communicating it to our end users in a way that adds value to each individual signature. We categorise signatures according to their type (for example, Family, Domain or Repeat) and annotate entries with links to other databases, abstracts and protein matches.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The InterPro database also identifies relationships between entries. For example, signatures at a general Family level are related to more specific subfamilies through a Parent/Child relationship. Families may also Contain...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5330/version/1

Role of CellML and FieldML in VPH/Physiome Applications
Provedor de dados: 17
Autores: Peter J. Hunter.
Discusses the use of the VPH/Physiome markup languages in VPH applications.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5911/version/1

Agenda of the &amp;#x201c;BioSharing workshop - Unifying Bio-Resources Descriptors&amp;#x201d;
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Location: ISMB/ECCB,...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6148/version/1

JSBML update
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Nicolas Rodriguez.
This presentation gives an overview about the major changes in JSBML since the release of version 0.8-b1, which will become part of the first release candidate.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6358/version/1

Effect of Crohn&amp;#x27;s Disease Risk Alleles on Enteric Microbiota Marker Paper
Provedor de dados: 17
Autores: Ellen Li; Erica Sodergren; George Weinstock; Thaddeus Stappenbeck; Daniel Frank; Charles Robertson; Norman Pace; Wei Zhu; Edgar Boedeker; R. Balfour Sartor; Phillip Tarr; Lloyd Mayer; David Dietz.
This UH2/UH3 demonstration project entitled &amp;#x201c;Effects of Crohn&amp;#x2019;s disease risk alleles on enteric microbiota&amp;#x201d; is focused on characterizing intestinal associated microbiota in patients with ileal Crohn&amp;#x2019;s disease (ileal CD), ulcerative colitis (UC) and control patients without inflammatory bowel diseases (non-IBD).  We hypothesize that genetic factors that affect Paneth cell function, contribute to compositional changes in intestinal microbiota.  These changes in microbiota may lead to reduction of protective commensal organisms and increased numbers of aggressive organisms that incite intestinal inflammation. This hypothesis is being tested by high throughput 16S rRNA sequence analysis of de-identified ileal and...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4975/version/1

The System Biology Format Converter
Provedor de dados: 17
Autores: Ga&amp;#xeb;l Jalowicki; Nicolas Rodriguez; Martina Kutmon; Jean-Baptiste Pettit; Lu Li; Arnaud Henry; Kedar Nath Natarajan; Camille Laibe; Chris T. Evelo; Nicolas Le Nov&amp;#xe8;re.
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

Nationwide Study of Breast Cancer Risk Factors in Latinas
Provedor de dados: 17
Autores: Michael Dean; Latoya Silverton; Julie Sawitzke.
Breast cancer is the most common cancer among American women. Any woman can be affected by breast cancer, with risk for the disease increasing with age.  Risk for breast cancer is also exacerbated in women who have certain genetic alterations. Mutations in the BRCA1 and BRCA2 genes predispose women to breast and ovarian cancer, and are increasingly recognized in prostate and pancreatic cancers (1-3).  In Caucasian and Asian ethnicities BRCA mutations are associated with basal-type/triple-negative disease. However this association between BRCA gene mutations and basal/triple-negative disease has been understudied in other ethnicities (4-6). The incidence and mortality of breast cancer of Hispanics and Native Americans are lower than other ethnicities;...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5691/version/2

UniProt Knowledgebase: a hub of integrated data
Provedor de dados: 17
Autores: Michele Magrane; UniProt Consortium.
Data integration plays an increasingly important role in bringing together the large amounts of diverse information spread across disparate resources and presenting a comprehensive overview of these data to the scientific community. The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialised data collections. UniProtKB also integrates data such as protein sequences, protein-protein interactions, Gene Ontology terms and official gene...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5092/version/1

Managing Multiple Parameter Sets in SBML
Provedor de dados: 17
Autores: Frank Bergmann.
This document describes the elements of a SBML annotation, for storing multiple parameter sets in an SBML model. A user might wish to store different parameter sets that exhibit interesting behavior of computational models. One common example would be to store parameter values for steady states, or even oscillating regimes.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4233/version/1

Publishing re-usable phylogenetic trees, in theory and practice
Provedor de dados: 17
Autores: Brian O&amp;#x27;Meara; Jamie Whitacre; Ross Mounce; Dan F. Rosauer; Rutger A. Vos; Arlin Stoltzfus.
Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information (&amp;#x27;data&amp;#x27;), including empirical data as well as computed inferences such as phylogenetic trees. &amp;#xd;&amp;#xa;Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6048/version/1

Socio-economic determinants of anthropometric measures of abdominal adiposity among older people in England
Provedor de dados: 17
Autores: Jose Iparraguirre; Sam SzeLam.
Objective: to look into the socio-economic determinants of levels of three anthropometric measures of abdominal adiposity among older people in England -body mass index, waist circumference (WC), and waist-hip ratio (WHR)- and of changes along two health risk classifications: the World Health Organisation classification based on BMI levels and the WHO combined classification based on BMI and waist circumference measurements.&amp;#xd;&amp;#xa;Design: quantile regression and multinomial analysis using data from the English Longitudinal Study of Ageing (ELSA), wave 2 (2004-05) and wave 4 (2008-09)&amp;#xd;&amp;#xa;Results: The quantile analysis on levels led to disparate results depending on the wave, which would question results previously published based on...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6897/version/1

The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish
Provedor de dados: 17
Autores: Claire M. Fraser-Liggett; Alan  R. Shuldiner.
Emerging evidence that the gut microbiota may contribute in important ways to human health and disease has led us and others to hypothesize that both symbiotic and pathological relationships between gut microbes and their host may by key contributors to obesity and the metabolic complications of obesity. Our &amp;#x201c;Thrifty Microbiome Hypothesis&amp;#x201d; posits that gut microbiota play a key role in human energy homeostasis. Specifically, constituents of the gut microbial community may introduce a survival advantage to its host in times of nutrient scarcity, promoting positive energy balance by increasing efficiency of nutrient absorption and improving metabolic efficiency and energy storage. However, in the presence of excess nutrients, fat...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4957/version/1

Systems Biology Graphical Notation: Entity Relationship language Level 1
Provedor de dados: 17
Autores: Nicolas Le Nov&amp;#xe8;re; Stuart Moodie; Anatoly Sorokin; Falk Schreiber; Huaiyu Mi.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/3719/version/2

Diet, Genetic Factors, and the Gut Microbiome in Crohn&amp;#x27;s Disease
Provedor de dados: 17
Autores: Gary D. Wu; James D. Lewis; Frederic D. Bushman.
This manuscript is part of a pilot effort on the part of NIH staff and the Nature publishing group to provide a more convenient archive for &amp;#x22;marker papers&amp;#x22; to be published.  These &amp;#x22;marker papers&amp;#x22; are designed to provide the users of community resource data sets with information regarding the status and scope of individual community resource projects.  For further information see editorial in September 2010 edition of Nature Genetics (Nature Genetics, 42, 729 (2010)), and the Nature Precedings HMP summary page.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Project IDs: 46313, 46879&amp;#xd;&amp;#xa;Publication moratorium: 1 year&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;     We propose to investigate the hypothesis that consistent changes...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5006/version/1

Types, models and instances: a perspective from neuroscience
Provedor de dados: 17
Autores: Robert C. Cannon.
In order to share neuroscience models effectively, there is a need to clearly separate out the structure, equations and parameters so that each model only specifies those bits that are unique to itself. This will enable specialized simulation tools to recognize structures they can handle without having to process the equations directly. Two projects, NeuroML2 and NineML are working in this direction. As an example, we show how the Hodgkin Huxley equations can be decomposed into separate component type definitions and parameter sets in such as way that the majority of Hodgkin-Huxley style ion channel models can be expressed in only a few lines.
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5119/version/1

The Human Microbiome and Recurrent Abdominal Pain in Children
Provedor de dados: 17
Autores: James Versalovic; Robert J. Shulman; Kevin Riehle; Delphine M. Saulnier; Toni-Ann Mistretta; Maria A. Diaz; Sabeen Raza; Debasmita Mandal; Xiang Qin; Susan Lynch; Joseph Petrosino; Richard Gibbs.
This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS).  Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain.  3. Perform functional gut metagenomics by evaluation of whole...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5228/version/2

The SBML Level 3 Annotation package: an initial proposal
Provedor de dados: 17
Autores: Neil Swainston.
The SBML Level 3 Annotation package proposal intends to extend the current Level 3 Core annotations by increasing the range of RDF features supported.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Such an extension will support RDF Reification, annotation of SBML attributes, specification of relationships between annotations, negation of annotations and cross-references and cross-element annotations.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5001/version/1

Minimum Information about a Neuroscience Investigation (MINI): Electrophysiology
Provedor de dados: 17
Autores: Frank Gibson; Paul G. Overton; Tom V. Smulders; Simon R. Schultz; Stephen J. Eglen; Colin D. Ingram; Stefano Panzeri; Phil Bream; Miles Whittington; Evelyne Sernagor; Mark Cunningham; Christopher Adams; Christoph Echtermeyer; Jennifer Simonotto; Marcus Kaiser; Daniel C. Swan; Martyn Fletcher; Phillip Lord.
This module represents the formalised opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission&amp;#xd;&amp;#xa;to the CARMEN system (&amp;#x22;http://www.carmen.org.uk&amp;#x22;:www.carmen.org.uk).
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/1720/version/2

ENA as an Information Hub
Provedor de dados: 17
Autores: Petra ten Hoopen; Ruth Akhtar; Richard Gibson; Bob Vaughan; Nadeem Faruque; Guy Cochrane.
The European Nucleotide Archive (ENA; &amp;#x22;http://www.ebi.ac.uk/ena/&amp;#x22;:http://www.ebi.ac.uk/ena/) is a comprehensive repository for public nucleotide sequence data from nearly four hundred thousand taxonomic nodes. Together with partners in the International Nucleotide Sequence Database Collaboration (INSDC; EBI, NCBI and DDBJ) we provide a broad spectrum of sequences, from raw reads (Sequence Read Archive data class), assembled contigs (Whole Genome Shotgun data class), assemblies of EST transcripts (Transcriptome Shotgun Assembly data set), to partial or complete assembled nucleic acid molecules with functional annotation derived from direct and third party experimental evidence (Standard and TPA data classes, respectively). Resources beyond...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5108/version/1

We Need A Web For Data
Provedor de dados: 17
Autores: John Wilbanks.
The Web has many forums for sharing personal data, but not for scientific data and not in a way that allows the data to be accessed by &amp;#x22;machines as users.&amp;#x22; A Web of data could add tremendous value by integrating disparate disciplines or conduct data-driven queries. Doing this is very complex and requires more robust standards than currently exist. The intended user for most data is not a person; it is a software application that can manipulate the data into something useful for humans. Such software could be &amp;#x22;search engines, analytic software, visualization tools, database back ends, and more.&amp;#x22; This need creates a much different requirement for standards than those that were developed for displaying web data to people....
Tipo: Manuscript
Palavras-chave: Biotechnology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5499/version/1

KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-accumulation Analysis
Provedor de dados: 17
Autores: Nozomu Sakurai.
Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation are considered to be useful for uncovering unknown functions of genes and regulatory systems of the metabolic pathways. Although many databases and tools are available to interpret quantitative data of transcriptome and metabolome, there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We developed a new metabolic pathway database, KaPPA-View4 (&amp;#x22;http://kpv.kazusa.or.jp/kpv4/&amp;#x22;:http://kpv.kazusa.or.jp/kpv4/), that enables to overlay gene-to-gene and/or metabolite-to-metabolite relationships as quadratic Bez&amp;#xed;er curves on metabolic pathway maps. For up to 4 maps...
Tipo: Presentation
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5065/version/1

The Role of the Gut Microbiota in Ulcerative Colitis
Provedor de dados: 17
Autores: Vincent B. Young; Eugene B. Chang; Folker Meyer; Mitchell L. Sogin; Thomas M. Schmidt; James Tiedje.
The overall goal of our Demonstration Project is to address the hypothesis that the gut microbiota plays a critical role in the pathogenesis of inflammatory bowel disease (IBD). To circumvent the confounding effects of mucosal inflammation and medications that independently bias microbial selection, we have set out to study a unique clinical model of ulcerative colitis (pouchitis) where the development and status of the gut microbiota can be assessed prospectively and relative to the outcome of disease. Pouchitis is an inflammatory condition of a surgically-created pseudorectum that is unique to ulcerative colitis and rarely occurs when this procedure is performed for treatment of other non-IBD diseases.  Since the incidence of developing pouchitis within...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5254/version/1

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Stefan Hoops; Sarah M. Keating; Nicolas Le Nov&amp;#xe8;re; Sven Sahle; Darren Wilkinson.
With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2715/version/1

Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net
Provedor de dados: 17
Autores: Michael Hucka.
Systems biology has arisen through the convergence of theoretical, computational, and mathematical modeling of systems and the need to understand the wealth of information being rapidly generated in biology.  Systems biology by its nature requires collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics, and physics.  Successful integration of these disciplines depends on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, software tools that permit analysis of vast and complex data, and agreed-upon standards that enable researchers to communicate and reuse each other&amp;#x27;s results in practical and unambiguous ways....
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/20/version/1

BRIF Workshop Introduction
Provedor de dados: 17
Autores: Anne Cambon-Thomsen.
This presentation aims at introducing the place of BRIF in the landscape of data sharing, the BRIF concept, a presentation of the working group, the ongoing debates and the workshop objectives.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5658/version/1

The Hymenoptera Genome Database
Provedor de dados: 17
Autores: Monica C. Munoz-Torres; Justin T. Reese; Christopher P. Childers; Anna K. Bennett; Jaideep P. Sundaram; Donald  C. Vile; Christine G. Elsik.
The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of hymenopteran insect species. This relational database implements open-source software and components providing access to curated data contributed by an extensive, active research community. HGD includes the genome sequences and annotation data of honey bee _Apis mellifera_ and its pathogens (&amp;#x22;http://BeeBase.org&amp;#x22;:BeeBase.org) the parasitoid wasp _Nasonia vitripennis_ (&amp;#x22;http://NasoniaBase.org&amp;#x22;:NasoniaBase.org) and a portal to the genomes of six species of ants. Together, these species cover approximately 200 MY in the phylogeny of Hymenoptera, allowing to leverage genetic, genome sequence, and gene expression data, as well as the...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5182/version/1

Manual Curation of Vertebrate Proteins  in the UniProt Knowledgebase.
Provedor de dados: 17
Autores: Michael  J. Gardner; Lionel  Breuza; The UniProt  Consortium.
The UniProt Knowledgebase (UniProtKB) aims to provide the scientific community with a comprehensive, consistent and authoritative resource for protein sequence and functional information. Given the importance of human and vertebrate model data in biomedical research, a major focus is the high-quality manual curation of human proteins and their vertebrate orthologues. Manual curation involves (1) the extraction of experimental results from scientific literature to enrich protein records with a wide range of information including function, structure, interactions and subcellular location, (2) the manual verification of each sequence and clarification of discrepancies between sequence reports, and (3) the assessment of the output of a range of analysis...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5165/version/1

Annotating Whole Genome Sequencing in COSMIC (The Catalogue of Somatic Mutations in Cancer)
Provedor de dados: 17
Autores: 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.
&amp;#x22;COSMIC, the Catalogue Of Somatic Mutations In Cancer&amp;#x22;: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 &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5106/version/1

caNanoLab &amp;#x2013; A Tool To Benefit Biomedical Nanomaterials Research
Provedor de dados: 17
Autores: Michal Lijowski.
The cancer Nanotechnology Laboratory Web portal (&amp;#x22;http://cananolab.nci.nih.gov/caNanoLab/welcome.do&amp;#x22;:http://cananolab.nci.nih.gov/caNanoLab/welcome.do) is designed to promote sharing of nanomedicine data and to provide support for the annotation of nanoparticles with information about their composition, function, and characterization. The project is a part of NCI cancer Biomedical Informatics Grid (caBIG&amp;#xae;), and includes a collaboration among the NCI Center for Biomedical Informatics and Information Technology (CBIIT), the NCI Nanotechnology Characterization Laboratory (NCL), and the NCI Alliance for Nanotechnology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Currently, caNanolab contains nanomaterial data of 765 &amp;#x22;public&amp;#x22;...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5175/version/1

COMBINE - a vision
Provedor de dados: 17
Autores: Nicolas Le Novere.
A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and re-used models in systems biology. The robustness and versatility of this format, coupled to a wide software support, fostered the emergence of an entire area of research centered on model processing such as encoding, annotation, merging, comparison and integration with other datasets. Recently, new languages appeared that complement the model description, such as SED-ML to describe the simulation experiments or SBRML to encode the numerical results. In neuroscience, other fledgling efforts cover for instance multi-compartment neurons with NeuroML, and neuronal networks with NineML. More are needed to cover the wide spectrum of...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5992/version/1

MIREOT: the Minimum Information to Reference an External Ontology Term
Provedor de dados: 17
Autores: Melanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan R. Brinkman; Alan Ruttenberg.
While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3574/version/1

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5271/version/1

DDBJ Sequence Read Archive / DDBJ Omics Archive
Provedor de dados: 17
Autores: Yuichi Kodama; Satoshi Saruhashi; Eli Kaminuma; Hideaki Sugawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura.
Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields.  DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI.  In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms.  DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy.  Since 2004, DDBJ has operated CIBEX as a repository database for...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5085/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondr&amp;#xe9;-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; Richard H. Scheuermann; Q. Alison Yao; Martin S. Zand; Christopher J. Mungall.
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology.  Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed both issues.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were set for structuring these cell type terms as cross-products with logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The methods and improvement to the CL in...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3635/version/1

UniRule - Automatic Annotation In UniProtKB
Provedor de dados: 17
Autores: Alan J. Bridge; Diego Poggioli; Claire O&amp;#x27;Donovan.
The UniProt KnowledgeBase (UniProtKB) provides a stable, comprehensive, freely accessible, centralized resource on protein sequences and functional annotation. UniProtKB consists of two sections: UniProtKB/SwissProt, a section containing records that are manually annotated with information extracted from the literature and curator-evaluated computational analysis, and UniProtKB/TrEMBL, a section containing computationally analysed records enriched with automatic annotation and classification. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Automatic annotation is an essential complement to manual annotation, which cannot keep pace with either current or projected rates of growth of UniProtKB. To this end UniProt is developing an integrated annotation system termed...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5247/version/1

The BRIF: Success Factors and Crucial Considerations for Ensuring Impact.
Provedor de dados: 17
Autores: Lisa  B. Miranda.
This presentation focused on the potential of the BRIF to capture data that demonstrates the initial and long term impact of bioresources and those who direct/operate them for support/participation in biomedical and clinical research and their effects on clinical care outcomes. The focus of this talk is also to share ideas and provide different ways to look at the BRIF. The BRIF can be used to measure impact but may also be utilized to ensure and accelerate impact. Implementing the BRIF would potentially lead to significant positive downstream effects. Many challenges exist for the biobanking area ahead of this. One central issue that is delaying/impeding impact is the ability to create economically viable and sustainable resources.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Pharmacology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5877/version/1

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY
Provedor de dados: 17
Autores: Nick Juty; Nicolas Le Nov&amp;#xe8;re; Dagmar Waltemath; Christian Knuepfer.
The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the &amp;#x27;Repressilator&amp;#x27; model (Elowitz and Leibler, 2000).
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5122/version/1

SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web
Provedor de dados: 17
Autores: Norio Kobayashi; Manabu Ishii; Yuko Yoshida; Yuko Makita; Akihiro Matsushima; Yoshiki Mochizuki; Tetsuro Toyoda.
Integration of various omics databases is a fundamental approach for comprehensive understanding of life phenomena.  Scientists&amp;#x2019; Networking System (SciNetS) is a Semantic Web-based data repository that realises database integration by collecting metadata of databases described as a set of triples consisting of two bio-items such as gene and ontology terms and a semantically defined relationship between these bio-items.  These triples are curated from various life-sciences databases including gene-publication relationships manually curated from MEDLINE and gene-phenotype relationships extracted from published databases by computer programs.  SciNetS internally forms a metadata network by maximally concatenating...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5083/version/1

BioMed Central - open data guidance for authors
Provedor de dados: 17
Autores: 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

Normalization And Matching Of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Meik Bittkowski; Henriette Slogsnat; Jasmin Saric; Isabel Rojas; Wolfgang M&amp;#xfc;ller.
We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the normalized name forms. The tool is capable of normalizing a given name  of a chemical compound and matching it against names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact name-to-name-match.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6505/version/1

Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn&amp;#x27;s Disease
Provedor de dados: 17
Autores: Claire  M. Fraser-Liggett.
Inflammatory bowel diseases (IBD), such as Crohn&amp;#x2019;s disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. In this application, we propose to develop and demonstrate the ability to profile Crohn&amp;#x2019;s disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4958/version/1

BioPax and SBML output from Reactome: where we are, where we are heading
Provedor de dados: 17
Autores: David Croft.
Reactome is a free, open-source, open access, pathway database. Currently, Reactome has over 5000 human proteins, involved in over 4000 manually curated reactions.  Additionally, it has nearly 30,000 reactions inferred by orthology projection from human to 20 other model organisms.  Facilities exist for exporting single pathways or the entire database to either BioPax or SBML.  SBML generation now uses libSBML, ensuring syntactic correctness, and has adopted MIRIAM URIs for references to external databases.  For the future, we anticipate that users will be able to submit a list of species to Reactome and obtain as an output customized BioPax or SBML, based on reactions extracted from Reactome.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6376/version/1

Data Management Plan for Monogram BioSciences
Provedor de dados: 17
Autores: Christos J. Petropoulos.
This is the data plan for access to data underlying published reports by Monogram BioSciences.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Pharmacology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5668/version/1

eagle-i: An Ontology-Driven Framework For Biomedical Resource Curation And Discovery
Provedor de dados: 17
Autores: Erik  Segerdell; Melanie L. Wilson; Ted Bashor; Daniela Bourges-Waldegg; Karen Corday; H. Robert Frost; Tenille Johnson; Christopher J. Shaffer; Larry Stone; Carlo Torniai; Melissa A. Haendel.
The eagle-i Consortium (&amp;#x22;http://www.eagle-i.org/home&amp;#x22;:www.eagle-i.org/home) comprises nine geographically and ethnically diverse universities across America working to build a federated network of research resources. Biomedical research generates many resources that are rarely shared or published, including: reagents, protocols, instruments, expertise, organisms, training opportunities, software, human studies, and biological specimens. The goal of eagle-i is to improve biomedical research by helping researchers more easily find scientific resources that are difficult to discover, reducing time-consuming and expensive duplication of resources. Now in early development, the system will ultimately expand to include research resources at...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5176/version/1

*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol*
Provedor de dados: 17
Autores: Thomas Perls; Nir Barzilai.
The &amp;#x22;Archon Genomics X PRIZE Validation Protocol&amp;#x22;: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 &amp;#x3e;=105 years as the source of DNAs for the competition.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5756/version/1

COMBINE and MIRIAM Registry
Provedor de dados: 17
Autores: Nicolas Le Novere.
N/A
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6152/version/1

JSBML: a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Nicolas Rodriguez; Marine Dumousseau; Alexander D&amp;#xf6;rr; Clemens Wrzodek; Roland Keller; Sebastian Fr&amp;#xf6;hlich; Nicolas Le Nov&amp;#xe8;re; Andreas Zell; Michael Hucka.
The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java&amp;#x2122; programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6372/version/1

Disruptive Strategies for Removing Drug Discovery Bottlenecks
Provedor de dados: 17
Autores: Sean Ekins; Chris L. Waller; Mary  P. Bradley; Antony J. Williams.
Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6961/version/1

ExO: An Ontology for Exposure Science
Provedor de dados: 17
Autores: Carolyn J. Mattingly; Thomas  E. McKone; Michael Callahan; Judith  Blake; Elaine A. Cohen Hubal.
An ontology is a formal representation of knowledge within a domain and typically consists of classes, the properties of those classes, and the relationships between them.  Ontologies are critically important for specifying data of interest in a consistent manner, thereby enabling data aggregation, analysis and exchange.  An exposure ontology, consistent with those being used in toxicology and other health sciences, is required to formally represent exposure concepts, the relationships between these concepts and most important, the relationships between exposure, susceptibility, and toxicology information.  A successful exposure ontology must facilitate the semantic retrieval of exposure data in the context of environmental health science, medical...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6321/version/1

Exposing The Cancer Genome Atlas (TCGA) as a SPARQL endpoint
Provedor de dados: 17
Autores: Helena Deus.
Automated discovery of candidate biomarkers from multiple databases has been the central challenge in the Life Sciences in general and in the study of systemic processes such as those documented by The Cancer Genome Atlas (TCGA) in particular. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The maturation of Semantic Web technologies offers solutions to those problems by allowing the query to be defined by navigating a normally represented domains of discourse instantiated by the data. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We address the systems challenge of The Cancer &amp;#xd;&amp;#xa;Genome Atlas initiative (http://cancergenome.nih.gov/), which generates a large scale repository of high throughput molecular biology data generated and processed at 5 academic...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6303/version/1

SBML and Synthetic Biology
Provedor de dados: 17
Autores: Chris Myers.
This talk describes the synthetic biology open language (SBOL).
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6343/version/1

Metacuration Standards and Minimum Information about a Bioinformatics Investigation
Provedor de dados: 17
Autores: Tin Wee Tan; Asif M. Khan; Shen Jean Lim; Yong Li Hu; Mark de Silva; Kuan Siong Lim.
Many bioinformatics databases published in journals are here this year and gone the next. There is generally (i) no requirement, mandatory or otherwise, by reviewers, editors or publishers for full disclosure of how databases are built and how they are maintained; (ii) no standardized requirement for data in public access databases to be kept as backup for release and access when a project ends, when funds expire and website terminates; (iii) the case of proprietary resources, there is no requirement for data to be kept in escrow for release under stated conditions such as when a published database disappears due to company closure. Consequently, much of the biological databases published in the past twenty years are easily lost, even though the...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5078/version/1

BRIF workshop working group.
Provedor de dados: 17
Autores: Laurence Mabile.
Number of attendees, geographical origin of the group, skills and areas represented, tools developed to help the BRIF progress.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5582/version/1

BioModels Database: curation and annotation
Provedor de dados: 17
Autores: Michael Schubert; Ishan Ajmera; Vijayalakshmi Chelliah; Lukas Endler; Nicolas Rodriguez; Camille Laibe; Nicolas Le Nov&amp;#xe8;re.
The BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published, peer-reviewed quantitative models of biological processes.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

Managing Bio-Models: &amp;#xb;Model Storage, Retrieval, Ranking and Versioning
Provedor de dados: 17
Autores: Ron Henkel; Dagmar Waltemath; Olaf Wolkenhauer.
In this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models - tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently  addressed in existing systems.&amp;#xd;&amp;#xa;To validate our techniques, we have been implemented a framework called Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The design is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6325/version/1

Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Provedor de dados: 17
Autores: Samiran Bisai; Kaushik  Bose.
This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa.  The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars.  Height and weight were measured following standard techniques.  The body mass index (BMI) was computed following standard equation.  Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI.  We followed the World Health Organization&amp;#x27;s classification (1995) of the public health problem of low BMI, based on adult populations worldwide.  Our results show that, in general, among the tribes...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7068/version/2

Principles for the post-GWAS functional characterisation of risk loci
Provedor de dados: 17
Autores: Matthew L. Freedman; Alvaro N. A. Monteiro; Simon A. Gayther; Gerhard A. Coetzee; Angela Risch; Christoph Plass; Graham Casey; Mariella De Biasi; Chris Carlson; Dave Duggan; Michael James; Pengyuan Liu; Jay W.  Tichelaar; Haris G. Vikis; Ming You; Ian G. Mills.
Several challenges lie ahead in assigning functionality to susceptibility SNPs. For example, most effect sizes are small relative to effects seen in monogenic diseases, with per allele odds ratios usually ranging from 1.15 to 1.3. It is unclear whether current molecular biology methods have enough resolution to differentiate such small effects. Our objective here is therefore to provide a set of recommendations to optimize the allocation of effort and resources in order to maximize the chances of elucidating the functional contribution of specific loci to the disease phenotype. It has been estimated that 88% of currently identified disease-associated SNPs are intronic or intergenic. Thus, in this paper we will focus our attention on the analysis of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5162/version/2

LibSBGN Status Update
Provedor de dados: 17
Autores: Martijn van Iersel; Tobias Czauderna; Alice C. Villeger.
LibSBGN is a library for reading, writing and validating maps that use the Systems Biology Graphical Notation (SBGN). The goals of LibSBGN are to 1) increase interoperability between pathway visualization tools, 2) increase the amount of code re-used, and 3) make it easier for tool developers to adopt the SBGN standard. This presentation is a status update of the project, presented at the COMBINE 2011 meeting.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6373/version/1

Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
Provedor de dados: 17
Autores: Dagmar Waltemath; Frank T. Bergmann; Richard Adams; Nicolas Le Novere.
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the experimental task to run, and which result to produce.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5846/version/1

Natural Environment Research Council - Data Policy
Provedor de dados: 17
Autores: Mark Thorley.
The Natural Environment Research Council (NERC) has a policy on data in order to:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(a) Ensure the continuing availability of environmental data of long-term value for research, teaching, and for wider exploitation for the public good, by individuals, government, business and other organisations;&amp;#xd;&amp;#xa;(b) Support the integrity, transparency and openness of the research it supports;&amp;#xd;&amp;#xa;(c) Help in the formal publication of data sets, as well as enabling the tracking of their usage through citation and data licences;&amp;#xd;&amp;#xa;(d) Meet relevant legislation and Government guidance on the management and distribution of environmental information.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6017/version/1

1st INCF Workshop on Sustainability of Neuroscience Databases
Provedor de dados: 17
Autores: 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

SBGN PD: Current status, future changes and unresolved issues.
Provedor de dados: 17
Autores: Stuart L. Moodie.
The presentations reports and the current status of the SBGN-PD specification and highlights issues for further discussion.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6831/version/1

Integration of the scientific literature into the Semantic Web: Facts from biomedical data resources
Provedor de dados: 17
Autores: Dietrich Rebholz; Samuel Croset; Christoph Grabmueller.
Scientific literature is the primary resource for relevant and innovative information. The integration of the literature with other data resources in the biomedical research community generates overhead that can be avoided through the used of Semantic Web Technology generating openly accessible data. Projects such as SESL and CALBC have producted significant amount of data that that are ready for exploitation.&amp;#xd;&amp;#xa;The tutorial will teach different approaches on how to integrate the scientific literature with the content from biomedical databases, and will discuss the inferences that can be achieved. Furthermore, the tutorial will point to the resources that are ready for use and enable integration of the literature at your discretion. A good...
Tipo: Presentation
Palavras-chave: Biotechnology; Immunology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7011/version/1

Biological resource catalog: NIF and NeuroLex
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;NIF has developed a &amp;#x201c;resource...
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6238/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondr&amp;#xe9;-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; Richard H. Scheuermann; Q. Alison Yao; Martin S. Zand; Christopher J. Mungall.
The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed issues of both the content and structure of the CL.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were made for restructuring these cell type terms as cross-products with logical definitions based on relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The improvements to the CL in this area represent a paradigm for the future revision of the whole of the CL.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3543/version/2

SABIO-RK: Access to Biochemical Reaction Kinetics Data
Provedor de dados: 17
Autores: Martin Golebiewski.
SABIO-RK (http://sabio.h-its.org/) is a curated database for biochemical reaction kinetics data drawn from different sources: from literature or direct submission by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. New RESTful web services, as well as a new browser...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6506/version/1

Modularization for the Cell Ontology
Provedor de dados: 17
Autores: Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl.
One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6685/version/1

Wellcome Trust Policy on Data Management and Sharing
Provedor de dados: 17
Autores: David Carr.
The Wellcome Trust&amp;#x27;s policy statement on data management and sharing, which was originally published in January 2007 and revised in August 2010.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6007/version/1

Some Concepts of Graph Theory
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present some preliminary concepts of graph theory with interesting and easy examples.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7120/version/1

Evaluation of the cutaneous microbiome in psoriasis
Provedor de dados: 17
Autores: Martin  J. Blaser; Barbara Methe; Bruce  Strober; Guillermo I. Perez Perez; Stuart Brown; Alexander  Alekseyenko.
Psoriasis, a highly prevalent disease of humans of unknown cause, is a chronic inflammatory disorder primarily involving skin, with distinctive clinical characteristics. With the newly developed tools that facilitate microbiome research, it now is possible to assess whether the cutaneous microbiome plays a role in the pathogenesis of this disorder. Preliminary data from our studies suggest that the cutaneous microbiome in psoriasis is complex and possibly different from normal. To deal with this complexity, we propose to examine the cutaneous microbiome in relation to psoriasis with explorations at several taxonomic and informatic levels. Our overall objective is to examine how changes in the normal cutaneous microbiome contributes to the pathogenesis of...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5276/version/1

Near Infrared Reflectance Spectroscopy (NIRS) Determination of Isoflavone Contents for Selected Soybean Accessions
Provedor de dados: 17
Autores: I. C. Baianu; Jun  Guo; Tiefeng  You; Randall   L. Nelson.
Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. The rapid and economical determination of soybean isoflavone concentrations is essential for the investigation and development of soybean health foods as well as the selection of soybean seeds with optimal isoflavone levels for such foods. Fourier transforms near infrared reflectance spectroscopy (FT-NIRS) calibrations were developed for the rapid and cost-effective analysis of isoflavones in soybean seeds. FT-NIRS measurements were carried out in quadruplicate for 50 soybean lines selected from the USDA Soybean Germplasm Collection. The selected soybean seeds provided a wide range of isoflavone concentrations (from 0.3 to 6.0 mg/g) that is...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7048/version/1

SBRML- A Markup Language for Encoding Systems Biology Results
Provedor de dados: 17
Autores: Joseph  O. Dada.
Background:&amp;#xd;&amp;#xa;The wide acceptance of Systems Biology Markup Language (SBML) as standard format for models of biochemical systems makes it possible to build, share, evaluate and develop biochemical models cooperatively. However, there is currently no standard format for encoding the results of computational analyses of systems biology models. To address this issue, we present here the Systems Biology Results Markup Language (SBRML), an XML-based format for representing systems biology results.  SBRML provides a means of representing computational simulation results as well as encoding experimental data in the context of a particular model.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods &amp;#x26; Results:&amp;#xd;&amp;#xa;SBRML is based on XML...
Tipo: Poster
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6351/version/1

Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)
Provedor de dados: 17
Autores: Nicolas Le Novere; Emek Demir; Huaiyu Mi; Stuart Moodie; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5902/version/1

Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: 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 &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5731/version/1

Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era
Provedor de dados: 17
Autores: Andrea Califano; Atul Butte; Stephen Friend; Trey Ideker; Eric E. Schadt.
After completion of a number of large scale Genome-Wide Association Studies (GWAS), there is still a significant amount of trait and disease variance that cannot be explained by existing genetic variability. This review introduces new, Integrative Network-based Association Study (INAS) approaches that aim to minimize the impact from multiple hypothesis testing statistics, thus allowing the identification of rare variants/alterations and epistatic interactions. In particular we discuss methods that rely on the de novo computational, experimental, and integrative dissection of context specific molecular interaction networks (or interactomes, for short). We provide several examples of how these approaches may be used to tackle discovery of genetic variants...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5732/version/1

Quantization makes relativity compatible with superluminal phenomena
Provedor de dados: 17
Autores: Qi-Ren Zhang.
News shocked the physicist society that neutrinos may move faster than light. Most physicists affirm that this is impossible, according to the well-established relativity. Some try to find a new theory other than relativity to explain the phenomena. In the following we show it may be explained within relativity, if the quantum theory is also taken into account.
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6887/version/1

Double burden of malnutrition among urban Bengalee adolescent boys in Midnapore, West Bengal, India
Provedor de dados: 17
Autores: S Bisai; R Khongsdier; K Bose; D Mahalanabis.
Malnutrition is an important public health problem worldwide. Therefore a study was undertaken to assess the prevalence of adolescent thinness, overweight and obesity in Midnapore town, West Bengal, India. A total of 974 adolescent boys aged 10-18 years were selected following multistage cluster sampling method from three higher secondary schools. Data was collected using pretested questionnaire following standard technique. Presence of thinness was evaluated using the cut-off values of international survey as suggested by Cole et al (2007). While overweight and obesity was determine by using international cut-off values develop by Cole et al (2000) based on international surveys as recommended by IOTF.   Overall the prevalence of thinness, overweight and...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7106/version/1

Skin Microbiome in Disease States: Atopic Dermatitis and Immunodeficiency
Provedor de dados: 17
Autores: Julia Segre; Heidi Kong.
The Human Microbiome Project seeks to explore the diversity of microbiota that resides in and on the human body, including the skin, in health and disease. The NIH Intramural Skin Microbiome Consortium (NISMC) is a trans-disciplinary group of experts engaged in the practice of genomics, bioinformatics, large-scale DNA sequencing, dermatology, immunology, allergy, infectious disease, and clinical microbiology. Atopic dermatitis (AD, &amp;#x201c;eczema&amp;#x201d;) is a chronic relapsing skin disorder that affects ~15% of U.S. children and is associated with $1 billion of medical costs annually. AD is characterized by dry, itchy skin, infiltrated with immune cells. Colonization by _Staphylococcus aureus_ (_S. aureus_) is ten-fold more common in AD  patients...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5019/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/1

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Provedor de dados: 17
Autores: Mark Wilkinson; Benjamin Vandervalk; Luke McCarthy.
Background.  &amp;#xd;&amp;#xa;The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration.  There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics  community.  Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Description. &amp;#xd;&amp;#xa;SADI &amp;#x2013; Semantic Automated Discovery and Integration &amp;#x2013; is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6550/version/1

Biomedical Resource Ontology
Provedor de dados: 17
Autores: Trish  Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6354/version/1

SBML Editor&amp;#x2019;s Report: Principles for Package Development
Provedor de dados: 17
Autores: Lucian Smith.
In the last six months, the SBML Editors have developed several principles to guide the development of SBML Level 3 packages.  An update on what those principles are, and some controversies that have arisen as a result.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6403/version/1

Kinetic Simulation Algorithm Ontology
Provedor de dados: 17
Autores: Anna Zhukova; Dagmar Waltemath; Nick Juty; Camille Laibe; Nicolas Le Nov&amp;#xe8;re.
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

The Five Stars of Online Journal Articles  &amp;#x2013; an article evaluation framework
Provedor de dados: 17
Autores: David Shotton.
I propose five factors &amp;#x2013; peer review, open access, enriched content, available datasets and machine-readable metadata &amp;#x2013; as the Five Stars of Online Journal Articles, a constellation of five independent criteria within a multi-dimensional publishing universe against which online journal articles can be evaluated, to see how well they match up to current visions for research communications. Achievement along each of these publishing axes can vary, analogous to the different stars within the constellation shining with varying luminosities. I suggest a five-point scale for each by which a journal article can be evaluated, and a diagrammatic representation for such evaluations.  While the criteria adopted for these scales are somewhat...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6542/version/1

Incorporating Community Annotation Interfaces into the CIPRO2.5 Database with Comprehensible Sketches to Support Quick Annotations of Proteome Data.
Provedor de dados: 17
Autores: Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Toshinori Endo.
User annotation or comment interfaces are now widely used in several web sites such as journals, news, weblogs and Wikipedia. However, there are only a few biological databases with annotation interfaces. The _Ciona_ _intestinalis_ protein database (CIPRO) was created in order to provide integrated proteome data especially for experimental biologists. The current database contains 89,673 unique sequences covering all the known and predicted gene models. Typical tasks include which gene models are reliable and which function is plausible. The human-curated annotation is most important for the meaningful database.&amp;#xd;&amp;#xa;Here we incorporate three new functions into the CIPRO2.5 database (http://cipro.ibio.jp/2.5/), providing enriched resources for...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5064/version/1

Management and provision of computational models
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

The Vaginal Microbiome: Disease, Genetics and the Environment
Provedor de dados: 17
Autores: Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James  P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael  D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico A. Puma; Mark A. Reimers; Maria C. Rivera; Seth B. Roberts; Myrna G. Serrano; Nihar Sheth; Judy L. Silberg; Logan Voegtly; Elizabeth C. Prom-Wormley; Bin Xie; Timothy  P. York; Cynthia N. Cornelissen; Jerome F. Strauss III; Lindon J. Eaves; Gregory A. Buck.
The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5150/version/2

LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Nov&amp;#xe8;re; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Vill&amp;#xe9;ger.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/4967/version/2

jlibSEDML - a Java library for working with SED-ML
Provedor de dados: 17
Autores: Richard Adams; Ion Moraru; Anuradha Lakshminaryana.
jlibSEDML is an open-source  Java library to support the emerging SED-ML standard to record the operations needed to run simulations and other operations on biochemical models. It is compatible with level 1 version 1 of the specification and is available from http://sourceforge.net/projects/jlibsedml
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4965/version/1

Identifiers.org and MIRIAM Registry: perennial identifiers for crossreferencing purposes
Provedor de dados: 17
Autores: 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

JSBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Andreas Dr&amp;#xe4;ger.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML&amp;#x27;s clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use&amp;#xd;&amp;#xa;library.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4986/version/1

Novel developments in SBGN-ED and applications
Provedor de dados: 17
Autores: Tobias Czauderna; Eva Grafahrend-Belau; Astrid Junker; Anja Hartmann; Matthias Klapperst&amp;#xfc;ck; Falk Schreiber.
Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.&amp;#xd;&amp;#xa;We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6415/version/1

General updates about SBML and SBML Team activities
Provedor de dados: 17
Autores: Michael Hucka.
In this presentation, I summarize very briefly some recent updates to SBML.org, SBML development, and software from the SBML Team.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6345/version/1

The Human Virome in Children and its Relationship to Febrile Illness
Provedor de dados: 17
Autores: Gregory A. Storch; George M. Weinstock; Erica  J. Sodergren; Kristine M. Wylie; Max Q. Arens; Richard S. Buller; David M. Jaffe; Jared T. Muenzer.
This study investigates the relationship of viruses to febrile illness in children.  Subjects are normal children 2-36 months of age with fever along with normal children of the same age without fever, plus immunocompromised children with fever along with immunocompromised children without fever.  Specimens obtained include blood, nasopharyngeal secretions, and feces.  Specimens are analyzed using a panel of virus-specific PCR assays and also by high throughput sequencing using 454 and Illumina platforms.
Tipo: Marker Paper / Data Plan
Palavras-chave: Biotechnology; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5319/version/1

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3
Provedor de dados: 17
Autores: 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.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;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

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Provedor de dados: 17
Autores: Jonathan M. J. Derry; Lara M. Mangravite; Christine Suver; Matt Furia; David  Henderson; Xavier  Schildwachter; Jonathan Izant; Solveig K. Sieberts; Michael R. Kellen; Stephen H. Friend.
The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5883/version/1

CellML + [CMISS | OpenCMISS]
Provedor de dados: 17
Autores: David P. Nickerson.
A brief introduction and comparison to the usage of CellML models in CMISS and OpenCMISS.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5896/version/1

FieldML &amp;#x2013; a meta-language for field interchange
Provedor de dados: 17
Autores: Richard Christie; Poul M. F. Nielsen; Chris P. Bradley; Caton Little; Randall Britten; Peter J. Hunter.
FieldML is being developed as an XML standard for communicating computational field descriptions and data. Important principles in its design include building models from as few and as fundamental a set of concepts as necessary, supporting maximum reuse, and allowing the functional derivation of fields to be of unlimited complexity.&amp;#xd;&amp;#xa;This talk introduces concepts from the FieldML data model (at version 0.3), and demonstrates how they combine to describe rich field representations.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5901/version/1

Rice Genes in Oryzabase
Provedor de dados: 17
Autores: Yukiko Yamazaki; Rie Tsuchiya; Yuka Takahashi; Takao Asanuma; Yo  Shidahara; Shingo Sakaniwa.
In addition to maintaining a rice gene list, Oryzabase, a database of rice science, has also been hosting a website to submit newly identified genes. The current rice gene dictionary is based on a traditional rice trait gene dictionary and extended through time with new genes which are manually retrieved from journal articles. Currently over 4000 genes are listed. However it is still insufficient in both quantity and quality. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;   Recently we started to apply automated extraction before manual annotation to enhance the efficiency of gene extraction. To improve the quality of information, we started collecting relevant DNA accessions and LOCUS-ID. In Oryzabase, we try to employ the help of users to overcome this information...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5069/version/1

Double burden of malnutrition among urban Bengalee adolescent boys in Midnapore, West Bengal, India
Provedor de dados: 17
Autores: S Bisai; R Khongsdier; K Bose; D Mahalanabis.
Malnutrition is an important public health problem worldwide. Therefore a study was undertaken to assess the prevalence of adolescent thinness, overweight and obesity in Midnapore town, West Bengal, India. A total of 974 adolescent boys aged 10-18 years were selected following multistage cluster sampling method from three higher secondary schools. Data was collected using pretested questionnaire following standard technique. Presence of thinness was evaluated using the cut-off values of international survey as suggested by Cole et al (2007). While overweight and obesity was determine by using international cut-off values develop by Cole et al (2000) based on international surveys as recommended by IOTF.   Overall the prevalence of thinness, overweight and...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7106/version/2

Biopax and Semantics
Provedor de dados: 17
Autores: Ismael Navas-Delgado; Maria Jes&amp;#xfa;s Garc&amp;#xed;a-Godoy; Maria del Mar Rold&amp;#xe1;n-Garc&amp;#xed;a; Jos&amp;#xe9; F. Aldana-Montes.
Biopax community is producing sets of data in RDF files, but most of them are not available through query interfaces. The publication of SPARQL endpoints is feasible with current sets of data, but the use of reasoning in these interfaces is unfeasible in many cases. The use of large scale reasoners is a need to take advantage of these data sets.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6320/version/1

JSBML:  a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Marine Dumousseau; Andreas Dr&amp;#xe4;ger; Clemens Wrzodek; Alexander D&amp;#xf6;rr; Sarah M. Keating; Akiya Jouraku; Nicolas Le Nov&amp;#xe8;re; Andreas Zell; Michael Hucka.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to its clearly defined specifications and the availability of libSBML, a portable, robust, and easy-to-use library.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API).  Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6718/version/1

ChEBI &amp;#x2013; an Open-access Chemistry Resource for the Life Sciences:&amp;#xb;Facilities for On-line Submission and Curation
Provedor de dados: 17
Autores: Marcus Ennis; Nico Adams; Adriano Dekker; Paula de Matos; Janna Hastings; Kenneth Haug; Duncan Hull; Zara Josephs; Gareth Owen; Steve Turner; Christoph Steinbeck.
ChEBI (Chemical Entities of Biological Interest) is a database of &amp;#x2018;small&amp;#x2019; molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5089/version/1

Data sharing: What about epidemiological cohorts?
Provedor de dados: 17
Autores: Marcel Goldberg; Marie Zins.
General-purpose population-based cohorts can be powerful scientific platforms. The Gazel Cohort Study, a French cohort of 20,000 adults followed-up since more than 20 years, was designed as an open epidemiologic laboratory, hosting more than 40 nested research projects from French and international teams.&amp;#xd;&amp;#xa;Formal rules were elaborated to define the way that the Gazel database can be accessed.&amp;#xd;&amp;#xa;One of the main problems faced by the Gazel team members is scientific recognition of their work, as the large majority of the publications come from external research groups.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5575/version/1

The Data Sharing Challenge. Learning Community From Consortia
Provedor de dados: 17
Autores: Winston Hide; Gabriel Altshuler; Oliver Hofmann; Kimberly Begley.
Today&amp;#x2019;s data generation and analysis environment is changing rapidly as the lure of technologies provide new opportunities to laboratory scientists. From physicians seeking rapid translation to the bedside, to environmentalists seeking new paradigms to understand the biome - large scale data generation is everywhere. How do we overcome the challenges of curation, management, interpretation and sharing of these data in the new multidisciplinary environment? One key approach is to leverage the expertise inherent in existing systems - bringing together tools and paradigms that work in subfields, and making them work together for the consortium. We will discuss the stem cell discovery engine. The approach brings together leading experts in stem cell...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5090/version/1

BioSharing - standards, policies and communication in bioscience
Provedor de dados: 17
Autores: 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 exist in both the regulatory arena and commercial science.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Proliferation of standards is a positive sign of stakeholders&amp;#x2019; 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...&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioSharing catalogue (www.biosharing.org)...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6153/version/1

Metagenomic study of the human skin microbiome associated with acne
Provedor de dados: 17
Autores: Huiying Li.
The human microbiota contributes to our normal postnatal development and plays a significant role in defining our physiology. To understand the role of microbiota in human health and disease, we study the skin microbiome in pilosebaceous units (hair follicles) and its association with acne.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Acne is one of the most common skin diseases. Although its etiology still needs to be defined, a bacterial factor has been suggested in the development of the disease. In fact, antibiotic therapy targeting _Propionibacterium acnes_ has been a mainstay treatment for more than 30 years.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our preliminary study shows that the microcomedone, a specialized skin compartment where acne arises, has a tractable...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5305/version/1

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu Mi; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/3721/version/4

1st INCF Workshop on NeuroImaging Database Integration
Provedor de dados: 17
Autores: 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

Open Standards and Resources in Systems Biology: collaborative scale-up toward virtual life
Provedor de dados: 17
Autores: Nicolas Le Novere.
The practise of Systems Biology relies on interfaces. Interfaces&amp;#xd;&amp;#xa;between the entities we study: the paradigm moved from a physical&amp;#xd;&amp;#xa;object centric view toward a relationship-centric one; interfaces&amp;#xd;&amp;#xa;between tools: From the retrieval of the primary data to the fine&amp;#xd;&amp;#xa;analysis of a model&amp;#x27;s behaviour, one uses many tools, more or less&amp;#xd;&amp;#xa;well connected; interfaces between individuals: To build any&amp;#xd;&amp;#xa;non-trivial mechanistic model requires to merge existing work and&amp;#xd;&amp;#xa;gather external expertise.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;If we want these interfaces to be generic enough to allow for anybody&amp;#xd;&amp;#xa;to leverage on existing...
Tipo: Presentation
Palavras-chave: Biotechnology; Data Standards.
Ano: 2006
URL: http://precedings.nature.com/documents/10/version/1

Omics Data Sharing - BioSharing: on Data Policies&amp;#x2019;s Plans and Reporting Standards
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Several data preservation, management and sharing policies have emerged in response to increased funding for high-throughput approaches in major genomics and functional genomics bioscience domain; and nowadays, several funding agencies also require inclusion of data-sharing plans in grant applications. But despite some commonalities, the policies are heterogeneous by nature, given the different types of communities served and the data types they generate. In parallel, an escalating number of community-driven standardization efforts (including biocurators, database developers and experimentalists, vendors etc), operate to develop minimal requirements checklists, ontologies, and file-formats to support the harmonization of the reporting process, so that...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5049/version/1

Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Provedor de dados: 17
Autores: Samiran Bisai; Kaushik  Bose.
This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa.  The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars.  Height and weight were measured following standard techniques.  The body mass index (BMI) was computed following standard equation.  Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI.  We followed the World Health Organization&amp;#x27;s classification (1995) of the public health problem of low BMI, based on adult populations worldwide.  Our results show that, in general, among the tribes...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7068/version/1

NCBO Overview and Biositemaps
Provedor de dados: 17
Autores: Patricia L. Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6355/version/1

1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy
Provedor de dados: 17
Autores: 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

The National Vegetation Classification Standard: Implementation and outreach for the state of Oklahoma
Provedor de dados: 17
Autores: Todd D. Fagin; Bruce W. Hoagland; David Lowther.
Efficient stewardship of the nation&amp;#x2019;s biological resources requires a systematic inventory and classification of the systems which support these resources.  However, until recently, a single classification system utilized across jurisdictional boundaries and throughout multiple collecting agencies was non-existent. Rather, conservation priorities were focused primarily at the local and regional scales, with inventory and mapping standards varying from one area to the next. Inconsistent standards of inventories and classifications compounded the difficulties inherent in management of biological resources, namely the ability to present multi-scale, synoptic views of vegetation resources.  In order to address these problems, the Federal Geographic...
Tipo: Presentation
Palavras-chave: Ecology; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3621/version/1

Best practices for building interoperable systems for translational research
Provedor de dados: 17
Autores: 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 &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5197/version/1

SBML Level 3 Hierarchical Model Composition
Provedor de dados: 17
Autores: Lucian P. Smith; Michael Hucka.
A new proposal for incorporating modularity (or &amp;#x27;model composition&amp;#x27;) into SBML Level 3.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5133/version/1

BBSRC Data Sharing Policy
Provedor de dados: 17
Autores: 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 &amp; 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

Bio-resources for sharing: which communities and what specific needs
Provedor de dados: 17
Autores: Andres Metspalu.
Biobanks are an important source to obtain samples and data for research purposes for a wide array of communities. In fact, sharing of bio-resources and data is an integral part of a biobank&amp;#x27;s role. For an effective partnership a list of requirements or needs have to be met, assuring quality of the resources shared as well as quality of the collaboration in general. Tracking and documenting bio-resource sharing and collaborations of a biobank can be seen as one indicator of the &amp;#x22;impact&amp;#x22; a biobank has to the field. As an example, the practice of the Estonian Genome Center of the University of Tartu is presented.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5659/version/1

Structural and Dynamic Studies of Amino Acids, Proteins and Nucleic Acids By Chemical-Hyperspectral Imaging, FT-IR/NIR, Vibro-Rotational Spectroscopy, Plasma, Microwave and Neutron Spectroscopy
Provedor de dados: 17
Autores: I. C. Baianu.
A detailed review of structural and dynamic studies of amino acids, proteins and nucleic acids by spectroscopic techniques: microwaves,  near infrared, UV, X-rays and neutrons, including also EXAFS, chemical-hyperspectral imaging and fluorescence correlation spectroscopy and FLIM, FRAP imaging with references, instrumentation diagrams and  application examples for several related areas.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7079/version/1

Functional annotation of bacterial sugars
Provedor de dados: 17
Autores: Frederique Lisacek.
Glyco-bioinformatics means different things to different people. It ranges, for example, from the mining of the genome for glycosylation pathway enzymes, through to analysis of microarray expression of glycosyltransferases, to glycoprotein identification data, to the development of tools that facilitate the interpretation of mass spectra and to the construction of structural glycan databases. Lastly, these data need to be mined so that the function of the glycan structures attached to the range of glycoconjugates in nature can be determined. The quality of the data in these databases needs to be maintained for this work to be meaningful.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For easier analysis, glycan structures are often characterised independent of the...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5107/version/1

Standards and infrastructure for managing experimental metadata
Provedor de dados: 17
Autores: Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar; Chris Taylor; Manon Delahaye; Richard Evans; Susanna-Assunta Sansone.
*See also the &amp;#x22;related presentation&amp;#x22;:http://precedings.nature.com/documents/3145/version/1*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We present an infrastructure that leverages synergistic reporting standards and ontologies^1,2,3,4,5^ to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The infrastructure&amp;#x2019;s components include: a data capture and editing tool (_ISAcreator_); validator (_ISAvalidator_); database (_BioInvestigation Index_); and converter (_ISAconverter_); and a BioConductor analysis package...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3144/version/1