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| Registros recuperados: 210 | |
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| Jonathan Cooper; Gary Mirams. |
| "Functional curation":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 
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 |
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| 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. 

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 |
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| 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. 
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 |
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| 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
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 |
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| Pascale Gaudet (Pascale.Gaudet@isb-sib.ch); Philippe Rocca-Serra (proccaserra@googlemail.com). |
| Members of the International Society for Biocuration (ISB, biocurator.org) and the BioSharing (biosharing.org) initiative work together to develop and implement BioDBcore (biodbcore.org), a community-defined, uniform system for describing the core attributes of biological databases, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. The BioSharing catalogue offers this “one-stop shop” for those seeking information about the standards and data sharing policies.

This presentation illustrates the rational for BioDBcore(P Gaudet) and the progresses for its implementation (P Rocca-Serra),... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6167/version/1 |
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| Allyson L. Lister; Phillip Lord; Matthew Pocock; Anil Wipat. |
| *Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3286/version/1 |
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| Registros recuperados: 210 | |
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