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Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates Nature Precedings
Bjoern Peters; Alan Ruttenberg; Jason Greenbaum; Melanie Courtot; Ryan Brinkman; Patricia Whetzel; Daniel Schober; Susanna Assunta Sansone; Richard Scheuerman; Philippe Rocca-Serra.
The developers of the Ontology of Biomedical Investigations (OBI) primarily use Protégé for editing. However, adding many classes with similar patterns of logical definition is time consuming, error prone, and requires the editor to have some expertise in OWL. Therefore, the process is poorly suited for a large number of domain experts who have limited experience Protégé and ontology development. We have developed a procedure to ease this task and allow such domain experts to add terms to the ontology in a way that both effectively includes complex logical definitions yet requires minimal manual intervention by OBI developers. The procedure is based on editing a Quick Term Template in a spreadsheet format which is...
Tipo: Presentation Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3970/version/1
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Standards and infrastructure for managing experimental metadata Nature Precedings
Susanna-Assunta Sansone; Philippe Rocca-Serra.
*See also "related poster":http://precedings.nature.com/documents/3144/version/1*

Today’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 ‘omics’). 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.

Standards initiatives normally cater to particular domains. However, several synergistic...
Tipo: Presentation Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2009 URL: http://precedings.nature.com/documents/3145/version/1
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BioSharing: Standards, Policies and Communication in Bioscience Nature Precedings
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
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Agenda of the "BioSharing workshop - Bringing catalogues of bio-resource and standards together" Nature Precedings
Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Pascale Gaudet.
This workshop has brought together representatives of groups developing catalogues of bio-resources and its aims were twofold:

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

2. Outline the technical implementations of the bioDBcore checklist (www.biodbcore.org), the proposed uniform system for describing the catalogues of tools and databases, in particular, how to ensure (bi-directional) linking to the BioSharing catalogue....
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6145/version/1
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BioSharing Overview Nature Precedings
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
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Agenda of the “BioSharing workshop - Unifying Bio-Resources Descriptors” Nature Precedings
Susanna-Assunta Sansone; Philippe Rocca-Serra; Pascale Gaudet; Dawn Field.
Organized by members of the BioSharing initiative (www.biosharing.org) and the International Society for Biocuration (ISB, www.biocurator.org), this workshop brought together developers, curators, journal editors and researchers to discuss the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications.

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

Location: ISMB/ECCB,...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6148/version/1
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Standards and infrastructure for managing experimental metadata Nature Precedings
Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar; Chris Taylor; Manon Delahaye; Richard Evans; Susanna-Assunta Sansone.
*See also the "related presentation":http://precedings.nature.com/documents/3145/version/1*

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. 

The infrastructure’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
Registros recuperados: 7
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