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	Provedor de dados Nature Precedings (8) Autor Christopher J. Mungall (8) Alexander D. Diehl (3) David Osumi-Sutherland (3) Alan Ruttenberg (2) Alison D. Augustine (2) Amelia Ireland (2) Anastasia Nijnik (2) Anna Maria Masci (2) Bali Pulendran (2) Bjoern Peters (2) Elizabeth S. Gold (2) Judith A. Blake (2) Lindsay G. Cowell (2) Martin S. Zand (2) Penelope A. Morel (2) Q. Alison Yao (2) Richard H. Scheuermann (2) Terrence F. Meehan (2) Timothy A. Gondré-Lewis (2) Carlo Torniai (1) Mais... Palavra-chave Bioinformatics (8) Data Standards (3) Immunology (2) Genetics & Genomics (1) Tipo do documento Manuscript (7) Presentation (1) Ano 2011 (2) 2010 (1) 2009 (5) País United Kingdom (8)		Ordenar por:  Relevância Autor Título Ano Registros recuperados: 8 Primeira ... 1 ... Última Hematopoietic Cell Types: Prototype for a Revised Cell Ontology Nature Precedings Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondré-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 Taking shortcuts with OWL using safe macros Nature Precedings Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland. Accurate representation of complex domains such as biology demands powerful and expressive ontology languages such as OWL. However, the complex nested class expressions required for modeling can be a hindrance to ontology authoring and adoption. These class expressions can appear opaque to domain experts, and even users proficient in OWL can benefit from some kind of syntactic sugar or "short-cut" strategy, especially when authoring large ontologies.

One solution is to have domain experts fill in simple templates (for example, in Excel) and translate the results into more complex axioms, but this has the disadvantage of being disconnected from full ontology authoring and reasoning... Tipo: Manuscript Palavras-chave: Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5292/version/2 The NCBO OBOF to OWL Mapping Nature Precedings Dilvan A. Moreira; Christopher J. Mungall; Nigam H. Shah; Stuart Aitken; John-Day Richter; Timothy Redmond; Mark A. Musen. Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.

OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.

This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL.... Tipo: Manuscript Palavras-chave: Bioinformatics. Ano: 2009 URL: http://precedings.nature.com/documents/3938/version/1 Modularization for the Cell Ontology Nature Precedings 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 Hematopoietic Cell Types: Prototype for a Revised Cell Ontology Nature Precedings Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondré-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 Evolution of the Sequence Ontology terms and relationships Nature Precedings Karen Eilbeck; Christopher J. Mungall. The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to better define the mereological, spatial and temporal aspects of biological sequence. Tipo: Manuscript Palavras-chave: Bioinformatics. Ano: 2009 URL: http://precedings.nature.com/documents/3495/version/1 Cross-Product Extensions of the Gene Ontology Nature Precedings Christopher J. Mungall; Michael Bada; Tanya Z. Berardini; Jennifer Deegan; Amelia Ireland; Midori A. Harris; David P. Hill; Jane Lomax. The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries. Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics. Ano: 2009 URL: http://precedings.nature.com/documents/3496/version/1 Taking shortcuts with OWL using safe macros Nature Precedings Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland. Accurate representation of complex domains such as biology demands
powerful and expressive ontology languages such as OWL. However, the
complex nested class expressions required for modeling can be a
hindrance to ontology authoring and adoption. These class expressions
can appear opaque to domain experts, and even users proficient in OWL
can benefit from some kind of syntactic sugar or "short-cut"
strategy, especially when authoring large ontologies.

One solution is to have domain experts fill in simple templates (for
example, in Excel) and translate the results into more complex... Tipo: Manuscript Palavras-chave: Bioinformatics. Ano: 2010 URL: http://precedings.nature.com/documents/5292/version/1 Registros recuperados: 8 Primeira ... 1 ... Última

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