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VO: Vaccine Ontology Nature Precedings
Yongqun He; Lindsay Cowell; Alexander D. Diehl; Harry Mobley; Bjoern Peters; Alan Ruttenberg; Richard H. Scheuermann; Ryan R. Brinkman; Melanie Courtot; Chris Mungall; Zuoshuang Xiang; Fang Chen; Thomas Todd; Lesley Colby; Howard Rush; Trish Whetzel; Mark A. Musen; Brian D. Athey; Gilbert S. Omenn; Barry Smith.
The collaborative, community-based Vaccine Ontology (VO) was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Currently VO covers a variety of aspects of the vaccine domain, with an emphasis on classification of vaccines and vaccine components, and on host immune response to vaccines. VO can be used for a number of applications, e.g., ontology-based vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI).
Tipo: Manuscript Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3553/version/1
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Development of an Ontology of Microbial Phenotypes (OMP) Nature Precedings
Michelle Giglio; Chris Mungall; Peter Uetz; Lanlan Yin; Johannes Goll; Deborah Siegele; Marcus Chibucos; James Hu.
*Abstract*
Phenotypic data are routinely used to elucidate gene and protein function in most organisms amenable to experimental manipulation. However, although phenotype ontologies exist for many eukaryotic model organisms, no standardized system exists for the capture of phenotypic information in bacteria. We propose to build an Ontology of Microbial Phenotypes and use it to annotate the prokaryotic model organism _Escherichia coli_.

*Introduction*
Phenotypes are the observable characteristics of an organism that result from the combination of a particular genotype and a particular environment, and thus are a basic and fundamental aspect of the biology of all organisms. The awesome power...
Tipo: Poster Palavras-chave: Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3639/version/1
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Uberon: towards a comprehensive multi-species anatomy ontology Nature Precedings
Melissa A. Haendel; Georgios G. Gkoutos; Suzanna E. Lewis; Chris Mungall.
The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies.
Tipo: Poster Palavras-chave: Developmental Biology; Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3592/version/1
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The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data Nature Precedings
Colin Batchelor; Thomas Bittner; Karen Eilbeck; Chris Mungall; Jane Richardson; Rob Knight; Jesse Stombaugh; Craig Zirbel; Eric Westhof; Neocles Leontis.
Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared...
Tipo: Manuscript Palavras-chave: Chemistry; Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3561/version/1
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Querying Drosophila In-Situ Expression Data using SPARQL and D2RQ Nature Precedings
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
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