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| Chris Freeland. |
| The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic name... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Earth & Environment. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3372/version/1 |
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| Phillip Lord. |
| The distinction between function and role is a vexed and difficult one. While the distinction appears to be useful, in practice it is hard to apply; this can be even worse when applying this distinction to biology. In this paper, I take an evolutionary approach, considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against work performed on the Ontology for Biomedical Investigations (OBI). Finally, I give an axiomatisation and discuss methods for applying these definitions in practice. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3228/version/1 |
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| Geoffrey Frank; William Wheaton; Vesselina Bakalov; Phillip Cooley; Diane Wagener. |
| Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications providing historical evidence about epidemics.
An ontology has been developed for MIDAS to support the collection, documentation, and dissemination of models. It uses relations to link taxonomies (including a subset of the infectious disease ontology) that define the scope of its models and supporting documentation.
The ontology is used to aid in the navigation process that is part of the user interface for identifying which studies and publications are available in the MIDAS repository... |
| Tipo: Presentation |
Palavras-chave: Immunology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3555/version/1 |
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| Thomas Wächter; Ursula G. Sauer; Andreas Doms; Barbara Grune; Michael R. Alvers; Horst Spielmann; Michael Schroeder. |
| EU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta version of Go3R ("www.Go3R.org":http://www.Go3R.org), the first knowledge-based semantic search engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory authorities involved in... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3148/version/1 |
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| Richard H. Scheuermann; Megan Kong; Carl Dahlke; David Karp. |
| The Ontology-Based eXtensible data model (OBX) was developed to serve as a framework for the development of a clinical research database in the Immunology Database and Analysis Portal (ImmPort) system. OBX was designed around the logical structure provided by the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). By using the logical structure provided by these two well-formulated ontologies, we have found that a relatively simple, extensible data model could be developed to represent the relatively complex domain of clinical research. In addition, the common framework provided by the BFO should make it straightforward to utilize OBX database data dictionaries based on reference and application ontologies from the OBO... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3482/version/1 |
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| Zeba Wunderlich; Leonid Mirny. |
| Peptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are members of large protein domain families. Members of these families are often quite similar to each other, but each domain recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein domains. The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family. Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically. Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical origin... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1881/version/1 |
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| Wanderley-Nogueira,Ana C.; Belarmino,Luis C.; Soares-Cavalcanti,Nina da M.; Bezerra-Neto,João P.; Kido,Ederson A.; Pandolfi,Valesca; Abdelnoor,Ricardo V.; Binneck,Eliseu; Carazzole,Marcelo F.; Benko-Iseppon,Ana M.. |
| Plants have the ability to recognize and respond to a multitude of pathogens, resulting in a massive reprogramming of the plant to activate defense responses including Resistance (R) and Pathogenesis-Related (PR) genes. Abiotic stresses can also activate PR genes and enhance pathogen resistance, representing valuable genes for breeding purposes. The present work offers an overview of soybean R and PR genes present in the GENOSOJA (Brazilian Soybean Genome Consortium) platform, regarding their structure, abundance, evolution and role in the plantpathogen metabolic pathway, as compared with Medicago and Arabidopsis. Searches revealed 3,065 R candidates (756 in Soybean, 1,142 in Medicago and 1,167 in Arabidopsis), and PR candidates matching to 1,261 sequences... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Pathogen response; Biotic stress; Bioinformatics; Glycine max; Medicago truncatula. |
| Ano: 2012 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200007 |
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| Hong-Sang Low; Christopher J. O. Baker; Alexander Garcia; Markus R. Wenk. |
| Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids. |
| Tipo: Presentation |
Palavras-chave: Chemistry; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3590/version/2 |
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| Hong Sang Low; Christopher J. O. Baker; Alex Garcia; Markus R. Wenk. |
| Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids. |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3542/version/1 |
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| Hong-Sang Low; Christopher J. O. Baker; Alexander Garcia; Markus R. Wenk. |
| Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids. |
| Tipo: Presentation |
Palavras-chave: Chemistry; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3590/version/1 |
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| Catherine Canevet; Artem Lysenko; Andrea Splendiani; Matthew Pocock; Chris Rawlings. |
| An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a distributed knowledge base which has the potential to advance biomedical research [1]. This potential, however, cannot be realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need for tools that provide data reduction, visualization and interactive analysis capabilities.
Ondex is a data integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated with... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5430/version/1 |
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| Praneetha Amburu; Dibyabhaba Pradhan; Vani Priyadarshini; Munikumar Manne; Umamaheswari Amineni. |
| Human parvovirus B19, a member of the Parvoviridae family, is a pathogen associated with a wide variety of diseases. Most commonly, it causes childhood rash erythema infectiosum, but in some cases more serious symptoms such as persistent arthropathy, critical failures of red cell production causing transient aplastic crisis, this infection in pregnancy causes hydrops fetalis and myocarditis. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of consideration. Functional annotation would provide role of viral proteome in its survival and pathogenic mechanisms. SVMProt functional family annotations of VP2 protein had deciphered its zinc-binding, coat protein, outer membrane, chlorophyll biosynthesis, DNA repair and... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5289/version/1 |
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| Matthew Holford; James P. McCusker; Kei Cheung; Michael Krauthammer. |
| Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancel cell's molecular state and its response to anti-cancer therapy. To study the problem, we have previously focused on data warehousing technologies and statistical data integration. In this paper, we present recent work on extending our analytical capabilities using Semantic Web technology. A key new component presented here is a SPARQL endpoint to our existing data warehouse. This endpoint allows the merging of observed quantitative data with existing data from semantic knowledge sources such as Gene Ontology (GO). We show how such variegated quantitative and functional data can be integrated and... |
| Tipo: Presentation |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5391/version/1 |
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| Andrey Ptitsyn; Jeffrey Gimble. |
| *Background*
It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. 

*Results*
We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/858/version/1 |
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| Eugene B. Postnikov; Alexander Y. Loskutov; Sergey A. Larionov; Evgeny V. Ryadchenko; Roman V. Kiseliov. |
| We propose the original method of the time-scale wavelet analysis of DNA sequence represented as a 2D walk on a complex plane. Namely, we consider the mapping of two irreducible A − T and G − C sequences into a walk trajectory in the plane AGTC (firstly proposed by M. Gates) as a unique complex-valued function. 
 This function is processed with the new algorithm of the continuous wavelet transform with the Morlet wavelet. This method is based on the representation of the transform’s result as a solution of the specific Cauchy problem for the system of PDE. 
 As an example, we applied the described algorithm to a part of the telomer region of the 22 human chromosome and demonstated... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1461/version/1 |
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| Shuye Pu; Karen Ronen; James Vlasblom; Jack Greenblatt; Shoshana J. Wodak. |
| Epistatic or genetic interactions, representing the effects of mutations on the phenotypes caused by other mutations, can be very helpful for uncovering functional relationships between genes. Recently, the Epistasis Miniarray Profile (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. As part of this approach, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles. Here we present an original biclustering algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2182/version/1 |
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| Registros recuperados: 1.312 | |
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