http://precedings.nature.com/tags/function Recently posted documents tagged with 'function' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3228/version/1 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. http://precedings.nature.com/documents/3228/version/1 Mon, 11 May 2009 09:03:16 UTC An evolutionary approach to Function hdl:10101/npre.2009.3228.1 2009-05-11 Phillip Lord Nature Precedings 2009-05-11T09:03:16Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2479/version/1 Conceived as follow-up to recent efforts destined to supply .owl ontologies with relational tools of greater complexity, the present article focuses on four main paths, all of them consisting in providing biomedical ontologies with formal means to express (1) deviations from normality, (2) topological connectedness, (3) inherence and (4) causality and function. http://precedings.nature.com/documents/2479/version/1 Thu, 06 Nov 2008 14:56:50 UTC Relation Ontology II hdl:10101/npre.2008.2479.1 2008-11-06 Cristian Cocos Nature Precedings 2008-11-06T14:56:50Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2311/version/1 BackgroundHigh throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures. ResultsWe developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.ConclusionsYeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products. http://precedings.nature.com/documents/2311/version/1 Fri, 19 Sep 2008 02:00:35 UTC Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics hdl:10101/npre.2008.2311.1 2008-09-19 Michel Dumontier Nature Precedings 2008-09-19T02:00:35Z Manuscript Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1941/version/1 Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general structure and use. http://precedings.nature.com/documents/1941/version/1 Tue, 03 Jun 2008 09:33:06 UTC Function, Role, and Disposition in Basic Formal Ontology hdl:10101/npre.2008.1941.1 2008-06-03 Robert Arp Nature Precedings 2008-06-03T09:33:06Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/