http://precedings.nature.com/tags/software Recently posted documents tagged with 'software' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3547.1 The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. These relationships and the Homolonto software are available at http://bgee.unil.ch/. http://dx.doi.org/10.1038/npre.2009.3547.1 Tue, 04 Aug 2009 13:06:04 UTC Generating Homology Relationships by Alignment of Anatomical Ontologies doi:10.1038/npre.2009.3547.1 2009-08-04 Frederic B. Bastian Nature Precedings 2009-08-04T13:06:04Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3517/version/1 Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new content. The communications and interactions of the participants with each other, directly or through the tool, were tracked and analyzed. Our initial analysis of the degree to which this new tool fulfills the practical requirements of collaborative ontology engineering suggests the approach is promising. We present some observations and recommendations for CP based upon this experience. http://precedings.nature.com/documents/3517/version/1 Wed, 29 Jul 2009 21:49:09 UTC Practical experiences in concurrent, collaborative ontology building using Collaborative Protégé hdl:10101/npre.2009.3517.1 2009-07-29 Daniel Schober Nature Precedings 2009-07-29T21:49:09Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3516.1 Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new content. The communications and interactions of the participants with each other, directly or through the tool, were tracked and analyzed. Our initial analysis of the degree to which this new tool fulfills the practical requirements of collaborative ontology engineering suggests the approach is promising. We present some observations and recommendations for CP based upon this experience. http://dx.doi.org/10.1038/npre.2009.3516.1 Wed, 29 Jul 2009 16:53:47 UTC Concurrent, Collaborative *Ontology Building* with Collaborative Protégé (CP) doi:10.1038/npre.2009.3516.1 2009-07-29 Daniel Schober Nature Precedings 2009-07-29T16:53:47Z Presentation Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3188.1 The boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap between text miners and biologists. Beyond the development of enhanced entity recognisers and the construction of relationship extraction systems, now, more than ever, it is the time for applying available tools to real-world scenarios. Moreover, it is crucial to develop end-user tools that can assist biologists in their research activities. Such tools should be able to emulate biologist conventional curation, recurring to the same knowledge bases and making the same assumptions that biologists usually do, whereas delivering automated capabilities. The search and selection of PubMed articles, the construction of dictionaries from the contents of available Molecular Biology repositories, the implementation of description environments for rule specification, the implementation of dictionary- and rule-based entity recognisers, the development of flexible and extensible relationship extraction systems and the development of easy-to-use manual curation environments are of foremost importance.Our software, named @Note, aims to be a framework and a workbench for BioTM, i.e., it has been conceived for delivering end-user applications, whereas enabling collaboration with other BioTM groups. As a framework, it provides a reusable design for BioTM software systems and a set of pre-assembled software building blocks that programmers can use, extend and customise for their specific needs. As a workbench, it helps developing BioTM applications by integrating Natural Language Processing and Data Mining tools and supporting major Information Retrieval and Information Extraction processes. Moreover, it encompasses a flexible and extensible manual curation environment that enables the interaction with biologists, correcting former annotations and enhancing dictionary contents. We successfully applied @Note in the study of the stringent response on Escherichia coli, an important subject within the analysis of stress responses in bacteria. This joint effort allowed biologists to contribute to the enhancement of our manual curation environment and to identify new functionalities for the existing plug-ins and the specification of new plug-ins. http://dx.doi.org/10.1038/npre.2009.3188.1 Tue, 28 Apr 2009 18:31:15 UTC Bringing Text Miners and Biologists Closer Together doi:10.1038/npre.2009.3188.1 2009-04-28 Anália Lourenço Nature Precedings 2009-04-28T18:31:15Z Presentation Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.670.1 The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is that a virtualized environment doesn’t affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning, using, developing and testing bioinformatics applications. http://dx.doi.org/10.1038/npre.2007.670.1 Mon, 13 Aug 2007 05:14:24 UTC DNALinux Virtual Desktop Edition doi:10.1038/npre.2007.670.1 2007-08-13 Sebastian Bassi Nature Precedings 2007-08-13T05:14:24Z Manuscript Biotechnology Bioinformatics http://creativecommons.org/licenses/by/2.5/