http://precedings.nature.com/users/5c38eefbb62d65c1d79682ad03cdfeed/ Documents posted by Phillip Lord Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3286/version/1 Motivation: The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.Results: We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.Availability: Detailed information including download and mapping of the ontologies as well as integration results is available from http://www.cisban.ac.uk/RBM http://precedings.nature.com/documents/3286/version/1 Fri, 29 May 2009 14:35:07 UTC Annotation of SBML Models Through Rule-Based Semantic Integration hdl:10101/npre.2009.3286.1 2009-05-29 Allyson L. Lister Nature Precedings 2009-05-29T14:35:07Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ 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/3231/version/1 This paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering. http://precedings.nature.com/documents/3231/version/1 Fri, 08 May 2009 09:47:22 UTC Developing ontologies in decentralised settings hdl:10101/npre.2009.3231.1 2009-05-08 Frank Gibson Nature Precedings 2009-05-08T09:47:22Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/