http://precedings.nature.com/users/0b6a37340c59a46cd7dc92623ab45828/ Documents posted by Allyson LIster Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3574/version/1 While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions. http://precedings.nature.com/documents/3574/version/1 Mon, 10 Aug 2009 15:16:25 UTC MIREOT: the Minimum Information to Reference an External Ontology Term hdl:10101/npre.2009.3574.1 2009-08-10 Melanie Courtot Nature Precedings 2009-08-10T15:16:25Z Manuscript Biotechnology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3576.1 While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions. http://dx.doi.org/10.1038/npre.2009.3576.1 Mon, 10 Aug 2009 14:42:27 UTC MIREOT: the Minimum Information to Reference an External Ontology Term doi:10.1038/npre.2009.3576.1 2009-08-10 Mélanie Courtot Nature Precedings 2009-08-10T14:42:27Z Presentation Biotechnology Bioinformatics http://creativecommons.org/licenses/by/3.0/ 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/