http://precedings.nature.com/tags/OBO%20Foundry Recently posted documents tagged with 'OBO Foundry' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3938/version/1 Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Page http://precedings.nature.com/documents/3938/version/1 Wed, 04 Nov 2009 16:35:19 UTC The NCBO OBOF to OWL Mapping hdl:10101/npre.2009.3938.1 2009-11-04 Dilvan A. Moreira Nature Precedings 2009-11-04T16:35:19Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3868.1 BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Protégé frames, and RDF. Features include browsing, searching, and visualization of ontologies. Searching of integrated data resources is also possible through ontology-based indexing of biomedical resources with BioPortal ontologies. http://dx.doi.org/10.1038/npre.2009.3868.1 Fri, 16 Oct 2009 11:30:09 UTC BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse doi:10.1038/npre.2009.3868.1 2009-10-16 Patricia L. Whetzel Nature Precedings 2009-10-16T11:30:09Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ 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/3496/version/1 The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries. http://precedings.nature.com/documents/3496/version/1 Wed, 29 Jul 2009 02:04:15 UTC Cross-Product Extensions of the Gene Ontology hdl:10101/npre.2009.3496.1 2009-07-29 Christopher J. Mungall Nature Precedings 2009-07-29T02:04:15Z Manuscript Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3495.1 The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to better define the mereological, spatial and temporal aspects of biological sequence. http://dx.doi.org/10.1038/npre.2009.3495.1 Wed, 29 Jul 2009 02:02:08 UTC Evolution of the Sequence Ontology terms and relationships doi:10.1038/npre.2009.3495.1 2009-07-29 Karen Eilbeck Nature Precedings 2009-07-29T02:02:08Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3169.1 The Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways, complexes, or in disease modeling. This is useful for proteomics studies where isoforms and modified forms must be differentiated and for biological pathway/network representation where the cascade of events often depends on a specific protein modification. The PRO framework is designed to allow the community to curate any protein entities of interest and will provide a stable unique identifier to any protein type. PRO is manually curated starting with content derived from various data sources coupling with scientific literature. Only annotation with experimental evidence is included, and is in the form of relationship to other ontologies (such as Gene Ontology, Sequence Ontology, and PSI-MOD). We have developed a web-based curation editor for PRO community annotation. In the tutorial, we will first give a brief introduction to the ontology and its relevance to the research communities – OBO ontologies, MOD, pathway and other databases, and any resources that need references/links to protein types. We will show the components of the PRO entry report, and how to search the ontology. Then, we will walk through an example where we will teach the basic curation steps: accessing the web editor, entering the protein to be defined with source attribution, and adding functional annotation. We will provide the necessary tools and documentation so that the user will be able to start curating the protein types of interest. PRO URL: http://pir.georgetown.edu/pro/ http://dx.doi.org/10.1038/npre.2009.3169.1 Fri, 24 Apr 2009 16:16:11 UTC Protein Ontology and Community Curation doi:10.1038/npre.2009.3169.1 2009-04-24 Cecilia Arighi Nature Precedings 2009-04-24T16:16:11Z Presentation Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3145.1 See also related posterToday’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the MIBBI project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development1. More than 60 groups participate in the OBO Foundry 2, which coordinates the orthogonal development of ontologies such as OBI for describing experimental (meta)data. And several groups participate in the development of ISA-Tab, a tabular framework for presenting experimental metadata3 (analogous to FuGE, a generic data model to underpin various XML file formats4).We have developed an infrastructure that leverages the aforementioned synergistic reporting standards to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies. View the public instance of our ISA-based infrastructure, running at EBI, and/or download the components for your local use.References1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. http://www.obofoundry.org3. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. http://isatab.sf.net4. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. http://fuge.sf.net http://dx.doi.org/10.1038/npre.2009.3145.1 Wed, 22 Apr 2009 21:18:50 UTC Standards and infrastructure for managing experimental metadata doi:10.1038/npre.2009.3145.1 2009-04-23 Susanna-Assunta Sansone Nature Precedings 2009-04-22T21:18:50Z Presentation Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3144.1 See also the related presentationWe present an infrastructure that leverages synergistic reporting standards and ontologies1,2,3,4,5 to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies. The infrastructure’s components include: a data capture and editing tool (ISAcreator); validator (ISAvalidator); database (BioInvestigation Index); and converter (ISAconverter); and a BioConductor analysis package (R-ISApackage). The components are designed for local installation, and can work independently, or as unified system.View the public instance running at EBI and/or download the components for your local use.References1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. http://www.obofoundry.org3. Ontology for Biomedical Investigations (OBI) http://obi-ontology.org 4. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. http://isatab.sf.net5. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. http://fuge.sf.net http://dx.doi.org/10.1038/npre.2009.3144.1 Wed, 22 Apr 2009 21:18:37 UTC Standards and infrastructure for managing experimental metadata doi:10.1038/npre.2009.3144.1 2009-04-23 Susanna-Assunta Sansone Nature Precedings 2009-04-22T21:18:37Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3128.1 We present a tool that automatically detects ontological terms in free text. Once candidate terms have been identified the results are displayed either overlaid on the original text or in a list organised by the ontology and frequency. The user can interactively accept or reject each match, or try to find a more appropriate match by exploring the network of ontology concepts themselves. In typical ontological resources, the parent(s) of a term represent broader concepts whilst the children of a term represent more specific concepts. In this way, the suggested match can used as a starting point for the user to find a more suitable term. The ontology browser interface incorporates a graphical visualisation which uses Flash to present an interactive view of the ontology.The Terminizer services offers the full set of ontologies are obtained from the OBO Foundry, a collection of over 40 biological ontologies in a common format. Any ontology available in the standard OBO format can easily be added to the database. In addition to the interactive mode, the software is also available as a Web service. Both the term detection service and the interactive presentation layer can be incorporated within other Web sites or programs. http://dx.doi.org/10.1038/npre.2009.3128.1 Wed, 22 Apr 2009 21:15:03 UTC Terminizer – Assisting Mark-Up of Text Using Ontological Terms doi:10.1038/npre.2009.3128.1 2009-04-22 David Hancock Nature Precedings 2009-04-22T21:15:03Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/