NCBO Web Services: Powering Semantically Aware Applications
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The National Center for Biomedical Ontology provides web services and tools to enable the application of ontologies in biomedical science and clinical care. It maintains a library of biomedical ontologies and builds tools for ontology development, data annotation, and data integration. Key web services include services for ontology search, traversal, and download, as well as annotation and mapping services.
NCBO Web Services: Powering Semantically Aware Applications
- 1. NCBO Web Services: Powering Semantically Aware Applications Trish Whetzel Outreach Coordinator THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY
- 2. National Center for Biomedical Ontology • Mission – To create software for the application of ontologies in biomedical science and clinical care • NCBO Partners – Stanford University - Dr. Mark A. Musen – Mayo Clinic - Dr. Christopher G. Chute – University of Buffalo - Dr. Barry Smith – University of Victoria - Dr. Margaret-Anne Storey
- 3. NCBO Key Activities • We create and maintain a library of biomedical ontologies • We build tools and Web services to enable the use of ontologies • We collaborate with scientific communities that develop and use ontologies
- 4. National Centers for Biomedical Computing (http://www.ncbcs.org)
- 6. Outline • NCBO Web services Overview • Ontology Development and Visualization • Data Annotation • Data Integration
- 7. http://rest.bioontology.org Ontology Services • Search • Traverse • Comment • Download Mapping Services Widgets • Tree-view • Auto-complete • Graph-view Annotation Data Access • Create • Upload • Download Term recognition Search “data” annotated with a given term http://bioportal.bioontology.org
- 8. Outline • NCBO Web services • Ontology Development and Visualization • Data Annotation • Data Integration
- 14. Outline • NCBO Web services • Ontology Development and Visualization • Data Annotation • Data Integration
- 19. Outline • NCBO Web services • Ontology Development and Visualization • Data Annotation • Data Integration
- 24. Thank you! • Web service documentation: http://www.bioontology.org/wiki/index.php/ NCBO_REST_services • Keep in touch – Software support: support@bioontology.org – Twitter: @bioontology – Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group
Editor's Notes
- #10: BioPortal Import Plugin
- #11: designed to aid ontology developers during the knowledge elicitation stage and allows ontology developers to search for terms from a repository of ontologies and compare similar classes, properties, and instances. The plugin was developed as part of the Open architecture for Accessible Services Integration and Standardization project, which facilitates interoperability across service providers, mobile devices (wearable devices, phones, palm, etc.) smart home technology, and medical care providers for elderly and disabled population ------- Improve the quality of life for the elderly Utilizes key technologies in order to provide holistic services to older people to support their physical and psychological independence, stimulate their social or psychological engagement and foster their emotional well being. http://www.oasis-project.eu/ OASIS – Open architecture for Accessible Services Integration and Standardization project It is an Integrated Project with the scope to revolutionise the interoperability, quality, breadth and usability of services for all daily activities of older people. Brings together a consortium of 33 partners across 11 countries.
- #13: Ontology Generation Tool for OBO-Edit and Protégé (NEW) generates ontology terms, definitions, and relationships based on natural language text found in PubMed, the Web, or PDF documents and therefore supports the extension of existing ontologies with terms from resources commonly used in biocuration
- #17: A ‘user-friendly’ standalone Java application that assists the experimentalists to annotate the experimental metadata. Depending on the configuration (set via the ISAconfigurator tool), certain fields prompt a pop-up browser to search and select terms from ontologies that are accessed in real time via the Ontology Lookup Service and BioPortal.
- #18: The CVRG ECG Gadget is a Web 2.0 mashup application built using the GoogleWeb Toolkit and Visualization API. †It integrates the CVRG ECG Storage &Analysis Workflows with ECG Visualization/Annotation using REST services available from the NCBO Bioportal. †The application can be executed using an Apache Tomcat server, allowing the application to be run locally and/or remotely. †The application has been tested in Internet Explorer 7 & 8.Questions and feedback on the tool itself are welcome.
- #21: Structured annotations enable pathway analysis, statistical analyses, cross-species comparisons
- #22: Uses Jump To widget to access information from BioPortal and then search through databases