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NCBO Web services: Powering Semantically Aware Applications
The National Center for Biomedical Ontology provides several web services to enable semantically aware applications, including services for ontology development and visualization, data annotation, and data integration. These services include tools for ontology search, traversal, mapping, and comment as well as services for term recognition, annotation, and access to annotated data. Documentation for using these services is available on the NCBO website.
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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. 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
- 3. National Centers forBiomedical Computing (http://www.ncbcs.org)
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- 5. Outline • NCBOWeb services Overview • Ontology Development and Visualization • Data Annotation • Data Integration
- 6. http://http://rreesstt..bbiioooonnttoollooggyy..oorrgg Ontology Services Ontology Services • Search • Traverse • Comment • Download • Search • Traverse • Comment • Download Mapping Services Mapping Services WWididggeettss • Create • Upload • Download • Tree-view • Auto-complete • Graph-view • Tree-view • Auto-complete • Graph-view AAnnnnoottaattioionn DDaattaa A Acccceessss • Create • Upload • Download TTeerrmm r reeccooggnnititioionn Search “data” annotated with a given term Search “data” annotated with a given term hhttttpp::////bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg
- 7. Outline • NCBOWeb services • Ontology Development and Visualization • Data Annotation • Data Integration
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- 23. 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
- #9 BioPortal Import Plugin – enables term re-use by being able to select ontology terms from BioPortal for use in your own ontology project
- #10 The plugin was developed as part of the Open architecture for Accessible Services Integration and Standardization (OASIS) 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. 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. The plugin 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. 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.
- #11 Notes (comments and term proposals) submitted in BioPortal are accessible in Web Protégé
- #12 DOG4DAG - Ontology Generation Tool for OBO-Edit and Protégé 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
- #13 Custom view of RadLex ontology implemented using the NCBO Web services. Therefore, the ontology is stored and managed in BioPortal, but the display is customized by using the Web services to access the content of RadLex and format as the community prefers
- #15 RightField – data annotation with fields limited to selected ontologies
- #16 ISACreator - 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. New – OntoMaton, ISAcreator functionality in GoogleDocs
- #17 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.
- #18 RedFly – database of transcription regulatory elements in Drosophila
- #20 GeneWiki - Structured annotations enable pathway analysis, statistical analyses, cross-species comparisons
- #21 Knowledge Egg - Uses Jump To widget to access information from BioPortal and then search through databases
- #22 GeneWeaver, developed by the Jackson Laboratory, uses the Annotator to identify ontology terms from metadata descriptions and uses these in analysis of gene relationships
- #23 ODiSSea – application within SciVerse Hub that uses the NCBO Annotator to identify ontology terms in SciVerse content and also links these to data records via the NCBO Resource Index