NCBO Web Services and the Development of Semantic Applications

Venue

• This tutorial will take place in association with the ICBO conference taking place in Graz, Austria. Registration details are provided here

Abstract

The National Center for Biomedical Ontology (NCBO) offers a range of Web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets (data annotation), and to recommend particular terminologies and ontologies that would be appropriate for data-annotation tasks. The BioPortal ontology repository provides a Web-based interface that utilizes the NCBO Web services and allows users to visualize ontologies, to map terms in ontologies to one another, and to add comments on ontologies that can guide ontology developers and offer assistance to ontology users.

Our Web services are used to create a searchable ontology-based index of data records, to create UIMA components for concept recognition, and to create structured data entry interfaces. This tutorial will provide hands-on experience using the NCBO Web services, and will offer participants in-depth understanding of how ontologies and terminologies are used to solve problems in biomedical informatics. The tutorial will demonstrate the use of Web services provided by NCBO to perform tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management.

Schedule

• 1:30 - Semantically Aware applications - who and how people are incorporating ontology web services in their software
• 2:00 - Review of NCBO BioPortal
• 2:30 - Review of NCBO REST Web services
  • Ontology Web services - Search, Traverse, Download
  • View Extraction Web service - Subset ontologies
  • Notes Web service - Propose Terms, Comment
  • Mapping Web services - Create, Upload, Download
  • Widgets - Tree view, Auto-complete, Graph view
• 3:30 - Review of Annotator and Resource Index
  • Annotator - Ontology Term recognition
  • Resource Index - Fetch ontology-indexed data
• 4:00 Break
• 4:30 - Access Ontologies via SPARQL BioPortal SPARQL Endpoint

What You Need to Participate

• Computer with Internet connection
• BioPortal API Key - get your API Key by registering for an account on BioPortal
• Software editor of your choice
• Sample code will be demonstrated in both Java and Perl https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F
• Nice to Have
  • Firefox HTTP Resource Test Plugin
  • Firefox API Key Add-on
  • Some experience with parsing XML
    • Java - Sax/DOM
    • Perl - LibXML

Slides

• Applications Using NCBO Web Services http://www.bioontology.org/wiki/index.php/File:Whetzel_ICBO_WebServiceUsageinApps-Intro.pdf
• NCBO Web service tutorial http://www.bioontology.org/wiki/index.php/File:Whetzel_ICBO-Tutorial_NCBOWebServices.pdf
• BioPortal SPARQL tutorial http://www.bioontology.org/wiki/index.php/File:Whetzel_SPARQL.pdf
• Sample programming tasks http://www.bioontology.org/wiki/index.php/File:ICBO-ProgrammingTasks.pdf

NCBO Sample Code Cookbook

• Visit the Sample Code Cookbook to see ontology-based uses cases and solutions using the NCBO Web services
• Add your own use case!

Keep in Touch

• NCBO Announce mailing list: https://mailman.stanford.edu/mailman/listinfo/bioportal-announce
  • Software release announcements
• Software support: NCBO User Group
  • Submit bug and feature requests
• Follow NCBO on Twitter: http://twitter.com/#!/bioontology
• "Like" NCBO on Facebook: http://on.fb.me/bioontology
• Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

Back to Dissemination/Outreach Main Wiki page

http://www.bioontology.org/wiki/index.php/Dissemination_Wiki