1. NCBO Tools and Web Services
Trish Whetzel
Outreach Coordinator

2. Outline
• NCBO Background
• Ontology Web Services
• Ontology Widgets
• NCBO Annotator
• NCBO Resource Index
• Ontology Recommender
• Lexicon Builder

3. National Centers for Biomedical Computing

4. 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

5. RESTful Web Services
• Accessed via HTTP
– http://rest.bioontology.org/bioportal/
• Each unique URL is a representation of some
object
• Operations include GET, POST, PUT, DELETE
• Lightweight, easy to build

6. Web Services
Code
UI
Browser

8. BioPortal
http://bioportal.bioontology.org/

9. Ontology Widgets
• See BioPortal (
http://bioportal.bioontology.org/ontologies/42490#widgets)
– Term selection - autocomplete widget
– Jump To - view term details in BioPortal
– Visualization - view ontology
– RSS feed - track updates to ontology, e.g. upload
of new versions, notes, mappings

10. Ontology Web Services
• Ontology Metadata - get information about an
ontology
• Term - get details about a term
• Search - find term in any ontology
• Hierarchy - traverse ontology hierarchy
• Notes - get contents of notes
• Mappings - get mapped terms
http://www.bioontology.org/wiki/index.php/NCBO_REST_services

11. Applications Using
NCBO Web Services
• Microsoft Word 2007 Add-in for
Ontology Recognition
• BioLit
• ISAcreator
• For full list, see
http://www.bioontology.org/tools

12. Microsoft Word 2007 Add-in
Automated recognition of
ontology terms and database
IDs before publication with
manual curation by author
http://ucsdbiolit.codeplex.com/

13. BioLit
Automated recognition of
ontology terms and database
IDs after publication with
manual curation by author
http://biolit.ucsd.edu

14. ISAcreator editor
http://isatab.sourceforge.net/

15. NCBO Annotator
• Open access, ontology-based Web service that
annotates or “tags” textual metadata
• Annotation is done using ontologies from
BioPortal, which includes OBO Foundry and
Unified Medical Language System ontologies
• Variety of parameters that can be customized

16. Annotator Workflow

17. Access to Annotator
• BioPortal
– User-friendly interface to test Annotator
• Web service (REST)
– Direct programmatic access
• User Guide and Sample Client Code
– http://www.bioontology.org/wiki/index.php/Annotator_Web_service

18. Annotator User Interface

19. Annotator Usage
• Production release
– April 2009
• Data processed
– 66 million calls
– more than 259 gigabytes of data

20. Annotator Users
• Rat Genome Database - example use case
• See
http://www.bioontology.org/wiki/index.php/
NCBO_Annotator_community for additional
use cases from the Annotator user community

21. Rat Genome Database
• Use case
– Are any of these genes associated with my disease or
phenotype?
– Is this candidate gene expressed in my tissue of interest?
• Annotate Gene Expression Omnibus (GEO) records
with the Annotator using
– Mouse Gross Adult anatomy ontology, Rat strain ontology,
Medical Subject Headings (MeSH), NCI Thesaurus
– Pilot test to annotate 30 GEO datasets and associated
sample records

22. Rat Genome Database
• Results
– Rat Strain ontology
• High number of false positives due to short length of many rat
strains (2-3 letters) and similarity to common words and variety of
words used to describe strains that were not included as
synonyms
– Mouse adult gross anatomy
• Low number of false positives
• Annotation of 192 datasets resulted in precision and recall of
84.0% and 94.8%
• Ability to link expression results of a gene (based on Affymetrix
probe set) to anatomical location
– Manual curation of results needed, but much less
burdensome by the initial automated results

23. NCBO Resource Index
• Ontology-based index of publicly available
biomedical resources
• Provides a mechanism to search across
resources by ontology terms

24. Ontology Recommender
• Identify ontology relevant to annotate data

25. Lexicon Builder
http://www.bioontology.org/wiki/index.php/
Lexicon_Builder

26. Acknowledgements
• Annotator Development
– Nigam Shah
– Clement Jonquet
– Fan Meng
– Mark Musen
• Feedback
– Simon Twigger
– Karen Dowell
– Robin Smith

27. References
• BioPortal
– http://bioportal.bioontology.org
• NCBO REST Web services
– http://www.bioontology.org/wiki/index.php/NCBO_REST_
services
• NCBO Annotator Web Service
– http://www.bioontology.org/wiki/index.php/Annotator_
Web_service
• NCBO Resource Index Web Service
– http://www.bioontology.org/wiki/index.php/Resource_In
dex