The National Center for Biomedical Ontology (NCBO) provides several software tools to enable semantically aware applications. These include BioPortal, an online library of biomedical ontologies, Ontology Widgets which allow integration of ontologies into websites, and the Annotator, a web service that semantically tags text with ontology terms. The NCBO also plans to develop a comprehensive index of online biomedical resources.

1. Enabling Semantically Aware
Software Applications
Trish Whetzel, PhD
Outreach Coordinator
THE NATIONAL CENTER FOR
BIOMEDICAL ONTOLOGY

2. Outline
• Overview of NCBO
• NCBO Software
– BioPortal
– Ontology Widgets
– Annotator
– Resource Index
• Future Plans
2

3. 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 Victoria - Dr. Margaret-Anne
Storey
– University of Buffalo - Dr. Barry Smith

4. National Centers for Biomedical Computing
(http://www.ncbcs.org)

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

6. BioPortal
• Library of Ontologies
– NCBO BioPortal includes Biomedical ontology
content, e.g. UMLS terminologies
• Architecture
– Backend includes LexEVS and Protégé
– Web Interface uses Ruby on Rails, Flex, and PHP
• Web services
– REST Web services
6

7. BioPortal
• Functionality
– Search across all ontologies
7

8. BioPortal
• Functionality
– Browse ontology hierarchy
– Details about a concept
8

9. BioPortal
• Functionality
– Visualize the ontology graph
9

10. BioPortal
• Functionality
– Mappings to/from other ontologies
10

11. BioPortal
• Functionality
– Notes
11

12. BioPortal Notes
• Notes
– Provide a mechanism to collect structured
information
– Integration with ontology editing programs
– Alerts – Email and RSS

13. Use Case for BioPortal Notes
• Ontology Enrichment
– Expansion of the ontology based on user need for
terms
• Constraints
– Existing trackers do not collect structured
information
– No programmatic access to tracker
– Lack of integration with ontology editing
programs
13

14. BioPortal Notes

15. Ontology Widgets
• Ontology Widgets
– Code to use in your web site
• Types
– Jump To
– Term auto-completion
– View ontology graph
– Ontology change alerts
• Available for all ontologies in BioPortal
– Click on the Widgets tab
15

16. Ontology Widgets
• BioPortal Widgets
RSS feed
Term-selection
Jump To

17. Ontology Widgets
• BioPortal Widgets
Tree widget
Visualization

18. NCBO Annotator
• Open access, ontology-based Web service that
annotates or “tags” textual metadata
• Annotation is done using ontologies from
BioPortal, including Unified Medical Language
System terminologies
• Variety of parameters that can be customized
18

19. Annotator: The Basic Idea
• Tag textual metadata with ontology terms
19

20. Annotator Workflow

21. Annotator - Parameters
• longestOnly (boolean) - match longest term phrase
– E.g. Purkinje cell versus Purkinje cell and cell
• stopWords (list) - words not to match
• withDefaultStopWords (boolean)
– http://rest.bioontology.org/obs/stopwords
• scored (boolean) - reflects the accuracy of the
annotation
– E.g. Direct match scored higher than synonym

22. Annotator - Parameters
• ontologiesToExpand (list) - ontologies to check for
mappings for expanded annotation
• ontologiesToKeepInResult (list) - ontologies to show
in result
• semanticTypes (list) - refers to UMLS ontologies
– http://rest.bioontology.org/obs/semanticTypes
• levelMax (integer) - hierarchy level to traverse for
expanded annotation
• format - annotation result format
– xml, text, or tabDelimited

23. Semantic Expansion
• is-a transitive closure
– Traverses the ontology parent-child hierarchy creating new
annotations with the parent terms

24. Semantic Expansion
• Mapping expansion
– Creates new annotations based on existing mappings
between ontologies

25. Annotator Web service
Code
UIMA
platform
Excel
User
Interface

26. Resource Index: The Basic Idea
26

27. Resource Index: Use Case
27

28. Resource Index: Use Case
28

29. Resource Index: Use Case
29

30. Future Plans
• Services that allow use of ontologies via an
enhanced version of BioPortal
• Integration of ontology authoring, publishing,
and peer review
• A comprehensive ontology-based index of
online biomedical resources
• Analytic methods to summarize and profile
biomedical data sets

31. References
• BioPortal
– http://bioportal.bioontology.org
• Annotator
– http://www.bioontology.org/wiki/index.php/Annotator_Web_s
ervice
• Resource Index
– http://www.bioontology.org/wiki/index.php/NCBO_Biomedical_
Resources_Index
• Web service documentation:
– http://www.bioontology.org/wiki/index.php/NCBO_REST_servic
es
• Trish Whetzel
– whetzel@stanford.edu