The document describes ontology web services created by the National Center for Biomedical Ontology to facilitate the application of ontologies in biomedical science. The services provide access to ontologies and related functions like searching, term details, hierarchies and mappings. Additional services allow the creation of ontology-based annotations using tools like the annotator and ontology recommender. All services are accessible via RESTful web APIs.

1. Ontology Web Services for
Semantic Applications
Trish Whetzel, PhD
Outreach Coordinator

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

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

6. Web Services
Code
User
Interface
Browser
http://bioportal.bioontology.org

7. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

8. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
– RDF
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

9. Ontology Web Services
• Access Ontologies and Views (Value sets or Slims)
– Search – search by term or term identifier across all
ontologies in BioPortal
– Term – get details about a term including it’s URI,
super- and sub-classes, properties
– Hierarchy – get parent or children terms
– Mapping – get mappings between terms
– Notes – get comments/new term proposals added to
the ontology
– RDF – get RDF snippet for term or entire ontology

10. Ontology Web Services
• BioPortal Search Demo
10

11. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
– RDF
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

12. Ontology Web Services
• Widgets
– Jump To – auto-complete function to select term
and Jump To BioPortal to view term details
– Term-selection widget – auto-complete function
and can return term URI, term ID or term name
– Visualize widget – view the ontology structure and
relations
– Tree widget – view the ontology tree
Code for widgets is available on BioPortal

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

14. Ontology Widgets
• BioPortal Widgets
Tree widget
Visualization

15. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
– RDF
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

16. Annotator: The Basic Idea
• Tag textual metadata with ontology terms
16

17. Annotator Workflow

18. Code
Annotator
Web service
UIMA
platform
Excel
User
Interface

19. Annotator Addin

20. Annotator Addin

21. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
– RDF
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
–Ontology
Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

22. Ontology Recommender
Clement Jonquet, Mark A. Musen and Nigam H. Shah
Building a Biomedical Ontology Recommender Web Service
Journal of Biomedical Semantics 2010, 1(Suppl 1):S1

23. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

24. Lexicon Builder
www.bioontology.org/wiki/inde
x.php/Lexicon_Builder

25. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of
annotations
– Resource Index

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. NCBO Resource Index

31. Ontology Web Services
• Access Ontologies and
Views (Value sets or
Slims)
– Search
– Term
– Hierarchy
– Mapping
– Notes
– RDF
• Widgets
– Auto-complete
– Visualization
• Create ontology-based
annotations
– Annotator
– Ontology Recommender
– Lexicon Builder
• Access ontology-based
index of annotations
– Resource Index

32. Tools using NCBO Technology
32
http://www.bioontology.org/technology

33. Thank you!
• Using NCBO Technology in Your Project:
http://www.bioontology.org/wiki/index.php/Using_
NCBO_Technology_In_Your_Project
• Web service documentation:
http://www.bioontology.org/wiki/index.php/NCBO_
REST_services
• Questions:
support@bioontology.org