Presentation from the Genomics Standards Consortium meeting, 2011.

1. Ontology Web Services
Trish Whetzel, PhD
Outreach Coordinator
THE NATIONAL CENTER FOR
BIOMEDICAL ONTOLOGY

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
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

9. Ontology View
• A View is a subset of one or more ontologies
– also referred to as a value set or slim
• Anyone can create a View
– does not need to be the ontology “owner”
9

10. View Extraction Web service
• Given a term identifier, extracts all children
• Parameters
– Ontology version identifier
– Term identifier
– Output ontology name
10
http://www.bioontology.org/wiki/in
dex.php/View_Extraction

11. Views in BioPortal
11

12. Views in BioPortal
12

13. Using Views in Your Application
• List all views
– Get list of all views in BioPortal
– Get all versions of a given View
• Views are accessible via all BioPortal web
services
– Get term – get all details about a term
– Search – find terms in a View
– Widgets – form field auto-complete widget
13

14. Ontology Web Services
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

15. BioPortal
• Functionality
– Notes
15

16. 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

17. Ontology Web Services
• BioPortal Search Demo
17

18. Ontology Web Services
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

19. 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

20. Ontology Widgets
• BioPortal Widgets
Term-selection

21. Ontology Widgets
• BioPortal Widgets
RSS feed
Jump To

22. Ontology Widgets
• BioPortal Widgets
Tree widget
Visualization

23. Ontology Web Services
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

24. Annotator: The Basic Idea
• Tag textual metadata with ontology terms
24

25. Annotator Workflow

26. Code
Annotator
Web service
UIMA
platform
Excel
User
Interface

27. Annotator Addin

28. Annotator Addin

29. Ontology Web Services
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

30. 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

31. Ontology Web Services
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

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

33. Ontology Web Services
• List Ontologies
– Get ontology metadata
• Create Views
– View Extraction
• 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

34. Resource Index: Use Case
34

35. Resource Index: Use Case
35

36. Resource Index: Use Case
36

37. Resource Index: The Basic Idea
37

38. Resource Index: Use Case
38

39. Resource Index: Use Case
39

40. Resource Index: Use Case
40

41. NCBO Resource Index

42. 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

43. Tools using NCBO Technology
43
http://www.bioontology.org/technology

44. 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