Tutorial presentation of NCBO Technology for the EBI Industry Programme meeting, 2013.

1. NCBO Technology
Trish Whetzel
Outreach Coordinator
THE NATIONAL CENTER FOR
BIOMEDICAL ONTOLOGY

2. Outline
• NCBO Overview
• BioPortal and NCBO Web Services
• BioPortal SPARQL Endpoint
• Applications using NCBO Technology

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

4. NCBO Key Activities
• We create and maintain a library of
biomedical ontologies
• We build tools and Web services to
enable the use of ontologies
• We collaborate with scientific
communities that develop and use
ontologies

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

6. www.bioontology.or
g

7. Social Media

8. Outline
• NCBO Overview
• BioPortal and NCBO Web Services
• BioPortal SPARQL Endpoint
• Applications using NCBO Technology

9. bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg

10. BioPortal
• Repository of biomedical ontologies
• Infrastructure is domain independent
• Stores ontologies developed in OWL, Protégé
frames, OBO format, and Rich Release Format
• Access to ontologies via Web interface, Web
services, and SPARQL
• Access control for private ontologies
• Supports subsets/views of ontologies

11. BioPortal Architecture
Ruby on Rails
Tomcat
Spring Framework
Hibernate ORM
Protégé DB RDF Data Store LexEVS
OWL, RDF,
Protégé frames
Restlet
OBO format,
UMLS RRF,
LexGrid XML
Third party
applications
SPARQL
Access

12. Virtual Appliance Installations

13. Virtual Appliance User Locations

14. Outline
• NCBO Overview
• BioPortal and NCBO Web Services
• BioPortal SPARQL Endpoint
• Applications using NCBO Technology

15. 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

16. http://http://rreesstt..bbiioooonnttoollooggyy..oorrgg
Ontology
Services
Ontology
Services
• Search
• Traverse
• Comment
• Download
• Search
• Traverse
• Comment
• Download
Mapping
Services
Mapping
Services
WWididggeettss
• Create
• Upload
• Download
• Tree-view
• Auto-complete
• Graph-view
• Tree-view
• Auto-complete
• Graph-view
AAnnnnoottaattioionn
DDaattaa A Acccceessss
• Create
• Upload
• Download
TTeerrmm r reeccooggnnititioionn
Search “data”
annotated with a
given term
Search “data”
annotated with a
given term
hhttttpp::////bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg

17. Ontology Web Services
Accessing, browsing, searching and traversing ontologies in Your application

18. Ontology Web Services
• Search
– Search by term or term identifier across all ontologies
in BioPortal
– Results are ranked by Web page views
– Parameters to expand or constrict search

20. Ontology Web Services
• Term
– Get details about a term including it’s definition,
synonyms, URI, super- and sub-classes, and other
properties

22. Ontology Web Services
• Hierarchy
– Get parent, children, and sibling terms

24. Notes Web Services
Propose new terms and comment on ontologies

25. Notes Web Service
• Add comments or terms proposals to an
ontology
• Maintained as metadata associated with the
ontology

27. WebProtégé
http://protegewiki.stanford.eedduu//wwiikkii//WWeebbPPrrootteeggee

28. VIEWs
Custom subset of large ontologies

29. Views and Value Sets
• Users can submit their own derivatives of
BioPortal ontologies
– these which become first-class objects in BioPortal and
can be used as all other Web services

30. Views in BioPortal

31. Views and Value Sets
• View Extraction Web service
– Given a root node term, extracts all child terms
• Access directly from Protégé via the BioPortal
Import plugin
http://protegewiki.stanford.edu/wiki/BioPortal_I
mport_Plugin

32. MAPPING Web Services
Using NCBO technology to integrate terminologies and ontologies

33. MMaappppiinnggss
Root
Term-1 Term-2
Term-3 Term-4
Term-5
R
t1 t2
t4
t3
t5 t6 t7
Term-2 t1
Term-5 t5
Ontology A Upload or Download
mapping subsets
Ontology B

34. Mapping Access
• Get a list of mappings for an ontology to all
other ontologies
• Get a list of mappings between two ontologies
• Get a list of mappings for a single term
• Get a list of mappings between two terms

35. widgets
Using NCBO technology on your web pages

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

37. Widgets
Form auto-complete
RSS feed
Jump To

38. Widgets
Tree widget
Visualization

39. Annotator web service
Using Ontologies to Annotate Your Data

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

41. Annotator Workflow

42. Data service
Using Ontologies to Access Public Data

43. Resource Index: The Basic Idea
• The index can be used for
• Search
• Data mining

44. Outline
• NCBO Overview
• BioPortal and NCBO Web Services
• BioPortal SPARQL Endpoint
• Applications using NCBO Technology

45. hhttttpp::////ssppaarrqqll..bbiioooonnttoollooggyy..oorrgg//

46. BioPortal SPARQL Data (beta)
• Ontology Content
• Ontology Metadata
• Ontology Term Mapping Data

47. BioPortal SPARQL Data (beta)
• All ontologies from BioPortal
– Original ontology format transformed into RDF
• OBO and OWL converted via OWL API
• RRF converted via UMLS2RDF custom code
– Latest version only in beta release
• Statistics (as of Dec. 2012)
– 415 ontologies
– 4.2M terms
– 2419 different predicates
– 80M triples

48. BioPortal Ontology Metadata

49. BioPortal Metadata Ontology

50. Globals
• Provides rdfs:subPropertyOf reasoning to enable
querying over multiple ontologies while using the
same predicate
– http://bioportal.bioontology.org/ontologies/globals
• Implemented for:
– Preferred name – skos:prefLabel
– Synonyms – skos:altLabel
– Term definition – skos:definition
– Term author – dc:author

51. Outline
• NCBO Overview
• BioPortal and NCBO Web Services
• BioPortal SPARQL Endpoint
• Applications using NCBO Technology

52. Applications using NCBO Technology

53. Applications using NCBO Technology
• Ontology Development and Visualization
• Data Annotation
• Data Integration

54. http://protegewiki.stanford.edu/wiki/
BioPortal_Import_Plugin

55. hhttttpp::////oollss22oowwll..ssoouurrcceeffoorrggee..nneett//

56. hhttttpp::////wweebbpprrootteeggee//

57. http://www.biotec.tu-dresden.de/research/
schroeder/dog4dag/

58. hhttttpp::////rraaddlleexx..oorrgg//

59. Applications using NCBO Technology
• Ontology Development and Visualization
• Data Annotation
• Data Integration

60. http://www.sysmo-db.
org/rightfield

61. http://isatab.sourceforge.nneett//iissaaccrreeaattoorr..hhttmmll

62. http://wiki.cvrgrid.org/iinnddeexx..pphhpp//EECCGGGGaaddggeett

63. http://rreeddffllyy..ccccrr..bbuuffffaalloo..eedduu//iinnddeexx..pphhpp

64. Applications using NCBO Technology
• Ontology Development and Visualization
• Data Annotation
• Data Integration

65. Annotator
http://en.wikipedia.oorrgg//wwiikkii//PPoorrttaall::GGeennee__WWiikkii

66. KKnnoowwlleeddggee EEgggg
hhttttpp::////wwwwww..kkuunnnnsskkaappsseeggggeett..nnoo//

67. http://ontologicaldiscovery.oorrgg//

68. ODiSSea
hhttttpp::////wwwwww..hhuubb..sscciivveerrssee..ccoomm//

69. Thank you!
• Web service documentation:
http://www.bioontology.org/wiki/index.php/
NCBO_REST_services
• Keep in touch
– Software support:
support@bioontology.org
–Twitter: @bioontology
– Facebook: http://on.fb.me/bioontology
– LinkedIn: http://linkd.in/ncbo-group