Presentation for the 15th Genomics Standards Consortium meeting, 2013.

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

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

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

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. www.bioontology.or
g

6. Outline
• NCBO Overview
• BioPortal
• NCBO Web Services
• Applications using NCBO Technology

7. bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg

8. BioPortal
• Repository of biomedical ontologies
• Stores ontologies developed in OWL or OBO
format
• View, browse, and search across ontologies
through the Web interface
• Programmatic access to ontologies via Web
services and SPARQL endpoint
• Access control for private ontologies

9. Outline
• NCBO Overview
• BioPortal
• NCBO Web Services
• Applications using NCBO Technology

10. 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

11. Outline
• NCBO Overview
• BioPortal
• NCBO Web Services
• Applications using NCBO Technology

12. Applications using NCBO Technology

13. These 3 software
components of
use BioPortal Web services
to access, browse ontology
and provide term-tagging
features
http://isatab.sourceforge.nneett//iissaaccrreeaattoorr..hhttmmll

14. http://mmeettaaggeennoommiiccss..aannll..ggoovv//

15. http://ontogrator.oorrgg//cclliinniiccaallttrriiaallss

16. https://submit.ncbi.nlm.nih.gov/biosample/t
emplates/all_attributes/

17. http://biosharing.org/standards/tteerrmmiinnoollooggyy__aarrttiiffaacctt

18. Summary
• NCBO provides access to ontologies via Web
services
• Web services are easy to integrate into
software applications
• Use of common ontologies across projects
better facilitates data integration and analysis

19. 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