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NCBO Technology 
Trish Whetzel 
Outreach Coordinator 
THE NATIONAL CENTER FOR 
BIOMEDICAL ONTOLOGY
Outline 
• NCBO Overview 
• BioPortal and NCBO Web Services 
• BioPortal SPARQL Endpoint 
• Applications using NCBO Technology
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
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
National Centers for Biomedical Computing 
(http://www.ncbcs.org)
www.bioontology.or 
g
Social Media
Outline 
• NCBO Overview 
• BioPortal and NCBO Web Services 
• BioPortal SPARQL Endpoint 
• Applications using NCBO Technology
bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg
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
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
Virtual Appliance Installations
Virtual Appliance User Locations
Outline 
• NCBO Overview 
• BioPortal and NCBO Web Services 
• BioPortal SPARQL Endpoint 
• Applications using NCBO Technology
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
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
Ontology Web Services 
Accessing, browsing, searching and traversing ontologies in Your application
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
NCBO Technology
Ontology Web Services 
• Term 
– Get details about a term including it’s definition, 
synonyms, URI, super- and sub-classes, and other 
properties
NCBO Technology
Ontology Web Services 
• Hierarchy 
– Get parent, children, and sibling terms
NCBO Technology
Notes Web Services 
Propose new terms and comment on ontologies
Notes Web Service 
• Add comments or terms proposals to an 
ontology 
• Maintained as metadata associated with the 
ontology
NCBO Technology
WebProtégé 
http://protegewiki.stanford.eedduu//wwiikkii//WWeebbPPrrootteeggee
VIEWs 
Custom subset of large ontologies
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
Views in BioPortal
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
MAPPING Web Services 
Using NCBO technology to integrate terminologies and ontologies
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
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
widgets 
Using NCBO technology on your web pages
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
Widgets 
Form auto-complete 
RSS feed 
Jump To
Widgets 
Tree widget 
Visualization
Annotator web service 
Using Ontologies to Annotate Your Data
Annotator: The Basic Idea 
• Tag textual metadata with ontology terms
Annotator Workflow
Data service 
Using Ontologies to Access Public Data
Resource Index: The Basic Idea 
• The index can be used for 
• Search 
• Data mining
Outline 
• NCBO Overview 
• BioPortal and NCBO Web Services 
• BioPortal SPARQL Endpoint 
• Applications using NCBO Technology
hhttttpp::////ssppaarrqqll..bbiioooonnttoollooggyy..oorrgg//
BioPortal SPARQL Data (beta) 
• Ontology Content 
• Ontology Metadata 
• Ontology Term Mapping Data
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
BioPortal Ontology Metadata
BioPortal Metadata Ontology
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
Outline 
• NCBO Overview 
• BioPortal and NCBO Web Services 
• BioPortal SPARQL Endpoint 
• Applications using NCBO Technology
Applications using NCBO Technology
Applications using NCBO Technology 
• Ontology Development and Visualization 
• Data Annotation 
• Data Integration
http://protegewiki.stanford.edu/wiki/ 
BioPortal_Import_Plugin
hhttttpp::////oollss22oowwll..ssoouurrcceeffoorrggee..nneett//
hhttttpp::////wweebbpprrootteeggee//
http://www.biotec.tu-dresden.de/research/ 
schroeder/dog4dag/
hhttttpp::////rraaddlleexx..oorrgg//
Applications using NCBO Technology 
• Ontology Development and Visualization 
• Data Annotation 
• Data Integration
http://www.sysmo-db. 
org/rightfield
http://isatab.sourceforge.nneett//iissaaccrreeaattoorr..hhttmmll
http://wiki.cvrgrid.org/iinnddeexx..pphhpp//EECCGGGGaaddggeett
http://rreeddffllyy..ccccrr..bbuuffffaalloo..eedduu//iinnddeexx..pphhpp
Applications using NCBO Technology 
• Ontology Development and Visualization 
• Data Annotation 
• Data Integration
Annotator 
http://en.wikipedia.oorrgg//wwiikkii//PPoorrttaall::GGeennee__WWiikkii
KKnnoowwlleeddggee EEgggg 
hhttttpp::////wwwwww..kkuunnnnsskkaappsseeggggeett..nnoo//
http://ontologicaldiscovery.oorrgg//
ODiSSea 
hhttttpp::////wwwwww..hhuubb..sscciivveerrssee..ccoomm//
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

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NCBO Technology

Editor's Notes

  1. "Like" NCBO on Facebook: http://on.fb.me/bioontology Follow NCBO on Twitter: http://twitter.com/#!/bioontology Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
  2. http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceontology=1009&targetontology=1032&pagesize=10&pagenum=1&apikey=24e037b6-54e0-11e0-9d7b-005056aa3316
  3. GSE12391 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12391
  4. Documentation at http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal#Preferred_Label.2C_Synonyms_and_other_common_predicates
  5. BioPortal Import Plugin – enables term re-use by being able to select ontology terms from BioPortal for use in your own ontology project
  6. The plugin was developed as part of the Open architecture for Accessible Services Integration and Standardization (OASIS) project, which facilitates interoperability across service providers, mobile devices (wearable devices, phones, palm, etc.) smart home technology, and medical care providers for elderly and disabled population. Utilizes key technologies in order to provide holistic services to older people to support their physical and psychological independence, stimulate their social or psychological engagement and foster their emotional well being. The plugin designed to aid ontology developers during the knowledge elicitation stage and allows ontology developers to search for terms from a repository of ontologies and compare similar classes, properties, and instances. http://www.oasis-project.eu/ OASIS – Open architecture for Accessible Services Integration and Standardization project It is an Integrated Project with the scope to revolutionise the interoperability, quality, breadth and usability of services for all daily activities of older people. Brings together a consortium of 33 partners across 11 countries.
  7. Notes (comments and term proposals) submitted in BioPortal are accessible in Web Protégé
  8. DOG4DAG - Ontology Generation Tool for OBO-Edit and Protégé generates ontology terms, definitions, and relationships based on natural language text found in PubMed, the Web, or PDF documents and therefore supports the extension of existing ontologies with terms from resources commonly used in biocuration
  9. Custom view of RadLex ontology implemented using the NCBO Web services. Therefore, the ontology is stored and managed in BioPortal, but the display is customized by using the Web services to access the content of RadLex and format as the community prefers
  10. RightField – data annotation with fields limited to selected ontologies
  11. ISACreator - A ‘user-friendly’ standalone Java application that assists the experimentalists to annotate the experimental metadata. Depending on the configuration (set via the ISAconfigurator tool), certain fields prompt a pop-up browser to search and select terms from ontologies that are accessed in real time via the Ontology Lookup Service and BioPortal. New – OntoMaton, ISAcreator functionality in GoogleDocs
  12. The CVRG ECG Gadget is a Web 2.0 mashup application built using the GoogleWeb Toolkit and Visualization API. It integrates the CVRG ECG Storage & Analysis Workflows with ECG Visualization/Annotation using REST services available from the NCBO BioPortal. The application can be executed using an Apache Tomcat server, allowing the application to be run locally and/or remotely. The application has been tested in Internet Explorer 7 & 8.
  13. RedFly – database of transcription regulatory elements in Drosophila
  14. GeneWiki - Structured annotations enable pathway analysis, statistical analyses, cross-species comparisons
  15. Knowledge Egg - Uses Jump To widget to access information from BioPortal and then search through databases
  16. GeneWeaver, developed by the Jackson Laboratory, uses the Annotator to identify ontology terms from metadata descriptions and uses these in analysis of gene relationships
  17. ODiSSea – application within SciVerse Hub that uses the NCBO Annotator to identify ontology terms in SciVerse content and also links these to data records via the NCBO Resource Index