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Web services and the Development of Semantic Applications
1. Web Services and Development
of Semantic Applications
Trish Whetzel
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
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
7. Outline
• Learning Objectives
• REST Web services
• BioPortal
• NCBO Web Services
8. Learning Objectives
• Learn what Web services are available from
NCBO
• Learn how to programmatically use these
Web services
• Learn how to combine these Web services to
perform tasks
9. REST Web Services
• Accessed via HTTP
– http://rest.bioontology.org/{parameters}
• Each unique URL is a representation of some
object
• Operations include GET, POST, PUT, DELETE
• Lightweight, easy to build
13. Outline
• REST Web services
• BioPortal
• NCBO Web Services
• BioPortal SPARQL Endpoint
14. 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
VVieiewwss
TTeerrmm r reeccooggnnititioionn
Fetch “data”
annotated with a
given term
Fetch “data”
annotated with a
given term
hhttttpp::////bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg
15. Ontology Web Services
Accessing, browsing, searching and traversing ontologies in Your application
16. Ontology Web Services
• List All Ontologies
– List all ontologies in BioPortal
– Documentation: http://bit.ly/sxL2Qi
– GoogleDoc Excel example:
http://bit.ly/ncbo-list-all-ontologies
17. One ontology id
has many ontology
version ids
Ontology version id
Ontology id
18. Ontology Web Services cont.
• Search
– Search by term or term identifier across all ontologies
in BioPortal
• Documentation: http://bit.ly/tMDkr6
• Example clients
– Java: http://bit.ly/ttTb1G
– Perl: http://bit.ly/sPXC2X
19. Ontology Web Services cont.
• Term
– get details about a term including it’s definition,
synonyms, URI, super- and sub-classes, and other
properties http://bit.ly/teedbd
• Hierarchy
– get parent, children, and sibling terms
http://bit.ly/tPzm75
30. 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
42. 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
44. Views and Value Sets
• View Extraction Web service
– Given a root node term, extracts all child terms
http://bit.ly/uXeh2s
• Access directly from Protégé via the BioPortal
Import plugin
http://protegewiki.stanford.edu/wiki/BioPortal_Import_
45. MAPPING Web Services
Using NCBO technology to integrate terminologies and ontologies
46. 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
48. Mappings
• Mappings Web service
– Documentation:
http://www.bioontology.org/wiki/index.php/BioPortal_• Functions
– Get/Download
– Create/Upload
• Example Perl client to Get mappings:
http://bit.ly/tDKPQd
52. Annotator Web Service
• Tag free text with ontology terms
• Documentation:
http://www.bioontology.org/wiki/index.php/Annotator_• Example clients:
– Perl: http://bit.ly/vKYpCP
– Java: http://bit.ly/rRFoKd
53. Gene Wiki
Annotator
http://en.wikipedia.oorrgg//wwiikkii//PPoorrttaall::GGeennee__WWiikkii
54. Statistical Tracking of
Ontological Phrases (STOP)
http://www.mooneygroup.oorrgg//ccoonntteenntt//wweebbttoooollss
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.Questions and feedback on the tool itself are welcome.
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.
Ontology Generation Tool for OBO-Edit and Protégé (NEW)
cgMDR is developed by Steve Harris’ group at the University of Oxford.
It is an Excel Add-in that allows users to annotate data elements with terms from BioPortal.
The screenshots:
Main screen from where a user chooses to add conceptual reference to a registry item
User can select a specific Terminology from the drop down list – Bioportal-SNOMEDCT, Bioportal-HL7, etc
Shows the results of query for a specific term in a specific terminology from Bioportal – some basic information and link back to parent source URL.
eMERGE - a national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research.
This allows researchers to harmonize their local phenotype data dictionaries to existing metadata and terminology standards such as the caDSR (Cancer Data Standards Registry and Repository), NCIT (NCI Thesaurus) and SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms). Use this tool to search/browse metadata related to different studies, create new study & its related metadata, users can also export metadata in excel format.
Indexing an element from GEO. The GEO element GDS1989 is annotated according to its title and its description, as well as by the ontology elements that comprise the transitive closure over the parent–child relationships subsumed by the direct annotations.