NCBO Technology

THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY

NCBO Technology

Trish WhetzelOutreach Coordinator

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.org

Social Media

Outline


bioportal.bioontology.orgbioportal.bioontology.org

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

OWL, RDF, Protégé frames

RDF Data Store LexEVSProtégé DB

Hibernate ORM

Spring Framework

Restlet

Tomcat

Ruby on Rails

OBO format, UMLS RRF, LexGrid XML

Third partyapplications

SPARQLAccess

Virtual Appliance Installations

Virtual Appliance User Locations

Outline


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:

//re

st.b

ioon

tolo

gy.o

rghtt

p://

rest

.bio

onto

logy

.org

Ontology ServicesOntology Services

• Search• Traverse• Comment• Download

• Search• Traverse• Comment• Download

WidgetsWidgets• Tree-view• Auto-complete• Graph-view

• Tree-view• Auto-complete• Graph-view

AnnotationAnnotation

Data AccessData Access

Mapping ServicesMapping Services

• Create• Upload• Download

• Create• Upload• Download

Term recognitionTerm recognition

Search “data” annotated with a given term

Search “data” annotated with a given term

http://bioportal.bioontology.orghttp://bioportal.bioontology.org

Ontology Web Services

Accessing, browsing, searching and traversing ontologies in Your application


• 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


• Term– Get details about a term including it’s definition,

synonyms, URI, super- and sub-classes, and other properties


• Hierarchy– Get parent, children, and sibling terms

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

WebProtégé

http://protegewiki.stanford.edu/wiki/WebProtegehttp://protegewiki.stanford.edu/wiki/WebProtege

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_Import_Plugin

MAPPING Web Services

Using NCBO technology to integrate terminologies and ontologies

MappingsMappings

Root

Term-1 Term-2

Term-3 Term-4

Term-5

R

t1 t2

t4

t5 t6 t7

t3

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

RSS feed

Form auto-complete

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


http://sparql.bioontology.org/http://sparql.bioontology.org/

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


Applications using NCBO Technology


• Ontology Development and Visualization• Data Annotation• Data Integration

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

http://ols2owl.sourceforge.net/ http://ols2owl.sourceforge.net/

http://webprotege/ http://webprotege/

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

http://radlex.org/http://radlex.org/

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

http://isatab.sourceforge.net/isacreator.htmlhttp://isatab.sourceforge.net/isacreator.html

http://wiki.cvrgrid.org/index.php/ECGGadgethttp://wiki.cvrgrid.org/index.php/ECGGadget

http://redfly.ccr.buffalo.edu/index.phphttp://redfly.ccr.buffalo.edu/index.php

Annotator

http://en.wikipedia.org/wiki/Portal:Gene_Wikihttp://en.wikipedia.org/wiki/Portal:Gene_Wiki

http://www.kunnskapsegget.no/http://www.kunnskapsegget.no/

Knowledge EggKnowledge Egg

http://ontologicaldiscovery.org/http://ontologicaldiscovery.org/

ODiSSea

http://www.hub.sciverse.com/http://www.hub.sciverse.com/

Thank you!

• Web service documentation: http://www.bioontology.org/wiki/

index.php/NCBO_REST_services• Keep in touch

– Software support: [email protected]

– Twitter: @bioontology– Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group

NCBO Technology

Software

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