NCBO Tools and Web Services

Trish Whetzel Outreach Coordinator

Outline

• NCBO Background• Ontology Web Services• Ontology Widgets• NCBO Annotator• NCBO Resource Index• Ontology Recommender• Lexicon Builder

National Centers for Biomedical Computing

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

RESTful Web Services

• Accessed via HTTP– http://rest.bioontology.org/bioportal/

• Each unique URL is a representation of some object

• Operations include GET, POST, PUT, DELETE • Lightweight, easy to build

Web Services

Code

UI

Browser

BioPortal

http://bioportal.bioontology.org/

Ontology Widgets

• See BioPortal (http://bioportal.bioontology.org/ontologies/42490#widgets) – Term selection - autocomplete widget – Jump To - view term details in BioPortal – Visualization - view ontology – RSS feed - track updates to ontology, e.g. upload

of new versions, notes, mappings

Ontology Web Services

• Ontology Metadata - get information about an ontology

• Term - get details about a term• Search - find term in any ontology• Hierarchy - traverse ontology hierarchy • Notes - get contents of notes• Mappings - get mapped terms

http://www.bioontology.org/wiki/index.php/NCBO_REST_services

Applications Using NCBO Web Services

• Microsoft Word 2007 Add-in for Ontology Recognition

• BioLit• ISAcreator• For full list, see

http://www.bioontology.org/tools

Automated recognition of ontology terms and database IDs before publication with manual curation by author

Microsoft Word 2007 Add-in

http://ucsdbiolit.codeplex.com/

BioLit

http://biolit.ucsd.edu

Automated recognition of ontology terms and database IDs after publication with manual curation by author

ISAcreator editor

http://isatab.sourceforge.net/

NCBO Annotator

• Open access, ontology-based Web service that annotates or “tags” textual metadata

• Annotation is done using ontologies from BioPortal, which includes OBO Foundry and Unified Medical Language System ontologies

• Variety of parameters that can be customized

Annotator Workflow

Access to Annotator

• BioPortal– User-friendly interface to test Annotator

• Web service (REST) – Direct programmatic access

• User Guide and Sample Client Code– http://www.bioontology.org/wiki/index.php/Annotator_Web_service

Annotator User Interface

Annotator Usage

• Production release– April 2009

• Data processed– 66 million calls – more than 259 gigabytes of data

Annotator Users

• Rat Genome Database - example use case • See

http://www.bioontology.org/wiki/index.php/NCBO_Annotator_community for additional use cases from the Annotator user community

Rat Genome Database

• Use case– Are any of these genes associated with my disease or

phenotype?– Is this candidate gene expressed in my tissue of interest?

• Annotate Gene Expression Omnibus (GEO) records with the Annotator using – Mouse Gross Adult anatomy ontology, Rat strain ontology,

Medical Subject Headings (MeSH), NCI Thesaurus – Pilot test to annotate 30 GEO datasets and associated

sample records

Rat Genome Database

• Results– Rat Strain ontology

• High number of false positives due to short length of many rat strains (2-3 letters) and similarity to common words and variety of words used to describe strains that were not included as synonyms

– Mouse adult gross anatomy• Low number of false positives• Annotation of 192 datasets resulted in precision and recall of

84.0% and 94.8% • Ability to link expression results of a gene (based on Affymetrix

probe set) to anatomical location– Manual curation of results needed, but much less

burdensome by the initial automated results

NCBO Resource Index

• Ontology-based index of publicly available biomedical resources

• Provides a mechanism to search across resources by ontology terms

Ontology Recommender

• Identify ontology relevant to annotate data

Lexicon Builder

http://www.bioontology.org/wiki/index.php/Lexicon_Builder

Acknowledgements

• Annotator Development– Nigam Shah– Clement Jonquet– Fan Meng– Mark Musen

• Feedback– Simon Twigger– Karen Dowell– Robin Smith

References

• BioPortal – http://bioportal.bioontology.org

• NCBO REST Web services– http://www.bioontology.org/wiki/index.php/

NCBO_REST_services • NCBO Annotator Web Service

– http://www.bioontology.org/wiki/index.php/Annotator_Web_service

• NCBO Resource Index Web Service– http://www.bioontology.org/wiki/index.php/

Resource_Index