ontology web services

THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY

Ontology Web Services

Trish Whetzel, PhDOutreach Coordinator

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

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

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

Web Services

Code

User Interface

Browser

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

Ontology Web Services• List Ontologies

– Get ontology metadata• Create Views

– View Extraction• Access Ontologies and

Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes

• Widgets– Auto-complete– Visualization

• Create ontology-based annotations– Annotator – Ontology Recommender – Lexicon Builder

• Access ontology-based index of annotations– Resource Index

Ontology View

• A View is a subset of one or more ontologies– also referred to as a value set or slim

• Anyone can create a View – does not need to be the ontology “owner”

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View Extraction Web service

• Given a term identifier, extracts all children • Parameters

– Ontology version identifier– Term identifier– Output ontology name

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

Views in BioPortal

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Views in BioPortal

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Using Views in Your Application

• List all views– Get list of all views in BioPortal – Get all versions of a given View

• Views are accessible via all BioPortal web services– Get term – get all details about a term – Search – find terms in a View – Widgets – form field auto-complete widget

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Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes– RDF




BioPortal

• Functionality– Notes

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• Access Ontologies and Views (Value sets or Slims) – Search – search by term or term identifier across all

ontologies in BioPortal – Term – get details about a term including it’s URI,

super- and sub-classes, properties– Hierarchy – get parent or children terms – Mapping – get mappings between terms – Notes – get comments/new term proposals added to

the ontology– RDF – get RDF snippet for term or entire ontology


• BioPortal Search Demo

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• Widgets– Jump To – auto-complete function to select term

and Jump To BioPortal to view term details– Term-selection widget – auto-complete function

and can return term URI, term ID or term name– Visualize widget – view the ontology structure and

relations– Tree widget – view the ontology tree

Code for widgets is available on BioPortal

Ontology Widgets

• BioPortal Widgets

Term-selection

Ontology Widgets


RSS feed

Jump To

Ontology Widgets


Tree widget

Visualization




Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF




Annotator: The Basic Idea

• Tag textual metadata with ontology terms

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Annotator Workflow

Code

Annotator Web service

Excel

UIMA platform

User Interface

Annotator Addin






• Create ontology-based annotations– Annotator – Ontology

Recommender – Lexicon Builder


Ontology Recommender

Clement Jonquet, Mark A. Musen and Nigam H. ShahBuilding a Biomedical Ontology Recommender Web ServiceJournal of Biomedical Semantics 2010, 1(Suppl 1):S1






• Create ontology-based annotations– Annotator – Ontology Recommender

– Lexicon Builder • Access ontology-based

index of annotations– Resource Index

Lexicon Builder

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

Resource Index: Use Case

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Resource Index: The Basic Idea

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NCBO Resource Index

Ontology Web Services• Access Ontologies and

Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF




Tools using NCBO Technology

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http://www.bioontology.org/technology

Thank you!

• Using NCBO Technology in Your Project: http://www.bioontology.org/wiki/index.php/

Using_NCBO_Technology_In_Your_Project

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

NCBO_REST_services

• Questions: [email protected]

ontology web services

Software