Ontology Web services for Semantic Applications

Ontology Web Services for Semantic Applications

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• 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 Web Services• Access Ontologies and

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

• Widgets– Auto-complete– Visualization

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

• Access ontology-based index of annotations– Resource Index

Ontology Web Services

• 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

Ontology Web Services

• BioPortal Search Demo

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Ontology Web Services• Access Ontologies and

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

• Widgets– Auto-complete– Visualization

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

• Access ontology-based index of annotations– Resource Index

Ontology Web Services

• 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

RSS feed

Term-selection

Jump To

Ontology Widgets

• BioPortal Widgets

Tree widget

Visualization

Ontology Web Services• Access Ontologies and

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

• Widgets– Auto-complete– Visualization

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

• Access ontology-based index of annotations– Resource Index

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

Annotator Addin

Ontology Web Services• Access Ontologies and

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

• Widgets– Auto-complete– Visualization

• Create ontology-based annotations– Annotator – Ontology

Recommender – Lexicon Builder

• Access ontology-based index of annotations– Resource Index

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

Ontology Web Services• 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

Lexicon Builder

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

Ontology Web Services• 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

Resource Index: The Basic Idea

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Resource Index: Use Case

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Resource Index: Use Case

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Resource Index: Use Case

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NCBO Resource Index

Ontology Web Services• Access Ontologies and

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

• Widgets– Auto-complete– Visualization

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

• Access ontology-based index of annotations– Resource Index

Tools using NCBO Technology

32http://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: support@bioontology.org