ontology web services for semantic applications
DESCRIPTION
Overview of NCBO Technology presented at the PhUSE 2011 meeting in San Francisco.TRANSCRIPT
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
10
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
27
Resource Index: Use Case
28
Resource Index: Use Case
29
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: [email protected]