ontology web services
DESCRIPTION
Presentation from the Genomics Standards Consortium meeting, 2011.TRANSCRIPT
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 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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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– RDF
• Widgets– Auto-complete– Visualization
• Create ontology-based annotations– Annotator – Ontology Recommender – Lexicon Builder
• Access ontology-based index of annotations– Resource Index
BioPortal
• Functionality– Notes
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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• List Ontologies
– Get ontology metadata• Create Views
– View Extraction• 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
Term-selection
Ontology Widgets
• BioPortal Widgets
RSS feed
Jump To
Ontology Widgets
• BioPortal Widgets
Tree widget
Visualization
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 – 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• List Ontologies
– Get ontology metadata• Create Views
– View Extraction• 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• 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
Lexicon Builder
www.bioontology.org/wiki/index.php/Lexicon_Builder
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
Resource Index: Use Case
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Resource Index: Use Case
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Resource Index: Use Case
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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
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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]