Difference between revisions of "Introduction to Bio-Ontologies and Their Applications"

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The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold an Introduction and Application of Bio-Ontologies tutorial as part of its [http://www.bioontology.org/wiki/index.php/Meetings_and_Events series of training and dissemination events].
 
The [http://www.bioontology.org/ National Center for Biomedical Ontology] will hold an Introduction and Application of Bio-Ontologies tutorial as part of its [http://www.bioontology.org/wiki/index.php/Meetings_and_Events series of training and dissemination events].
  
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'''Venue:''' [http://bmir.stanford.edu/ Stanford Center for Biomedical Informatics Research, Stanford University]
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:'''Venue:''' Oak Lounge West, 2nd Floor, Tresidder Union, Stanford University, [http://maps.google.com/maps/ms?ie=UTF8&fb=1&gl=us&hq=tresidder+student+union&hnear=Stanford,+CA&ecpose=37.42454663,-122.17057424,443.63,0,0,0&oe=UTF8&msa=0&msid=216493105589739392573.00049fcfb8d85601edcea Directions].
  
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'''Date: Tutorial: March 15, 2012'''  
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:'''Date: Tutorial: March 15, 2012'''  
  
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'''Organization:''' Barry Smith (NCBO / Buffalo), Trish Whetzel (NCBO / Stanford University), and Nigam Shah (NCBO / Stanford University)
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:'''Organization:''' Barry Smith (NCBO / Buffalo), Trish Whetzel (NCBO / Stanford University), and Nigam Shah (NCBO / Stanford University)
  
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'''Registration:''' Please write to [mailto:phismith@buffalo.edu Barry Smith]
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:'''Registration:''' Please write to [mailto:phismith@buffalo.edu Barry Smith]
  
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'''Audience:''' Some background in bioinformatics or medical informatics is required. No knowledge of ontology is presupposed.
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:'''Audience:''' Some background in bioinformatics or medical informatics is required. No knowledge of ontology is presupposed.
  
 
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----
  
 
'''Agenda:'''
 
'''Agenda:'''
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* 1:00pm What is an ontology and what is it useful for? (Barry Smith)
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* 1:00pm '''What is an ontology and what is it useful for?''' (Barry Smith) [http://ontology.buffalo.edu/smith/ppt/Bioontologies/What_Is_An_Ontology_NCBO_March_2012.ppt Slides]
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*We will provide an introduction to biomedical ontology with a focus on the conditions for successful development and application of ontologies. Topics to be covered include:
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**The reasons for the success of the Gene Ontology  (GO)
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**What is the difference between an ontology and a database?
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**Why you should use an ontology to support your research
  
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This section will provide an introduction to biomedical ontology with a focus on illustrations of success stories in the application of ontologies to supporting specific kinds of research. 
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* 2:20pm '''Break'''
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* 2:30pm NCBO Web Services and Development of Semantic Applications (Trish Whetzel)
 
  
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This section will describe NCBO technologies to support the use of ontologies in your research.
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* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah) [http://goo.gl/0zMjy Slides]
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** We will review the use of NCBO components to create an annotation workflow (specifically using the Annotator and Lexicon Builder components). We will then discuss the applications of this workflow to 9.5 million clinical documents--from the electronic health records of approximately one million adult patients from the STRIDE Clinical Data Warehouse, part of Stanford's CTSA Informatics platform--to identify statistically significant patterns of drug use and to conduct drug safety surveillance.
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** We will discuss how drug–disease co-occurrences and the temporal ordering of drugs and disease mentions in clinical notes can be examined for statistical enrichment and used to detect potential adverse events.
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** We will discuss how analysis such as GO enrichment analysis can be done using other ontologies, such as the Human Disease ontology, and generate biological insights.
  
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* 4:00pm Use of ontologies in biomedical research (Nigam Shah)
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* 3:30pm '''Break'''
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Links: http://bioportal.bioontology.org/
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* 3:40pm '''NCBO Web Services and Development of Semantic Applications''' (Trish Whetzel) [http://stanford.edu/~whetzel/downloads/Whetzel_NCBO-Tutorial.pdf.zip Slides]
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* We will provide an overview of NCBO Web services and of how they are being incorporated into software applications.
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** Introduction to REST Web services
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** [http://bioportal.bioontology.org NCBO BioPortal]
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** NCBO REST Web services
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*** [http://www.bioontology.org/wiki/index.php/NCBO_REST_services Ontology Web services] - Search, Traverse, Download
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*** [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction Web service] - Subset
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*** [http://www.bioontology.org/wiki/index.php/Ontology_Notes Notes Web service] - Propose Terms, Comment
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*** [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mapping Web services] - Create, Upload, Download
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*** [http://www.bioontology.org/wiki/index.php/NCBO_Widgets Widgets] - Tree view, Auto-complete, Graph view
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*** [http://www.bioontology.org/wiki/index.php/Annotator_Web_service Annotation] - Ontology Term recognition
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*** [http://www.bioontology.org/wiki/index.php/Resource_Index Data Access] - Fetch ontology-indexed data
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** [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - Access Ontologies via SPARQL

Latest revision as of 06:18, 16 March 2012

The National Center for Biomedical Ontology will hold an Introduction and Application of Bio-Ontologies tutorial as part of its series of training and dissemination events.

Venue: Oak Lounge West, 2nd Floor, Tresidder Union, Stanford University, Directions.
Date: Tutorial: March 15, 2012
Organization: Barry Smith (NCBO / Buffalo), Trish Whetzel (NCBO / Stanford University), and Nigam Shah (NCBO / Stanford University)
Registration: Please write to Barry Smith
Audience: Some background in bioinformatics or medical informatics is required. No knowledge of ontology is presupposed.

Agenda:

  • 1:00pm What is an ontology and what is it useful for? (Barry Smith) Slides
  • We will provide an introduction to biomedical ontology with a focus on the conditions for successful development and application of ontologies. Topics to be covered include:
    • The reasons for the success of the Gene Ontology (GO)
    • What is the difference between an ontology and a database?
    • Why you should use an ontology to support your research
  • 2:20pm Break
  • 2:30pm Examples of using ontologies in biomedical research (Nigam Shah) Slides
    • We will review the use of NCBO components to create an annotation workflow (specifically using the Annotator and Lexicon Builder components). We will then discuss the applications of this workflow to 9.5 million clinical documents--from the electronic health records of approximately one million adult patients from the STRIDE Clinical Data Warehouse, part of Stanford's CTSA Informatics platform--to identify statistically significant patterns of drug use and to conduct drug safety surveillance.
    • We will discuss how drug–disease co-occurrences and the temporal ordering of drugs and disease mentions in clinical notes can be examined for statistical enrichment and used to detect potential adverse events.
    • We will discuss how analysis such as GO enrichment analysis can be done using other ontologies, such as the Human Disease ontology, and generate biological insights.
  • 3:30pm Break
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