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:''' Oak Room, Tresidder Building, 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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:'''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].
  
 
:'''Date: Tutorial: March 15, 2012'''  
 
:'''Date: Tutorial: March 15, 2012'''  
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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]
 
*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:
 
*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   
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**The reasons for the success of the Gene Ontology  (GO)
 
**What is the difference between an ontology and a database?
 
**What is the difference between an ontology and a database?
 
**Why you should use an ontology to support your research
 
**Why you should use an ontology to support your research
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 +
* 2:20pm '''Break'''
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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.
 +
** 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.
 +
 +
* 3:30pm '''Break'''
 
   
 
   
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* 2:30pm '''NCBO Web Services and Development of Semantic Applications''' (Trish Whetzel)  
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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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* We will provide an overview of NCBO Web services and of how they are being incorporated into software applications.
 
** Introduction to REST Web services
 
** Introduction to REST Web services
 
** [http://bioportal.bioontology.org NCBO BioPortal]
 
** [http://bioportal.bioontology.org NCBO BioPortal]
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*** [http://www.bioontology.org/wiki/index.php/Resource_Index Data Access] - Fetch ontology-indexed data
 
*** [http://www.bioontology.org/wiki/index.php/Resource_Index Data Access] - Fetch ontology-indexed data
 
** [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - Access Ontologies via SPARQL
 
** [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - Access Ontologies via SPARQL
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* 4:00pm '''Use of ontologies in biomedical research''' (Nigam Shah)
 
−
** 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.
 
−
** For the patterns of drug use, we validate the usage patterns learned from the data against FDA-approved indications as well as external sources of known off-label use such as Medi-Span. For drug safety surveillance, we show that 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.
 

Latest revision as of 07:18, 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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