Introduction to Bio-Ontologies and Their Applications - Revision history

Whetzel at 14:18, 16 March 2012

2012-03-16T14:18:04Z

2012-03-15T23:49:13Z

2012-03-15T23:42:27Z

2012-03-15T23:41:54Z

2012-03-15T21:50:03Z

2012-03-15T21:46:22Z

2012-03-15T21:15:52Z

2012-03-14T18:03:03Z

2012-03-14T16:42:52Z

2012-03-14T16:31:07Z

@@ Line 29: / Line 29: @@
 * 3:30pm '''Break'''
-* 3:40pm '''NCBO Web Services and Development of Semantic Applications''' (Trish Whetzel)
+* 3:40pm '''NCBO Web Services and Development of Semantic Applications''' (Trish Whetzel) [http://stanford.edu/~whetzel/downloads/Whetzel_NCBO-Tutorial.pdf.zip Slides]
 * We will provide an overview of NCBO Web services and of how they are being incorporated into software applications.
 ** Introduction to REST Web services
 ** [http://bioportal.bioontology.org NCBO BioPortal]

@@ Line 22: / Line 22: @@
 * 2:20pm '''Break'''
-* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah) [[File:Part-2.pdf]]
+* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah) [http://goo.gl/0zMjy 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.

@@ Line 22: / Line 22: @@
 * 2:20pm '''Break'''
-* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah) [[File:Part-2.pptx]]
+* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah) [[File:Part-2.pdf]]
 ** 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.

@@ Line 22: / Line 22: @@
 * 2:20pm '''Break'''
-* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah)
+* 2:30pm '''Examples of using ontologies in biomedical research''' (Nigam Shah) [[File:Part-2.pptx]]
 ** 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.

@@ Line 14: / Line 14: @@
 '''Agenda:'''
-* 1:00pm '''What is an ontology and what is it useful for?''' (Barry Smith)
+* 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:
 **The reasons for the success of the Gene Ontology  (GO)

@@ Line 1: / Line 1: @@
 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].
-:'''Venue:''' Oak Room, 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].
+:'''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'''

@@ Line 16: / Line 16: @@
 * 1:00pm '''What is an ontology and what is it useful for?''' (Barry Smith)
 *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
+**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 '''NCBO Web Services and Development of Semantic Applications''' (Trish Whetzel)
+* 3:40pm '''NCBO Web Services and Development of Semantic Applications''' (Trish Whetzel)
 *We will provide an overview of NCBO Web services and of how they are being incorporated into software applications.
 ** Introduction to REST Web services
@@ Line 35: / Line 42: @@
 *** [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