From BFO to IAO - Revision history

Phismith at 16:12, 25 December 2009

2009-12-25T16:12:10Z

Phismith at 14:11, 25 July 2009

2009-07-25T14:11:33Z

Alanr at 23:13, 19 July 2009

2009-07-19T23:13:54Z

Alanr at 22:06, 19 July 2009

2009-07-19T22:06:11Z

Alanr at 22:04, 19 July 2009

2009-07-19T22:04:56Z

Alanr at 21:58, 19 July 2009

2009-07-19T21:58:31Z

Alanr at 21:58, 19 July 2009

2009-07-19T21:58:13Z

Phismith at 20:34, 19 July 2009

2009-07-19T20:34:03Z

Phismith at 16:15, 19 July 2009

2009-07-19T16:15:42Z

Alanr at 05:08, 20 March 2009

2009-03-20T05:08:14Z

← Older revision		Revision as of 16:12, 25 December 2009
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	Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].		Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].
		+
		+	Now available in streaming video format [http://org.buffalo.edu/Presentations.html#ICBOvideos here].

	Slides: [http://icbo.buffalo.edu/presentations/Smith.ppt Smith] [http://icbo.buffalo.edu/presentations/Ceusters.ppt Ceusters]		Slides: [http://icbo.buffalo.edu/presentations/Smith.ppt Smith] [http://icbo.buffalo.edu/presentations/Ceusters.ppt Ceusters]

← Older revision		Revision as of 14:11, 25 July 2009
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	Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].		Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].
		+
		+	Slides: [http://icbo.buffalo.edu/presentations/Smith.ppt Smith] [http://icbo.buffalo.edu/presentations/Ceusters.ppt Ceusters]
		+	[http://icbo.buffalo.edu/presentations/Ruttenberg.pdf Ruttenberg]

	Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time.		Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time.

@@ Line 16: / Line 16: @@
 '''Session 3: Thursday 9am to 12.30pm'''
-*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations]  (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based  integrated ontology for the description of life-science and clinical investigations and has as its domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies.
+*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations]  (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based  integrated ontology for the description of life-science and clinical investigations. Its domain encompasses materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the investigation to the natural world as represented in other OBO ontologies.
 * IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.
-* Attendees will finish this session with a understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.
+* Attendees will finish these sessions with an understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.
 '''Session 4: Thursday 1.30pm to 5pm'''

@@ Line 16: / Line 16: @@
 '''Session 3: Thursday 9am to 12.30pm'''
-*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations]  (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based  integrated ontology for the description of life-science and clinical investigations and has as it's domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies.
+*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations]  (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based  integrated ontology for the description of life-science and clinical investigations and has as its domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies.
 * IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.

@@ Line 16: / Line 16: @@
 '''Session 3: Thursday 9am to 12.30pm'''
-*Alan Ruttenberg: introduction to the Ontology for Biomedical Investigations(OBI) and the Information Artifact Ontology(IAO). OBI is a BFO-based  integrated ontology for the description of life-science and clinical investigations and has as it's domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies.
+*Alan Ruttenberg: Introduction to the [http://obi-ontology.org/ Ontology for Biomedical Investigations]  (OBI) and the [http://code.google.com/p/information-artifact-ontology/ Information Artifact Ontology] (IAO). OBI is a BFO-based  integrated ontology for the description of life-science and clinical investigations and has as it's domain materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the the investigation to the natural world as represented in other OBO ontologies.
-* IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.
+* IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.
-* Attendees should finish this session with a understanding of upper level entities essential to read the ontologies in more detail, a picture of that current state of the ontology, a picture of expected future work, being cognizant of issues that need to be resolved and perhaps primed to help solve them.
+* Attendees will finish this session with a understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.
 '''Session 4: Thursday 1.30pm to 5pm'''
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 '''Literature and Links'''
-[http://obofoundry.org OBO Foundry]
+* [http://obofoundry.org OBO Foundry]
 ----
 '''Faculty'''

@@ Line 1: / Line 1: @@
 '''From Basic Formal Ontology to the Information Artifact Ontology'''
-July 22-23, 2009
+Wednesday and Thursday, July 22-23, 2009
 Two-day Course organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology].
@@ Line 7: / Line 9: @@
 Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time.
-Day 1:
+'''Session 1: Wednesday 9am to 12.30pm'''
-*introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative,
+*Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative,
-*introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research
+'''Session 2: Wednesday 1.30pm to 5pm'''
-Day 2:
+'''Session 3: Thursday 9am to 12.30pm'''
-*introduction to the Information Artifact Ontology, a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies.
+'''Session 4: Thursday 1.30pm to 5pm'''
 ----

← Older revision		Revision as of 16:15, 19 July 2009
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	knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.		knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.

−	[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory ~~Boards~~ of the Gene Ontology Consortium, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.	+	[http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.

@@ Line 31: / Line 31: @@
 [http://org.buffalo.edu/ceusters/ Werner Ceusters] is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties.
-[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons], a Coordinating Editor of the OBO Foundry, and Co-chair of the W3C OWL
+[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org/ Science Commons]. His project, the Neurocommons, prototypes the use of
 Semantic Web technology for integrating and querying biomedical
 knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.
 [http://ontology.buffalo.edu/smith/ Barry Smith] is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Boards of the Gene Ontology Consortium, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.