Formal Ontology 2017: Difference between revisions

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Preliminary details


'''PHI 548 (seminar, 3 credits). Registration number: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=24057 24057]'''
'''Course Title:''' PHI 547 Formal Ontology
'''Faculty: Barry Smith'''
'''Date and Time:''' This course is an on-line course to be taught on Mondays from January 30 to May 8, 2017. Registered students will be assumed to have watched the course videos the URLs for which will be provided in advance of each week's class (which will be assumed to take place in the interval from 4 to 6pm). The final session or sessions (depending on the number of class participants) will consist in youtube videos (ca 20 minutes in length) created by the students in the class.


'''This course is cross-listed with BMI 507, which is offered as part of the newly accredited PhD program in UB's [http://www.smbs.buffalo.edu/biomedicalinformatics/index.php Department of Biomedical Informatics]
'''Course Description:''' The course will provide an introduction to formal ontology from both a philosophical and an application oriented point of view. Ontologies to be considered will include:  


'''Time''': 4:00-6:50pm, Mondays, Fall Semester 2016
::Basic Formal Ontology
::[http://obofoundry.org/ontology/iao.html Information Artifact Ontology]
::[http://geneontology.org Gene Ontology]
::[http://obofoundry.org OBO (Open Biomedical Ontologies) Foundry]
::The Environment Ontology


'''Room''': Baldy 200-G, UB North Campus
We will also consider formal languages used in ontology, with special focus on


'''Instructors''': [http://ontology.buffalo.edu/smith/ Barry Smith] (Philosophy) and [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters] (Biomedical Informatics)
OWL (Web Ontology Language)
CLIF (Common Logic Interchange Format; a version of First Order Logic)


'''Office hours''': BS: by appointment via [mailto:phismith@buffalo.edu email]; WC: TBA
'''Text:''' Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015, xxiv + 220pp. Freely available to UB persons under MIT Press Scholarship Online.


'''Course Description'''
Background reading on the roots of ontology in  
 
This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experiments and through patient care, and show how ontologies are used in accessing, maintaining and exploiting the results. We will describe how biomedical ontologies are developed and evaluated and provide a comparative critical analysis of the principal current ontology resources. We will also review the major theories, methods and tools for the development of ontologies, and illustrate how these are being used in different areas of biomedical research and healthcare. On completion of this course students will have a thorough understanding of strategies to manage and exploit biomedical data; they will have a knowledge of categorization, of the philosophy of experimentation, of the philosophy of medicine, and of computer-based reasoning with data.
 
=='''Recommended background reading''' ==
:R. Arp, B. Smith, A. D. Spear, ''[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]''
 
== '''Recommended background video content''' ==
 
Selections from: [http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013]
== '''Schedule''' ==
 
== 8/29/2016 Introduction to Ontology 1: General Overview ==
Roots of ontology in  
*artificial intelligence ([https://www.academia.edu/722721/The_second_naive_physics_manifesto Second Naive Physics Manifesto])
*artificial intelligence ([https://www.academia.edu/722721/The_second_naive_physics_manifesto Second Naive Physics Manifesto])
*Human Genome Project ([http://geneontology.org Gene Ontology])
*Human Genome Project ()
*library science ([https://www.nlm.nih.gov/mesh/subhierarchy.html MeSH])  
*library science ([https://www.nlm.nih.gov/mesh/subhierarchy.html MeSH])  
*Semantic Web ([https://en.wikipedia.org/wiki/Web_Ontology_Language OWL])
*Semantic Web ([https://en.wikipedia.org/wiki/Web_Ontology_Language OWL])


== 9/5/2016  Labor Day (no class) ==
Further readings are provided here: http://ontology.buffalo.edu/smith/
== 9/12/2016  Introduction to Ontology 2: Ontology in Buffalo ==
Example videos are provided here: https://www.youtube.com/user/hxo3nql/playlists
*[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]
*[http://obofoundry.org/ Open Biomedical Ontologies (OBO) Foundry]
*[http://obofoundry.org/ontology/iao.html Information Artifact Ontology]
*[http://www.referent-tracking.com/RTU/?page=index Referent Tracking]
*The methodology of ontological realism


== 9/19/2016  Ontology of Experiments ==
The generation and dissemination of new knowledge through biomedical research and clinical trials


== 9/26/2016  Ontology of Clinical Practice ==
'''Grading''': Students will be graded on the basis of their contributions to the on-line class discussion forum and by 20 minute youtube videos created by class participants which will be assembled for presentation at the end of the semester. Grading will be based on:
Disease vs. diagnosis; Electronic Health Records and other systems and techniques for modeling, representing and maintaining patient data


== 10/3/2016  Ontology of Social Entities ==
1. forum participation (25%)
Representation of race, gender, and other demographic entities; patient consent; healthcare organizations
2. 20 minute youtube video (25%)
 
3. associated powerpoint slides (25%)
== 10/10/2016  The Gene Ontology and the Open Biomedical Ontologies Foundry ==
4. associated essay (25%)
History and current theoretical foundations for the development of effective biomedical ontologies
 
== 10/17/2016 Using Ontologies to Represent Biomedical Data, Information and Knowledge==
Review of the logical principles for building consistent, structured ontological representations capable of interpretation by both humans and computers
 
== 10/24/2016 Representing Types and Representing Instances (WC) ==
Introduction to [http://www.referent-tracking.com/RTU/?page=reftrackparadigm.phtml Referent Tracking]
 
== 10/31/2016 Ontology Software ==
Use of Protege and other tools for ontology editing, search and reasoning
 
== 11/7/2016  The Unified Medial Language System (UMLS) and its Semantic Network==
== 11/14/2016  The SNOMED clinical terminology and ontology==
== 11/21/2016 Big Biomedical Data ==
== 11/28/2016  Student presentations ==
== 12/5/2016  Student presentations ==
 
All students will be required to take an active part in class discussions throughout the semester and to prepare a paper on some relevant topic. The paper should be submitted in a draft version on or before October 31, and in final form on or before December 5. A powerpoint version will be presented in class in one or other of the two closing sessions.
 
Your grade will be determined in three equal portions deriving from:
:1. class participation (2.5% per class attended)
:2. paper (3000 words; deadline for draft: March 29; deadline for final version: May 3)
:3. class presentation (graded according to quality of powerpoint slides, quality of delivery, and quality of response to questions)


*Information Artifact Ontology]
*[http://www.referent-tracking.com/RTU/?page=index Referent Tracking]
*The methodology of ontological realism
For policy regarding incompletes see [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html here]
For policy regarding incompletes see [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html here]


Revision as of 16:40, 21 July 2016

Preliminary details

Course Title: PHI 547 Formal Ontology Faculty: Barry Smith Date and Time: This course is an on-line course to be taught on Mondays from January 30 to May 8, 2017. Registered students will be assumed to have watched the course videos the URLs for which will be provided in advance of each week's class (which will be assumed to take place in the interval from 4 to 6pm). The final session or sessions (depending on the number of class participants) will consist in youtube videos (ca 20 minutes in length) created by the students in the class.

Course Description: The course will provide an introduction to formal ontology from both a philosophical and an application oriented point of view. Ontologies to be considered will include:

Basic Formal Ontology
Information Artifact Ontology
Gene Ontology
OBO (Open Biomedical Ontologies) Foundry
The Environment Ontology

We will also consider formal languages used in ontology, with special focus on

OWL (Web Ontology Language) CLIF (Common Logic Interchange Format; a version of First Order Logic)

Text: Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015, xxiv + 220pp. Freely available to UB persons under MIT Press Scholarship Online.

Background reading on the roots of ontology in

Further readings are provided here: http://ontology.buffalo.edu/smith/ Example videos are provided here: https://www.youtube.com/user/hxo3nql/playlists


Grading: Students will be graded on the basis of their contributions to the on-line class discussion forum and by 20 minute youtube videos created by class participants which will be assembled for presentation at the end of the semester. Grading will be based on:

1. forum participation (25%) 2. 20 minute youtube video (25%) 3. associated powerpoint slides (25%) 4. associated essay (25%)

  • Information Artifact Ontology]
  • Referent Tracking
  • The methodology of ontological realism

For policy regarding incompletes see here

For academic integrity policy see here

For accessibility services see here

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